C-DEBI Peer-Reviewed Publications

Chapter 2.3 – The Underground Economy (Energetic Constraints of Subseafloor Life)

Published: January 1, 2014

Developments in Marine Geology: Earth and Life Processes Discovered from Subseafloor Environments - A Decade of Science Achieved by the Integrated Ocean Drilling Program (IODP)

Authors: Steven L. D’Hondt, Guizhi Wang, Arthur J. Spivack

Editors: , , Fumio Inagaki,

C-DEBI Contribution Number: 230

Chapter 4.2.2 – Hydrogeologic Properties, Processes, and Alteration in the Igneous Ocean Crust

Published: January 1, 2014

Developments in Marine Geology: Earth and Life Processes Discovered from Subseafloor Environments - A Decade of Science Achieved by the Integrated Ocean Drilling Program (IODP)

Authors: Andrew T. Fisher, Jeffrey C. Alt, Wolfgang Bach

Editors: , , Fumio Inagaki,

C-DEBI Contribution Number: 228

New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph

Published: June 19, 2015

Applied and Environmental Microbiology

Authors: Roman A. Barco, David Emerson, Jason B. Sylvan, Beth N. Orcutt, Myrna E. Jacobson Meyers, Gustavo A. Ramírez, John D. Zhong, Katrina J. Edwards

Editors:

C-DEBI Contribution Number: 227

Dissolved hydrogen and methane in the oceanic basaltic biosphere

Published: November 1, 2014

Earth and Planetary Science Letters

Authors: Huei-Ting Lin, James P. Cowen, Eric J. Olson, Marvin D. Lilley, Sean P. Jungbluth, Samuel T. Wilson, Michael S. Rappé

C-DEBI Contribution Number: 226

Publications > Thesis

Published: January 1, 2013

Oceanography, M.S.

Dissolved Inorganic Carbon and Alkalinity in Marine Sedimentary Interstitial Water

Authors: Justine Sauvage

C-DEBI Contribution Number: 225

Chapter 2.4 – Life at Subseafloor Extremes

Published: January 1, 2014

Developments in Marine Geology: Earth and Life Processes Discovered from Subseafloor Environments - A Decade of Science Achieved by the Integrated Ocean Drilling Program (IODP)

Authors: Ken Takai, Kentaro Nakamura, Douglas E. LaRowe, Jan P. Amend

Editors: , , Fumio Inagaki,

C-DEBI Contribution Number: 224

Biosphere frontiers of subsurface life in the sedimented hydrothermal system of Guaymas Basin

Published: July 31, 2014

Frontiers in Microbiology

Authors: Andreas P. Teske, Amy V. Callaghan, Douglas E. LaRowe

C-DEBI Contribution Number: 223

Thermodynamic limitations on microbially catalyzed reaction rates

Published: August 1, 2012

Geochimica et Cosmochimica Acta

Authors: Douglas E. LaRowe, Andrew W. Dale, Jan P. Amend, Philippe Van Cappellen

C-DEBI Contribution Number: 222

Prokaryotic Populations in Arsenic-Rich Shallow-Sea Hydrothermal Sediments of Ambitle Island, Papua New Guinea

Published: January 1, 2012

Geomicrobiology Journal

Authors: D’Arcy R. Meyer-Dombard, Roy E. Price, Thomas Pichler, Jan P. Amend

C-DEBI Contribution Number: 221

Microbial diversity and potential for arsenic and iron biogeochemical cycling at an arsenic rich, shallow-sea hydrothermal vent (Tutum Bay, Papua New Guinea)

Published: June 1, 2013

Chemical Geology

Authors: D’Arcy R. Meyer-Dombard, Jan P. Amend, Magdalena R. Osburn

C-DEBI Contribution Number: 220

Archaeal and bacterial diversity in an arsenic-rich shallow-sea hydrothermal system undergoing phase separation

Published: January 1, 2013

Frontiers in Microbiology

Authors: Roy E. Price, Ryan A. Lesniewski, Katja S. Nitzsche, Anke Meyerdierks, Chad Saltikov, Thomas Pichler, Jan P. Amend

C-DEBI Contribution Number: 219

Catabolic and anabolic energy for chemolithoautotrophs in deep-sea hydrothermal systems hosted in different rock types

Published: October 1, 2011

Geochimica et Cosmochimica Acta

Authors: Jan P. Amend, Thomas M. McCollom, Michael Hentscher, Wolfgang Bach

C-DEBI Contribution Number: 218

Goldschmidt Abstracts 2013: Microbial metabolism in serpentinite fluids

Published: July 1, 2013

Mineralogical Magazine

Authors: Melitza Crespo-Medina, William J. Brazelton, Katrina I. Twing, M. D. Kubo, Tori M. Hoehler, Matthew O. Schrenk

C-DEBI Contribution Number: 217

Radiolyis and life in deep subseafloor sediment of the South Pacific Gyre

Published: July 1, 2013

Mineralogical Magazine

Authors: Justine Sauvage, Arthur J. Spivack, Ann G. Dunlea, Richard W. Murray, Robert Pockalny, Steven L. D’Hondt, IODP Expedition 329 Shipboard Scientific Party

C-DEBI Contribution Number: 216

Publications > Film

Published: January 1, 2013

North Pond: The Search for Intraterrestrials

Authors: Michael Brown, Ad Lucien Santell, Samuel M. Hulme

C-DEBI Contribution Number: 215

Deep biosphere research hits its stride

Published: January 1, 2013

Core Discoveries: The Newsletter for Scientific Ocean Drilling

Authors: Heath J. Mills, Beth N. Orcutt

C-DEBI Contribution Number: 214

Goldschmidt Abstracts 2013: Mysteries of subseafloor sedimentary life

Published: July 1, 2013

Mineralogical Magazine

Authors: Steven L. D’Hondt

C-DEBI Contribution Number: 213

Interactions of proteins with biogenic iron oxyhydroxides and a new culturing technique to increase biomass yields of neutrophilic, iron-oxidizing bacteria

Published: May 30, 2014

Frontiers in Microbiology

Authors: Roman A. Barco, Katrina J. Edwards

C-DEBI Contribution Number: 212

Expanding the telepresence paradigm: Interactive programming from R/V Atlantis and ROV Jason

Published: March 1, 2014

Oceanography

Authors: D. F. Coleman, D. Livelybrooks, Sharon K. Cooper, G. Mulder, Andrew T. Fisher, A. M. Trehu, D. R. Tooomey

C-DEBI Contribution Number: 211

Microbial Acceleration of Olivine Dissolution via Siderophore Production

Published: January 1, 2014

Procedia Earth and Planetary Science

Authors: Mark A. Torres, A. Joshua West, Kenneth H. Nealson

C-DEBI Contribution Number: 208

Chapter 2.5 – Life in the Ocean Crust: Lessons from Subseafloor Laboratories

Published: January 1, 2014

Earth and Life Processes Discovered from Subseafloor Environments - A Decade of Science Achieved by the Integrated Ocean Drilling Program (IODP)

Authors: Beth N. Orcutt, Katrina J. Edwards

C-DEBI Contribution Number: 207

Extracellular Enzyme Activity and Microbial Diversity Measured on Seafloor Exposed Basalts from Loihi Seamount Indicate the Importance of Basalts to Global Biogeochemical Cycling

Published: June 6, 2014

Applied and Environmental Microbiology

Authors: Myrna E. Jacobson Meyers, Jason B. Sylvan, Katrina J. Edwards

C-DEBI Contribution Number: 206

Iron mineral structure, reactivity, and isotopic composition in a South Pacific Gyre ferromanganese nodule over 4Ma

Published: December 1, 2015

Geochimica et Cosmochimica Acta

Authors: Matthew A. Marcus, Katrina J. Edwards, Bleuenn Gueguen, Sirine C. Fakra, Gregory Horn, Nicolas A. Jelinski, Olivier Rouxel, Jeffry Sorensen, Brandy M. Toner

C-DEBI Contribution Number: 205

Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin

Published: March 6, 2014

The ISME Journal

Authors: Anne-Kristen Kaster, Koshlan Mayer-Blackwell, Ben Pasarelli, Alfred M. Spormann

C-DEBI Contribution Number: 202

Carbon adsorption onto Fe oxyhydroxide stalks produced by a lithotrophic iron-oxidizing bacteria

Published: January 16, 2014

Geobiology

Authors: Sarah A. Bennett, Brandy M. Toner, Roman A. Barco, Katrina J. Edwards

C-DEBI Contribution Number: 201

IODP Deep Biosphere Research Workshop report – a synthesis of recent investigations, and discussion of new research questions and drilling targets

Published: April 29, 2014

Scientific Drilling

Authors: Beth N. Orcutt, Douglas E. LaRowe, Karen G. Lloyd, Heath J. Mills, William D. Orsi, Brandi Kiel Reese, Justine Sauvage, Julie A. Huber, Jan P. Amend

C-DEBI Contribution Number: 200

7. Archaea in deep marine subsurface sediments

Published: January 1, 2014

Microbial Life of the Deep Biosphere

Authors: Andreas P. Teske

Editors: Jens Kallmeyer,

C-DEBI Contribution Number: 199

Deep-sea hydrothermal vent Epsilonproteobacteria encode a conserved and widespread nitrate reduction pathway (Nap)

Published: January 16, 2014

The ISME Journal

Authors: Costantino Vetriani, James W. Voordeckers, Melitza Crespo-Medina, Charles E. O’Brien, Donato Giovannelli, Richard A. Lutz

C-DEBI Contribution Number: 198

Sulphide oxidation and carbonate dissolution as a source of CO2 over geological timescales

Published: March 19, 2014

Nature

Authors: Mark A. Torres, A. Joshua West, Gaojun Li

C-DEBI Contribution Number: 197

2. Life in the Oceanic Crust

Published: January 1, 2014

Microbial Life of the Deep Biosphere

Authors: Jennifer F. Biddle, Sean P. Jungbluth, Mark A. Lever, Michael S. Rappé

Editors: Jens Kallmeyer,

C-DEBI Contribution Number: 196

Metagenomic analysis of organic matter degradation in methane-rich Arctic Ocean sediments

Published: March 1, 2014

Limnology and Oceanography

Authors: David L. Kirchman, Thomas E. Hanson, Matthew T. Cottrell, Leila J. Hamdan

C-DEBI Contribution Number: 195

Deep subsurface microbiology: a guide to the research topic papers

Published: January 1, 2013

Frontiers in Microbiology

Authors: Andreas P. Teske, Jennifer F. Biddle, Virginia P. Edgcomb, Axel Schippers

C-DEBI Contribution Number: 194

Stabilizing the foundation of the house that ‘omics builds: the evolving value of cultured isolates to marine microbiology

Published: October 1, 2013

Current Opinion in Microbiology

Authors: Michael S. Rappé

C-DEBI Contribution Number: 193

The "Adopt-A-Microbe" Project: A multi-disciplinary science curriculum for middle school students

Published: January 1, 2013

Current: The Journal of Marine Education

Authors: Beth N. Orcutt, Sharon K. Cooper, Amanda G. Haddad, Cynthia Joseph, Stephanie Schroeder

C-DEBI Contribution Number: 192

Theme 4: Evolution and Survival

Published: January 1, 2013

Metcalf Instiute for Marine & Environmental Reporting

Authors: John B. Kirkpatrick, Sunshine Menezes, K. McDuffie, Sara Hickox

C-DEBI Contribution Number: 191

Published: January 1, 2013

Metcalf Instiute for Marine & Environmental Reporting

Theme 3: Limits of Life

Authors: John B. Kirkpatrick, Sunshine Menezes, K. McDuffie, Sara Hickox

C-DEBI Contribution Number: 190

Published: January 1, 2013

Metcalf Instiute for Marine & Environmental Reporting

Theme 2: Extent of Life

Authors: John B. Kirkpatrick, Sunshine Menezes, K. McDuffie, Sara Hickox

C-DEBI Contribution Number: 189

Theme 1: Activity in the Deep Subsea Biosphere

Published: January 1, 2013

Metcalf Instiute for Marine & Environmental Reporting

Authors: John B. Kirkpatrick, Sunshine Menezes, K. McDuffie, Sara Hickox

C-DEBI Contribution Number: 188

Ocean currents shape the microbiome of Arctic marine sediments

Published: November 29, 2012

The ISME Journal

Authors: Leila J. Hamdan, Richard B. Coffin, Masoumeh Sikaroodi, Jens Greinert, Tina Treude, Patrick M. Gillevet

C-DEBI Contribution Number: 187

Capitalizing on expertise in marine education and outreach to broaden impacts

Published: January 1, 2013

Current: The Journal of Marine Education

Authors: Peter R. Girguis, A. DeCharon, C. Herren

C-DEBI Contribution Number: 186

Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene

Published: May 6, 2013

Proceedings of the National Academy of Sciences

Authors: Marco J. L. Coolen, William D. Orsi, C. Balkema, C. Quince, Kate Harris, Sean P. Sylva, M. Filipova-Marinova, Liviu Giosan

C-DEBI Contribution Number: 185

Identity and mechanisms of alkane-oxidizing metalloenzymes from deep-sea hydrothermal vents

Published: January 1, 2013

Frontiers in Microbiology

Authors: Erin M. Bertrand, Ramaydalis Keddis, John T. Groves, Costantino Vetriani, Rachel Narehood Austin

C-DEBI Contribution Number: 184

The energetics of organic synthesis inside and outside the cell

Published: June 10, 2013

Philosophical Transactions of the Royal Society B: Biological Sciences

Authors: Jan P. Amend, Douglas E. LaRowe, Thomas M. McCollom, Everett L. Shock

C-DEBI Contribution Number: 183

Quantifying the degradation of organic matter in marine sediments: A review and synthesis

Published: August 1, 2013

Earth-Science Reviews

Authors: Sandra Arndt, Bo Barker Jørgensen, Douglas E. LaRowe, J. J. Middelburg, Richard D. Pancost, Pierre Regnier

C-DEBI Contribution Number: 182

Data report: microbial diversity in sediment near Grizzly Bare Seamount in Holes U1363B and U1363G

Published: September 5, 2011

Proceedings of the IODP

Authors: Sean P. Jungbluth, L. G. H. Johnson, James P. Cowen, Michael S. Rappé

C-DEBI Contribution Number: 181

Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano

Published: November 21, 2013

The ISME Journal

Authors: Julie L. Meyer, Julie A. Huber

C-DEBI Contribution Number: 181

Modeling microbial reaction rates in a submarine hydrothermal vent chimney wall

Published: January 1, 2014

Geochimica et Cosmochimica Acta

Authors: Douglas E. LaRowe, Andrew W. Dale, David R. Aguilera, Ivan L’Heureux, Jan P. Amend, Pierre Regnier

C-DEBI Contribution Number: 178

Predominant archaea in marine sediments degrade detrital proteins

Published: March 27, 2013

Nature

Authors: Karen G. Lloyd, Lars Schreiber, Dorthe G. Petersen, Kasper U. Kjeldsen, Mark A. Lever, Andrew D. Steen, Ramunas Stepanauskas, Michael Richter, Sara Kleindienst, Sabine Lenk, Andreas Schramm, Bo Barker Jørgensen

C-DEBI Contribution Number: 177

Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor

Published: October 4, 2013

Applied and Environmental Microbiology

Authors: Karen G. Lloyd, M. K. May, Richard T. Kevorkian, Andrew D. Steen

C-DEBI Contribution Number: 176

Extracellular enzymes in terrestrial, freshwater, and marine environments: perspectives on system variability and common research needs

Published: September 3, 2013

Biogeochemistry

Authors: Carol Arnosti, C. Bell, D. L. Moorhead, R. L. Sinsabaugh, Andrew D. Steen, M. Stromberger, M. Wallenstein, M. N. Weintraub

C-DEBI Contribution Number: 175

The Potential for Biologically Catalyzed Anaerobic Methane Oxidation on Ancient Mars

Published: April 1, 2014

Astrobiology

Authors: Jeffrey J. Marlow, Douglas E. LaRowe, Bethany L. Ehlmann, Jan P. Amend, Victoria J. Orphan

C-DEBI Contribution Number: 174

Characterizing borehole fluid flow and formation permeability in the ocean crust using linked analytic models and Markov chain Monte Carlo analysis

Published: September 1, 2013

Geochemistry, Geophysics, Geosystems

Authors: Dustin M. Winslow, Andrew T. Fisher, Keir Becker

C-DEBI Contribution Number: 173

Geochemistry: Subsurface sustenance

Published: May 26, 2013

Nature Geoscience

Authors: Steven L. D’Hondt

C-DEBI Contribution Number: 172

Serpentinites, Hydrogen, and Life

Published: April 1, 2013

Elements

Authors: Thomas M. McCollom, Jeffrey S. Seewald

C-DEBI Contribution Number: 171

RETINA: Illuminating elementary scientists with STEM modules

Published: January 1, 2013

Current: The Journal of Marine Education

Authors: Charles Geoffrey Wheat, Claudia Paul, Trevor Fournier, L. Arnow, Karen Monahan

C-DEBI Contribution Number: 170

13. Energetic constraints on life in marine deep sediments

Published: March 31, 2014

Microbial Life of the Deep Biosphere

Authors: Douglas E. LaRowe, Jan P. Amend

Editors: Jens Kallmeyer,

C-DEBI Contribution Number: 169

Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents

Published: March 28, 2013

The ISME Journal

Authors: Kiana L. Frank, Daniel R. Rogers, Heather C. Olins, Charles Vidoudez, Peter R. Girguis

C-DEBI Contribution Number: 168

Microbial communities associated with ferromanganese nodules and the surrounding sediments

Published: January 1, 2013

Frontiers in Microbiology

Authors: Benjamin J. Tully, John F. Heidelberg

C-DEBI Contribution Number: 167

Oxygen consumption rates in subseafloor basaltic crust derived from a reaction transport model

Published: September 27, 2013

Nature Communications

Authors: Beth N. Orcutt, Charles Geoffrey Wheat, Olivier Rouxel, Samuel M. Hulme, Katrina J. Edwards, Wolfgang Bach

C-DEBI Contribution Number: 166

Microbes: Out of the classroom and into the field

Published: January 1, 2013

Current: The Journal of Marine Education

Authors: Stephanie Schroeder, Cynthia Joseph

C-DEBI Contribution Number: 165

Microbiological characterization of post-eruption “snowblower” vents at Axial Seamount, Juan de Fuca Ridge

Published: January 1, 2013

Frontiers in Microbiology

Authors: Julie L. Meyer, Nancy H. Akerman, Giora Proskurowski, Julie A. Huber

C-DEBI Contribution Number: 164

New packer experiments and borehole logs in upper oceanic crust: Evidence for ridge-parallel consistency in crustal hydrogeological properties

Published: August 1, 2013

Geochemistry, Geophysics, Geosystems

Authors: Keir Becker, Andrew T. Fisher, Takeshi Tsuji

C-DEBI Contribution Number: 163

Assessment and use of NGR instrumentation on the JOIDES Resolution to quantify U, Th, and K concentrations in marine sediment

Published: March 29, 2013

Scientific Drilling

Authors: Ann G. Dunlea, Richard W. Murray, Robert N. Harris, Maxim A. Vasiliev, Helen Evans, Arthur J. Spivack, Steven L. D’Hondt

C-DEBI Contribution Number: 162

IODP Expedition 329: Life and Habitability Beneath the Seafloor of the South Pacific Gyre

Published: March 29, 2013

Scientific Drilling

Authors: Steven L. D’Hondt, Fumio Inagaki, Carlos A. Alvarez Zarikian

C-DEBI Contribution Number: 161

Interstitial fluid chemistry of sediments underlying the North Atlantic gyre and the influence of subsurface fluid flow

Published: March 1, 2012

Earth and Planetary Science Letters

Authors: Wiebke Ziebis, James McManus, Timothy Ferdelman, Friederike Schmidt-Schierhorn, Wolfgang Bach, Jesse Muratli, Katrina J. Edwards, Heinrich Villinger

C-DEBI Contribution Number: 160

Geochemistry of basalts from IODP site U1365: Implications for magmatism and mantle source signatures of the mid-Cretaceous Osbourn Trough

Published: July 1, 2012

Lithos

Authors: Guoliang Zhang, Christopher E. Smith-Duque, Suohan Tang, He Li, Carlos A. Alvarez Zarikian, Steven L. D’Hondt, Fumio Inagaki

C-DEBI Contribution Number: 159

Tracking microbial habitats in subseafloor sediments

Published: October 9, 2012

Proceedings of the National Academy of Sciences

Authors: Andreas P. Teske

C-DEBI Contribution Number: 158

Seawater recharge into oceanic crust: IODP Exp 327 Site U1363 Grizzly Bare outcrop

Published: June 1, 2013

Geochemistry, Geophysics, Geosystems

Authors: Charles Geoffrey Wheat, Samuel M. Hulme, Andrew T. Fisher, Beth N. Orcutt, Keir Becker

C-DEBI Contribution Number: 157

Olivine-Respiring Bacteria Isolated from the Rock-Ice Interface in a Lava-Tube Cave, a Mars Analog Environment

Published: January 1, 2012

Astrobiology

Authors: Radu Popa, Amy R. Smith, Rodica Popa, Jane Boone, Martin R. Fisk

C-DEBI Contribution Number: 155

Microbial activity in the marine deep biosphere: progress and prospects

Published: January 1, 2013

Frontiers in Microbiology

Authors: Beth N. Orcutt, Douglas E. LaRowe, Jennifer F. Biddle, Frederick S. Colwell, Brian T. Glazer, Brandi Kiel Reese, John B. Kirkpatrick, Laura L. Lapham, Heath J. Mills, Jason B. Sylvan, Scott D. Wankel, Charles Geoffrey Wheat

C-DEBI Contribution Number: 154

Microbial communities at the borehole observatory on the Costa Rica Rift flank (Ocean Drilling Program Hole 896A)

Published: January 1, 2012

Frontiers in Microbiology

Authors: Lisa M. Nigro, Kate Harris, Beth N. Orcutt, Andrew Hyde, Samuel Clayton-Luce, Keir Becker, Andreas P. Teske

C-DEBI Contribution Number: 153

Microbial distributions detected by an oligonucleotide microarray across geochemical zones associated with methane in marine sediments from the Ulleung Basin

Published: November 1, 2013

Marine and Petroleum Geology

Authors: Brandon R. Briggs, Michael F. Graw, Eoin L. Brodie, Jang-Jun Bahk, Sung-Han Kim, Jung-Ho Hyun, Ji-Hoon Kim, Marta Torres, Frederick S. Colwell

C-DEBI Contribution Number: 152

Mariana Forearc Serpentinite Mud Volcanoes Harbor Novel Communities of Extremophilic Archaea

Published: March 13, 2013

Geomicrobiology Journal

Authors: Andrea C. Curtis, Charles Geoffrey Wheat, Patricia Fryer, Craig L. Moyer

C-DEBI Contribution Number: 151

Low Temperature Geomicrobiology Follows Host Rock Composition Along a Geochemical Gradient in Lau Basin

Published: January 1, 2013

Frontiers in Microbiology

Authors: Jason B. Sylvan, Tiffany Y. Sia, Amanda G. Haddad, Lindsey J. Briscoe, Brandy M. Toner, Peter R. Girguis, Katrina J. Edwards

C-DEBI Contribution Number: 150

Ecology and Cultivation of Marine Oligotrophic Bacteria

Published: January 1, 2011

Extremophiles Handbook

Authors: Darin H. Hayakawa, Megan J. Huggett, Michael S. Rappé

Editors: Koki Horikoshi

C-DEBI Contribution Number: 149

Introduction to the Special Issue: From RIDGE to Ridge 2000

Published: March 1, 2012

Oceanography

Authors: Daniel Fornari, Stace Beaulieu, James Holden, Lauren Mullineaux, Maya Tolstoy

C-DEBI Contribution Number: 148

Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin

Published: March 23, 2012

Geobiology

Authors: Gilberto E. Flores, M. Shakya, J. Meneghin, Z. K. Yang, Jeffrey S. Seewald, Charles Geoffrey Wheat, Mircea Podar, A.-L. Reysenbach

C-DEBI Contribution Number: 147

Publications > Report

Published: January 9, 2012

IODP Expedition 336 Preliminary Report

Mid-Atlantic Ridge microbiology: Initiation of long-term coupled microbiological, geochemical, and hydrological experimentation within the seafloor at North Pond, western flank of the Mid-Atlantic Ridge

Authors: Expedition 336 Scientists

C-DEBI Contribution Number: 146

Characterizing Microbial Community and Geochemical Dynamics at Hydrothermal Vents Using Osmotically Driven Continuous Fluid Samplers

Published: May 7, 2013

Environmental Science & Technology

Authors: Julie Robidart, Stephen J. Callister, Pengfei Song, Carrie D. Nicora, Charles Geoffrey Wheat, Peter R. Girguis

C-DEBI Contribution Number: 145

Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l

Published: January 1, 2013

Frontiers in Microbiology

Authors: Esther Singer, John F. Heidelberg, Ashita Dhillon, Katrina J. Edwards

C-DEBI Contribution Number: 144

Archaea in Organic-Lean and Organic-Rich Marine Subsurface Sediments: An Environmental Gradient Reflected in Distinct Phylogenetic Lineages

Published: January 1, 2012

Frontiers in Microbiology

Authors: Alan M. Durbin, Andreas P. Teske

C-DEBI Contribution Number: 143

Nature and Extent of the Deep Biosphere

Published: January 1, 2013

Reviews in Mineralogy and Geochemistry

Authors: Frederick S. Colwell, Steven L. D’Hondt

C-DEBI Contribution Number: 142

Energy yields from chemolithotrophic metabolisms in igneous basement of the Juan de Fuca ridge flank system

Published: January 1, 2013

Chemical Geology

Authors: Jason Boettger, Huei-Ting Lin, James P. Cowen, Michael Hentscher, Jan P. Amend

C-DEBI Contribution Number: 141

Hydrothermal Discharge During Submarine Eruptions: The Importance of Detection, Response, and New Technology

Published: March 1, 2012

Oceanography

Authors: Edward Baker, William Chadwick, James P. Cowen, Robert Dziak, Kenneth Rubin, Daniel Fornari

C-DEBI Contribution Number: 140

Evidence for Microbial Carbon and Sulfur Cycling in Deeply Buried Ridge Flank Basalt

Published: March 14, 2013

Science

Authors: Mark A. Lever, Olivier Rouxel, Jeffrey C. Alt, N. Shimizu, Shuhei Ono, R. M. Coggon, W. C. Shanks, Laura L. Lapham, M. Elvert, X. Prieto-Mollar, Kai-Uwe Hinrichs, Fumio Inagaki, Andreas P. Teske

C-DEBI Contribution Number: 139

The Classroom Connection program: Bringing deep sea research to students of all learning levels

Published: January 1, 2012

Current: The Journal of Marine Education

Authors: Amanda G. Haddad, M. K. Turner, Cynthia Joseph, Beth N. Orcutt, L. Samuelson, Shipboard Parties of IODP Expedition 336 and MSM 20/5

C-DEBI Contribution Number: 138

Gene expression in the deep biosphere

Published: June 12, 2013

Nature

Authors: William D. Orsi, Virginia P. Edgcomb, Glenn D. Christman, Jennifer F. Biddle

C-DEBI Contribution Number: 137

Global distribution of microbial abundance and biomass in subseafloor sediment

Published: August 27, 2012

Proceedings of the National Academy of Sciences

Authors: Jens Kallmeyer, Robert Pockalny, Rishi R. Adhikari, David C. Smith, Steven L. D’Hondt

C-DEBI Contribution Number: 136

Discovering the roles of subsurface microorganisms: Progress and future of deep biosphere investigation

Published: August 16, 2012

Chinese Science Bulletin

Authors: Fengping Wang, ShuLin Lu, Beth N. Orcutt, Wei Xie, Ying Chen, Xiang Xiao, Katrina J. Edwards

C-DEBI Contribution Number: 135

Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank

Published: July 12, 2012

The ISME Journal

Authors: Sean P. Jungbluth, Jana Grote, Huei-Ting Lin, James P. Cowen, Michael S. Rappé

C-DEBI Contribution Number: 134

Summary of carbon, nitrogen, and iron leaching characteristics and fluorescence properties of materials considered for subseafloor observatory assembly

Published: November 16, 2012

Proceedings of the IODP

Authors: Beth N. Orcutt, Roman A. Barco, Samantha B. Joye, Katrina J. Edwards

C-DEBI Contribution Number: 133

CORK-Lite: Bringing Legacy Boreholes Back to Life

Published: September 28, 2012

Scientific Drilling

Authors: Charles Geoffrey Wheat, Katrina J. Edwards, Tom L. Pettigrew, Hans W. Jannasch, Keir Becker, Earl E. Davis, Heinrich Villinger, Wolfgang Bach

C-DEBI Contribution Number: 132

Design and deployment of borehole observatories and experiments during IODP Expedition 336, Mid-Atlantic Ridge flank at North Pond

Published: November 16, 2012

Proceedings of the IODP

Authors: Katrina J. Edwards, Charles Geoffrey Wheat, Beth N. Orcutt, Samuel M. Hulme, Keir Becker, Hans W. Jannasch, Amanda G. Haddad, Tom L. Pettigrew, W. Rhinehart, K. Grigar, Wolfgang Bach, W. Kirkwood, A. Klaus

C-DEBI Contribution Number: 131

Aerobic Microbial Respiration in 86-Million-Year-Old Deep-Sea Red Clay

Published: May 17, 2012

Science

Authors: Hans Røy, Jens Kallmeyer, Rishi R. Adhikari, Robert Pockalny, Bo Barker Jørgensen, Steven L. D’Hondt

C-DEBI Contribution Number: 130

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment

Published: March 18, 2012

Nature

Authors: Bente Aa. Lomstein, Alice T. Langerhuus, Steven L. D’Hondt, Bo Barker Jørgensen, Arthur J. Spivack

C-DEBI Contribution Number: 129

Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments above, within, and below the Sulfate–Methane Transition Zone

Published: April 3, 2012

Frontiers in Microbiology

Authors: Heath J. Mills, Brandi Kiel Reese, Alicia K. Shepard, Natascha Riedinger, Scot E. Dowd, Yuki Morono, Fumio Inagaki

C-DEBI Contribution Number: 128

The Deep Subsurface Biosphere in Igneous Ocean Crust: Frontier Habitats for Microbiological Exploration

Published: January 1, 2012

Frontiers in Microbiology

Authors: Katrina J. Edwards, Andrew T. Fisher, Charles Geoffrey Wheat

C-DEBI Contribution Number: 127

Characterization of Microbial Population Shifts during Sample Storage

Published: January 1, 2012

Frontiers in Microbiology

Authors: Heath J. Mills, Brandi Kiel Reese, Cruz St. Peter

C-DEBI Contribution Number: 126

Inorganic chemistry, gas compositions and dissolved organic carbon in fluids from sedimented young basaltic crust on the Juan de Fuca Ridge flanks

Published: May 1, 2012

Geochimica et Cosmochimica Acta

Authors: Huei-Ting Lin, James P. Cowen, Eric J. Olson, Jan P. Amend, Marvin D. Lilley

C-DEBI Contribution Number: 125

South Pacific Gyre Subseafloor Life

Published: December 13, 2011

Proceedings of the IODP

Authors: Steven L. D’Hondt, Fumio Inagaki, Carlos A. Alvarez Zarikian, Expedition 329 Scientists

C-DEBI Contribution Number: 124

Publications > Report

Published: August 8, 2011

IODP Expedition 329 Preliminary Report

South Pacific Gyre subseafloor life

Authors: Expedition 329 Scientists

C-DEBI Contribution Number: 123

Genomic Potential of Marinobacter aquaeolei, a Biogeochemical "Opportunitroph"

Published: February 18, 2011

Applied and Environmental Microbiology

Authors: Esther Singer, Eric A. Webb, William C. Nelson, John F. Heidelberg, N. Ivanova, A. Pati, Katrina J. Edwards

C-DEBI Contribution Number: 121

Chemistry of hot springs along the Eastern Lau Spreading Center

Published: February 1, 2011

Geochimica et Cosmochimica Acta

Authors: Michael J. Mottl, Jeffrey S. Seewald, Charles Geoffrey Wheat, Margaret K. Tivey, Peter J. Michael, Giora Proskurowski, Thomas M. McCollom, Eoghan Reeves, Jessica Sharkey, C.-F. You, L.-H. Chan, Thomas Pichler

C-DEBI Contribution Number: 120

Conditions and mechanism for the formation of iron-rich Montmorillonite in deep sea sediments (Costa Rica margin): Coupling high resolution mineralogical characterization and geochemical modeling

Published: March 1, 2011

Geochimica et Cosmochimica Acta

Authors: D. Charpentier, M. D. Buatier, E. Jacquot, A. Gaudin, Charles Geoffrey Wheat

C-DEBI Contribution Number: 119

Time-series analysis of two hydrothermal plumes at 9°50′N East Pacific Rise reveals distinct, heterogeneous bacterial populations

Published: January 4, 2012

Geobiology

Authors: Jason B. Sylvan, Benjamin C. Pyenson, Olivier Rouxel, Christopher R. German, Katrina J. Edwards

C-DEBI Contribution Number: 118

Oceanography: Carbon cycle at depth

Published: January 1, 2011

Nature Geoscience

Authors: Katrina J. Edwards

C-DEBI Contribution Number: 117

Life and Death of Deep-Sea Vents: Bacterial Diversity and Ecosystem Succession on Inactive Hydrothermal Sulfides

Published: January 24, 2012

mBio

Authors: Jason B. Sylvan, Brandy M. Toner, Katrina J. Edwards

C-DEBI Contribution Number: 116

The Deep, Dark Energy Biosphere: Intraterrestrial Life on Earth

Published: May 30, 2012

Annual Review of Earth and Planetary Sciences

Authors: Katrina J. Edwards, Keir Becker, Frederick S. Colwell

C-DEBI Contribution Number: 115

In situ enrichment of ocean crust microbes on igneous minerals and glasses using an osmotic flow-through device

Published: June 1, 2011

Geochemistry, Geophysics, Geosystems

Authors: Amy R. Smith, Radu Popa, Martin R. Fisk, Mark Nielsen, Charles Geoffrey Wheat, Hans W. Jannasch, Andrew T. Fisher, Keir Becker, Stefan M. Sievert, Gilberto E. Flores

C-DEBI Contribution Number: 114

Advanced instrument system for real-time and time-series microbial geochemical sampling of the deep (basaltic) crustal biosphere

Published: March 1, 2012

Deep Sea Research Part I: Oceanographic Research Papers

Authors: James P. Cowen, David A. Copson, James Jolly, Chih-Chiang Hsieh, Huei-Ting Lin, Brian T. Glazer, Charles Geoffrey Wheat

C-DEBI Contribution Number: 113

Prospects for the study of evolution in the deep biosphere

Published: January 1, 2012

Frontiers in Microbiology

Authors: Jennifer F. Biddle, Jason B. Sylvan, William J. Brazelton, Benjamin J. Tully, Katrina J. Edwards, Craig L. Moyer, John F. Heidelberg, William C. Nelson

C-DEBI Contribution Number: 112

IODP Expedition 327 and Atlantis Expedition AT 18-07:Observatories and Experiments on the Eastern Flank of the Juan de Fuca Ridge

Published: April 16, 2012

Scientific Drilling

Authors: Andrew T. Fisher, Takeshi Tsuji, Katerina Petronotis, Charles Geoffrey Wheat, Keir Becker, Jordan F. Clark, James P. Cowen, Katrina J. Edwards, Hans W. Jannasch

C-DEBI Contribution Number: 111

Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium

Published: September 23, 2011

PLoS ONE

Authors: Esther Singer, David Emerson, Eric A. Webb, Roman A. Barco, J. Gijs Kuenen, William C. Nelson, Clara S. Chan, Luis R. Comolli, Steve Ferriera, Justin Johnson, John F. Heidelberg, Katrina J. Edwards

Editors: Arkady B. Khodursky

C-DEBI Contribution Number: 110

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces

Published: February 13, 2013

PLoS ONE

Authors: William D. Orsi, Jennifer F. Biddle, Virginia P. Edgcomb

C-DEBI Contribution Number: 109

Under the sea: microbial life in volcanic oceanic crust

Published: September 6, 2011

Nature Reviews Microbiology

Authors: Katrina J. Edwards, Charles Geoffrey Wheat, Jason B. Sylvan

C-DEBI Contribution Number: 108

The ‘Adopt-A-Microbe’ Project: Web-based interactive microbiology education connected with scientific ocean drilling

Published: January 1, 2011

Current: The Journal of Marine Education

Authors: Beth N. Orcutt, Dinah Bowman, Katherine Inderbitzen, Amanda G. Haddad, Andrew T. Fisher, Leslie Peart

C-DEBI Contribution Number: 107

Tracing iron-fueled microbial carbon production within the hydrothermal plume at the Loihi seamount

Published: October 1, 2011

Geochimica et Cosmochimica Acta

Authors: Sarah A. Bennett, Roberta L. Hansman, Alex L. Sessions, Ko-ichi Nakamura, Katrina J. Edwards

C-DEBI Contribution Number: 106

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

Published: June 1, 2011

Microbiology and Molecular Biology Reviews

Authors: Beth N. Orcutt, Jason B. Sylvan, Nina J. Knab, Katrina J. Edwards

C-DEBI Contribution Number: 105

The Need for Scientific Ocean Drilling

Published: March 8, 2011

Eos, Transactions American Geophysical Union

Authors: Susan E. Humphris, Peter B. deMenocal, Katrina J. Edwards, Andrew T. Fisher, Demian Saffer

C-DEBI Contribution Number: 104

Fluid sampling from oceanic borehole observatories: design and methods for CORK activities (19902010)

Published: September 5, 2011

Proceedings of the IODP

Authors: Charles Geoffrey Wheat, Hans W. Jannasch, M. Kastner, Samuel M. Hulme, James P. Cowen, Katrina J. Edwards, Beth N. Orcutt, Brian T. Glazer

C-DEBI Contribution Number: 103

Preparation and injection of fluid tracers during IODP Expedition 327, eastern flank of Juan de Fuca Ridge

Published: September 5, 2011

Proceedings of the IODP

Authors: Andrew T. Fisher, James P. Cowen, Charles Geoffrey Wheat, Jordan F. Clark

C-DEBI Contribution Number: 102

Design, deployment, and status of borehole observatory systems used for single-hole and cross-hole experiments, IODP Expedition 327, eastern flank of Juan de Fuca Ridge

Published: September 5, 2011

Proceedings of the IODP

Authors: Andrew T. Fisher, Charles Geoffrey Wheat, Keir Becker, James P. Cowen, Beth N. Orcutt, Samuel M. Hulme, Katherine Inderbitzen, Amanda G. Haddad, Tom L. Pettigrew, Earl E. Davis, Hans W. Jannasch, K. Grigar, R. Aduddell, R. Meldrum, R. Macdonald, Katrina J. Edwards

C-DEBI Contribution Number: 101

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

The ISME Journal

Authors: Joel A. Boyd, Sean P. Jungbluth, Andy O. Leu, Paul N. Evans, Ben J. Woodcroft, Grayson L. Chadwick, Victoria J. Orphan, Jan P. Amend, Michael S. Rappé, Gene W. Tyson

Published: January 16, 2019

C-DEBI Contribution Number: 457

Abstract

The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane, and potentially propane. The number of archaeal clades encoding the MCR continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; Ca. Polytropus marinifundus gen. nov. sp. nov.) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Ca. Bathyarchaeota and Ca. Syntrophoarchaeum MAGs. Ca. P. marinifundus is basal to members of the class Archaeoglobi, and encodes the genes for β-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. Ca. P. marinifundus also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. Phylogenetic analysis suggests that the Ca. P. marinifundus MCR operons were horizontally transferred, changing our understanding of the evolution and distribution of this complex in the Archaea.

Source: http://dx.doi.org/10.1038/s41396-018-0343-2

Geology and Fluid Discharge at Dorado Outcrop, a Low Temperature Ridge-Flank Hydrothermal System

Geochemistry, Geophysics, Geosystems

Authors: Charles Geoffrey Wheat, Anne M. Hartwell, James McManus, Andrew T. Fisher, Beth N. Orcutt, Lucy E. Schlicht, Sara Niedenzu, Wolfgang Bach

Published: January 12, 2019

C-DEBI Contribution Number: 456

Abstract

Two expeditions to Dorado Outcrop on the eastern flank of the East Pacific Rise and west of the Middle America Trench collected images, video, rocks and sediment samples and measured temperature and fluid discharge rates to document the physical and biogeochemical characteristics of a regional, low‐temperature (~15°C) hydrothermal system. Analysis of video and images identified lava morphologies: pillow, lobate, and sheet flows. Glasses from collected lavas were consistent with an off‐axis formation. Hydrothermal discharge generally occurs through pillow lavas, but is patchy, sporadic, and sometimes ceases at particular sites of discharge. Year‐long temperature measurements at five of these discharge sites show daily ranges that oscillate with tidal frequencies by 6°C or more. Instantaneous fluid discharge rates (0.16 to 0.19 L s^‐1) were determined resulting in a calculated discharge of ~200 L s^‐1 when integrated over the area defined by the most robust fluid discharge. Such discharge has a power output of 10‐12 MW. Hydrothermal seepage through thin sediment adjacent to the outcrop accounts for <3% of this discharge, but seepage may support an oxic sediment column. High extractable Mn concentrations and depleted δ¹³C in the low but variable organic solid phase suggest hydrothermal fluids provide a source for manganese accumulation and likely enhance the oxidation of organic carbon. Comparisons of the physical and geochemical characteristics at Dorado and Baby Bare Outcrops, the latter being the only other site of ridge‐flank hydrothermal discharge that has been sampled directly, suggest commonalities and differences that have implications for future discoveries.

Source: http://dx.doi.org/10.1029/2018gc007933

Related Items

Awards

Award Dates: August 25, 2013 — February 24, 2016

Awards

Discrimination of detrital genes from marine sediments

Award Dates: December 31, 2016 — December 30, 2018

Awardee: Gustavo A. Ramírez (University of Rhode Island)

Degree: Ph.D. Marine Biology and Biological Oceanography, University of Southern California (2016)

Advisor: Steven L. D’Hondt (University of Rhode Island)

Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea

Frontiers in Microbiology

Published: December 3, 2018

C-DEBI Contribution Number: 449

Abstract

Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases. Based on characterized homologs and the lack of associated energy conserving complexes, the sulfate reduction pathways in ANME are likely used for assimilation but not dissimilation of sulfate. Environmental metaproteomic analysis confirmed the expression of 6 proteins in the sulfate assimilation pathway of ANME. The highest expressed proteins related to sulfate assimilation were two sulfite reductases, namely assimilatory-type low-molecular-weight sulfite reductase (alSir) and a divergent group of coenzyme F₄₂₀-dependent sulfite reductase (Group II Fsr). In methane seep sediment microcosm experiments, however, sulfite and zero-valent sulfur amendments were inhibitory to ANME-2a/2c while growth in their syntrophic SRB partner was not observed. Combined with our genomic and metaproteomic results, the passage of sulfur species by ANME as metabolic intermediates for their SRB partners is unlikely. Instead, our findings point to a possible niche for ANME to assimilate inorganic sulfur compounds more oxidized than sulfide in anoxic marine environments.

Source: http://dx.doi.org/10.3389/fmicb.2018.02917

Microbial organic matter degradation potential in Baltic Sea sediments influenced by depositional conditions and in situ geochemistry

Applied and Environmental Microbiology

Authors: Laura A. Zinke, Clemens Glombitza, Jordan T. Bird, Hans Røy, Bo Barker Jørgensen, Karen G. Lloyd, Jan P. Amend, Brandi Kiel Reese

Published: November 30, 2018

C-DEBI Contribution Number: 448

Abstract

Globally, marine sediments are a vast repository of organic matter which is degraded through various microbial pathways, including polymer hydrolysis and monomer fermentation. The sources, abundances, and quality (i.e. labile or recalcitrant) of the organic matter and the composition of the microbial assemblages vary between sediments. Here, we examine new and previously published sediment metagenomes from the Baltic Sea and the nearby Kattegat to determine connections between geochemistry and the community potential to degrade organic carbon. Diverse organic matter hydrolysis encoding genes were present in sediments between 0.25 to 67 meters below seafloor, and were in higher relative abundances in those sediments that contained more organic matter. New analysis of previously published metatranscriptomes demonstrated that many of these genes were transcribed in two organic-rich Holocene sediments. Some of the variation in deduced pathways in the metagenomes correlated to carbon content and depositional conditions. Fermentation-related genes were found in all samples, and encoded for multiple fermentation strategies. Notably, genes conferring alcohol metabolism were amongst the most abundant of these genes, indicating this is an important but underappreciated aspect of sediment carbon cycling. This study is a step towards a more complete understanding of microbial food webs and the impacts of depositional facies on present sedimentary microbial communities.

Source: http://dx.doi.org/10.1128/aem.02164-18

Take to the high seas: microbiology labs below the ocean surface

Environmental Microbiology Reports

Authors: Julie A. Huber, Christina Preston

Published: November 22, 2018

C-DEBI Contribution Number: 445

Abstract

Looking into the Crystal Ball, near term we see an expanding toolkit for microbial oceanographers and environmental microbiologists more broadly, allowing for improved spatial and temporal sampling, as well as in situ experimentation and analysis. Given many of the pieces exist in different instruments, we are confident that focused efforts to bring them together in one instrument to take us from sample collection to experiment to data is possible. Importantly, there will always be a need for expeditionary‐ and laboratory‐based work. The power of being at sea to take in a new study site and carefully collect those first few samples, thus building the hypotheses and experiments needed to answer the scientific questions, cannot be replaced. The oceans remain woefully under‐studied and under‐sampled, and the powerful microbial engines of the marine biosphere merit our attention and innovation. The next decade will provide important opportunities to observe, study and query marine microorganisms from afar, watching experiments unfold in real time as our instruments help carry out our mission to explore Earth's inner space below the ocean's surface.

Source: http://dx.doi.org/10.1111/1758-2229.12714

Geological storage of CO2 in sub-seafloor basalt: the CarbonSAFE pre-feasibility study offshore Washington State and British Columbia

Energy Procedia

Published: July 1, 2018

C-DEBI Contribution Number: 443

Microorganisms buried in marine sediments are known to endure starvation over geologic timescales. However, the mechanisms of how these microorganisms cope with prolonged energy limitation is unknown and therefore yet to be captured in a quantitative framework. Here, we present a novel mathematical model that considers (a) the physiological transitions between the active and dormant states of microorganisms, (b) the varying requirement for maintenance power between these phases, and (c) flexibility in the provenance (i.e., source) of energy from exogenous and endogenous catabolism. The model is applied to sediments underlying the oligotrophic South Pacific Gyre where microorganisms endure ultra‐low fluxes of energy for tens of millions of years. Good fits between model simulations and measurements of cellular carbon and organic carbon concentrations are obtained and are interpreted as follows: (a) the unfavourable microbial habitat in South Pacific Gyre sediments triggers rapid mortality and a transition to dormancy; (b) there is minimal biomass growth, and organic carbon consumption is dominated by catabolism to support maintenance activities rather than new biomass synthesis; (c) the amount of organic carbon that microorganisms consume for maintenance activities is equivalent to approximately 2% of their carbon biomass per year; and (d) microorganisms must rely solely on exogenous rather than endogenous catabolism to persist in South Pacific Gyre sediments over long timescales. This leads us to the conclusion that under oligotrophic conditions, the fitness of an organism is determined by its ability to simply stay alive, rather than to grow. This modelling framework is designed to be flexible for application to other sites and habitats, and thus serves as a new quantitative tool for determining the habitability of and an ultimate limit for life in any environment.

Source: http://dx.doi.org/10.1111/gbi.12313

Related Items

Awards

Develop a 1D biogeochemical-evolutionary model for deep sediments

Award Dates: October 10, 2016 — October 9, 2018

Awardee: James A. Bradley (University of Southern California)

Degree: Ph.D. Geographical Sciences, University of Bristol (2016)

Advisor: Douglas E. LaRowe (University of Southern California)

Three-dimensional models of hydrothermal circulation through a seamount network on fast-spreading crust

Earth and Planetary Science Letters

Authors: Rachel M. Lauer, Andrew T. Fisher, Dustin M. Winslow

Published: November 1, 2018

C-DEBI Contribution Number: 439

Abstract

We present results from three-dimensional, transient, fully coupled simulations of fluid and heat transport on a ridge flank in fast-spread ocean crust. The simulations quantify relationships between rates of fluid flow, the extent of advective heat extraction, the geometry of crustal aquifers and outcrops, and crustal hydrologic parameters, with the goal of simulating conditions similar to those seen on 18–24 M.y. old seafloor of the Cocos plate, offshore Costa Rica. Extensive surveys of this region documented a ∼14,500 km² area of the seafloor with heat flux values that are 10–35% of those predicted from conductive cooling models, and identified basement outcrops that serve as pathways for hydrothermal circulation via recharge of bottom water and discharge of cool hydrothermal fluid. Simulations suggest that in order for rapid hydrothermal circulation to achieve observed seafloor heat flux values, upper crustal permeability is likely to be ~10^-10 to 10^-9m², with more simulations matching observations at the upper end of this range. These permeabilities are at the upper end of values measured in boreholes elsewhere in the volcanic ocean crust, and higher than inferred from three-dimensional modeling of another ridge-flank field site where there is less fluid flow and lower advective power output. The simulations also show that, in a region with high crustal permeability and variable sized outcrops, hydrothermal outcrop-to-outcrop circulation is likely to constitute a small fraction of total fluid circulation, with most of fluid flow occurring locally through individual outcrops that both recharge and discharge hydrothermal fluid.

Source: http://dx.doi.org/10.1016/j.epsl.2018.08.025

Marine Shallow-Water Hydrothermal Vents: Geochemistry

Reference Module in Earth Systems and Environmental Sciences

Authors: Roy E. Price, Donato Giovannelli

Published: September 12, 2018

C-DEBI Contribution Number: 435

Abstract

Marine shallow-water hydrothermal vents are defined as occurring at less than ~ 200 m below sea level, and are often found off the coasts of island arc volcanoes, which provide the necessary heat source to drive circulation. Recent research suggests that marine shallow-water hydrothermal vents, also known as “shallow-sea” vents (SHVs), are abundant across the Earth. While they have many similarities to deep-sea hydrothermal vents (DHVs), they also have many important differences, primarily due to their occurrence at shallower depths. Here we introduce SHVs and describe some of the processes which influence their geochemistry. This information is summarized from Price and Giovannelli (2017), and is complementary to Giovannelli and Price (2018), which describes the microbiology of shallow-sea vents.

Source: http://dx.doi.org/10.1016/b978-0-12-409548-9.11015-2

Variation in electrode redox potential selects for different microorganisms under cathodic current flow from electrodes in marine sediments

Environmental Microbiology

Authors: Bonita R. Lam, Annette R. Rowe, Kenneth H. Nealson

Published: June 1, 2018

C-DEBI Contribution Number: 433

Abstract

Extracellular electron transport (EET) is a microbial process that allows microorganisms to transport electrons to and from insoluble substrates outside of the cell. Although progress has been made in understanding how microbes transfer electrons to insoluble substrates, the process of receiving electrons has largely remained unexplored. We investigated redox potentials favourable for donating electrons to dissolved and insoluble components in Catalina Harbor marine sediment by combining electrochemical techniques with geochemistry and molecular methods. Working electrodes buried in sediment microcosms were poised at seven redox potentials between −300 and −750 mV versus Ag/AgCl using a three‐electrode system. In electrode biofilms recovered after 2‐month incubations, overall community diversity increased with more negative redox potentials. Abundances of known EET‐capable groups (e.g., Alteromonadales and Desulfuromonadales) varied with redox potential. Motility and chemotaxis genes were found in greater abundance in electrode communities, suggesting a possible selective advantage of these pathways for colonization and utilization of the electrode. Our enrichments demonstrated the validity of this approach in capturing groups known, as well as novel groups (e.g., Campylobacterales) that perform EET. The diverse nature of the enriched cathode communities suggest that insoluble substrate oxidation may be a critical, although poorly described microbial metabolic process in marine sediment.

Source: http://dx.doi.org/10.1111/1462-2920.14275

Related Items

Awards

Investigating the diversity of extracellular electron transfer in deep sea marine sediment: A poorly understood microbial process with global implications

Award Dates: April 1, 2016 — June 30, 2017

PI: Kenneth H. Nealson (University of Southern California)

Passing electrons through marine sediments: Cultivation and characterization of microbes that utilize extracellular electron transport

Award Dates: May 1, 2013 — April 30, 2015

Awardee: Annette R. Rowe (University of Southern California)

Current Placement: Postdoc, USC, 2012-, USC

Degree: Ph.D. Microbiology, Cornell University (2011)

Advisor: Kenneth H. Nealson (University of Southern California)

Radiolytic H2 Production in Martian Environments

Astrobiology

Authors: Mary E. Dzaugis, Arthur J. Spivack, Steven L. D’Hondt

Published: July 26, 2018

C-DEBI Contribution Number: 388

Abstract

Hydrogen, produced by water radiolysis, has been suggested to support microbial communities on Mars. We quantitatively assess the potential magnitude of radiolytic H₂ production in wet martian environments (the ancient surface and the present subsurface) based on the radionuclide compositions of (1) eight proposed Mars 2020 landing sites, and (2) three sites that individually yield the highest or lowest calculated radiolytic H₂ production rates on Mars. For the proposed landing sites, calculated H₂ production rates vary by a factor of ∼1.6, while the three comparison sites differ by a factor of ∼6. Rates in wet martian sediment and microfractured rock are comparable with rates in terrestrial environments that harbor low concentrations of microbial life (e.g., subseafloor basalt). Calculated H₂ production rates for low-porosity (<35%), fine-grained martian sediment (0.12–1.2 nM/year) are mostly higher than rates for South Pacific subseafloor basalt (∼0.02–0.6 nM/year). Production rates in martian high-porosity sediment (>35%) and microfractured (1 μm) hard rock (0.03 to <0.71 nM/year) are generally similar to rates in South Pacific basalt, while yields for larger martian fractures (1 and 10 cm) are one to two orders of magnitude lower (<0.01 nM/year). If minerals or brine that amplify radiolytic H₂ production rates are present, H₂ yields exceed the calculated rates.

Source: http://dx.doi.org/10.1089/ast.2017.1654

Elemental sulfur reduction in the deep-sea vent thermophile, Thermovibrio ammonificans

Environmental Microbiology

Authors: Benjamin I. Jelen, Donato Giovannelli, Paul G. Falkowski, Costantino Vetriani

Published: June 1, 2018

C-DEBI Contribution Number: 434

Abstract

The reduction of elemental sulfur is an important energy‐conserving pathway in prokaryotes inhabiting geothermal environments, where sulfur respiration contributes to sulfur biogeochemical cycling. Despite this, the pathways through which elemental sulfur is reduced to hydrogen sulfide remain unclear in most microorganisms. We integrated growth experiments using Thermovibrio ammonificans, a deep‐sea vent thermophile that conserves energy from the oxidation of hydrogen and reduction of both nitrate and elemental sulfur, with comparative transcriptomic and proteomic approaches, coupled with scanning electron microscopy. Our results revealed that two members of the FAD‐dependent pyridine nucleotide disulfide reductase family, similar to sulfide‐quinone reductase and to NADH‐dependent sulfur reductase (NSR), respectively, are over‐expressed during sulfur respiration. Scanning electron micrographs and sulfur sequestration experiments indicated that direct access of T. ammonificans to sulfur particles strongly promoted growth. The sulfur metabolism of T. ammonificans appears to require abiotic transition from bulk elemental sulfur to polysulfide to nanoparticulate sulfur at an acidic pH, coupled to biological hydrogen oxidation. A coupled biotic‐abiotic mechanism for sulfur respiration is put forward, mediated by an NSR‐like protein as the terminal reductase.

Source: http://dx.doi.org/10.1111/1462-2920.14280

Related Items

Awards

Alternative carbon fixation strategies in the model organism Thermovibrio ammonificans: A model system to study energy limitation in the deep biosphere

Award Dates: June 1, 2014 — May 31, 2016

Awardee: Donato Giovannelli (Rutgers University)

Current Placement: Research Fellow, National Research Council, Institute for Marine Science CNR-ISMAR Ancona

Degree: Ph.D. Applied Biology, Ecology and Microbiology, University of Naples (2013)

Advisor: Costantino Vetriani (Rutgers University)

Data report: IODP Expedition 366 pore water trace element (V, Mo, Rb, Cs, U, Ba, and Li) compositions

Proceedings of the International Ocean Discovery Program

Authors: Charles Geoffrey Wheat, Trevor Fournier, Claudia Paul, Catriona Menzies, Roy E. Price, Jeffrey Ryan, Oliver Sissman

Published: August 13, 2018

C-DEBI Contribution Number: 429

Abstract

International Ocean Discovery Program (IODP) Expedition 366 focused, in part, on the study of geochemical cycling, matrix alteration and transport, and deep biosphere processes in the Mariana subduction zone. This research was accomplished by sampling the summit and flank regions of three active serpentinite mud volcanoes in the Mariana forearc: Yinazao (Blue Moon), Fantangisña (Celestial), and Asùt Tesoro (Big Blue) Seamounts. These mud volcanoes represent a transect with increasing distance from the trench. Because these mud volcanoes discharge fluids and materials from the subduction channel, they provide a means to characterize thermal, geochemical, and pressure conditions within the seismogenic zone. Previous coring on Ocean Drilling Program (ODP) Legs 125 and 195 at two other serpentinite mud volcanoes (Conical and South Chamorro Seamounts, respectively) and piston, gravity, and push cores from several other Mariana serpentinite mud volcanoes add to this transect of deep-sourced material that is discharged at the seafloor.

Pore waters were squeezed from cored serpentinite materials to determine the composition of deep-sourced fluid from the subduction channel and to assess the character, extent, and effect of diagenetic reactions and mixing with seawater on the flanks of three serpentinite seamounts (Yinazao, Fantangisña, and Asùt Tesoro). In addition, two water-sampling temperature probe (WSTP) fluid samples were collected in two of the cased boreholes, each with at least 30 m of screened casing that allowed formation fluids to discharge into the borehole. Here we report shore-based Li, Rb, Cs, Ba, V, Mo, and U measurements of pore waters and one of the WSTP samples. The alkali metals were analyzed to constrain the temperature of reaction in the subduction channel. The other elements were analyzed to assess potential biogenic and diagenetic reactions as the serpentinite material weathers and exchanges with bottom seawater via diffusion. Results were generally consistent with earlier coring and drilling operations, resulting in systematic changes in the composition of the deep-sourced fluid with distance from the trench.

Source: https://doi.org/10.14379/iodp.proc.366.201.2018

Influence of commercial DNA extraction kit choice on prokaryotic community metrics in marine sediment

Limnology and Oceanography: Methods

Authors: Gustavo A. Ramírez, Dennis Graham, Steven L. D’Hondt

Published: August 7, 2018

C-DEBI Contribution Number: 432

Abstract

Commercial DNA extraction kits are widely used for cultivation‐free surveys of marine sediment. However, the consequences of popular extraction‐kit choices for sequence‐based biological inferences about marine sedimentary communities have not previously been exhaustively assessed. To address this issue, we extracted DNA from multiple paired subsamples of marine sediment using two popular commercial extraction kits (MO BIO Laboratories PowerSoil^® DNA isolation kit and MP Biomedicals FastDNA^TM Spin Kit for Soil). We report comparisons of (1) total DNA yield, (2) extract purity, (3) gene‐targeted quantification, and (4) post‐sequencing ecological inferences in near‐seafloor (< 1 meter below seafloor [mbsf]) and subsurface (> 1 mbsf) marine sediment. In near‐seafloor sediment, the MP Biomedicals FastDNA^TM Spin Kit for Soil exhibits higher extraction yields, higher 16S rRNA gene loads, higher taxonomic diversity, and lower contaminant loads. In subseafloor sediment, both kits yield similar values for all of these parameters. The MO BIO Laboratories PowerSoil^® DNA isolation kit generally co‐extracts less protein with the DNA in both near‐seafloor and subseafloor sediment. For samples from all depths, both kits exhibit similar depth‐dependent community richness patterns, taxonomic composition, and ordination‐based similarity trends. We conclude that, despite kit‐specific differences in extract yields, purity and reagent contaminant loads, ecological inferences based on next‐generation sequencing of DNA extracted using these popular commercial kits are robustly comparable, particularly for subseafloor sediment samples.

Source: http://dx.doi.org/10.1002/lom3.10264

Low Energy Subsurface Environments as Extraterrestrial Analogs

Frontiers in Microbiology

Authors: Rose M. Jones, Jacqueline Goordial, Beth N. Orcutt

Published: July 18, 2018

C-DEBI Contribution Number: 431

Abstract

Earth’s subsurface is often isolated from phototrophic energy sources and characterized by chemotrophic modes of life. These environments are often oligotrophic and limited in electron donors or electron acceptors, and include continental crust, subseafloor oceanic crust, and marine sediment as well as subglacial lakes and the subsurface of polar desert soils. These low energy subsurface environments are therefore uniquely positioned for examining minimum energetic requirements and adaptations for chemotrophic life. Current targets for astrobiology investigations of extant life are planetary bodies with largely inhospitable surfaces, such as Mars, Europa, and Enceladus. Subsurface environments on Earth thus serve as analogs to explore possibilities of subsurface life on extraterrestrial bodies. The purpose of this review is to provide an overview of subsurface environments as potential analogs, and the features of microbial communities existing in these low energy environments, with particular emphasis on how they inform the study of energetic limits required for life. The thermodynamic energetic calculations presented here suggest that free energy yields of reactions and energy density of some metabolic redox reactions on Mars, Europa, Enceladus, and Titan could be comparable to analog environments in Earth’s low energy subsurface habitats.

Source: http://dx.doi.org/10.3389/fmicb.2018.01605

Organic Matter Degradation and Preservation

Encyclopedia of Earth Sciences Series: Encyclopedia of Geochemistry

Authors: Sandra Arndt, Douglas E. LaRowe

Editors: William M. White

Published: October 16, 2017

C-DEBI Contribution Number: 397

Abstract

Organic matter degradation and preservation play a key role in global biogeochemical cycles and climate. The degradation of OM generally proceeds via multiple enzymatic reactions involving millions of different organisms, billions of organic compounds, and a number of different oxidants, as well as intermediate compounds. As a result, OM degradation and preservation is controlled by a dynamic and complex interplay of different environmental factors. Attempts to isolate the impact of a single variable on the rate of OM degradation have often led to contradictory results. It is therefore becoming increasingly clear that OM degradability is not an intrinsic property of the organic matter itself but an ecosystem property. Correspondingly, the likelihood that a given organic compound will be degraded by a microbial community or be preserved will depend on the chemical formula and structure of that compound, in addition to the metabolic capabilities of the resident microorganisms in response to environmental factors such as electron acceptor and intermediate metabolite concentrations, temperature, and physical associations with minerals or other organic compounds.

Source: https://link.springer.com/referenceworkentry/10.1007%2F978-3-319-39193-9_184-1

Sediment Microbial Communities Influenced by Cool Hydrothermal Fluid Migration

Frontiers in Microbiology

Authors: Laura A. Zinke, Brandi Kiel Reese, James McManus, Charles Geoffrey Wheat, Beth N. Orcutt, Jan P. Amend

Published: June 13, 2018

C-DEBI Contribution Number: 430

Abstract

Cool hydrothermal systems (CHSs) are prevalent across the seafloor and discharge fluid volumes that rival oceanic input from rivers, yet the microbial ecology of these systems are poorly constrained. The Dorado Outcrop on the ridge flank of the Cocos Plate in the northeastern tropical Pacific Ocean is the first confirmed CHS, discharging minimally altered <15^∘C fluid from the shallow lithosphere through diffuse venting and seepage. In this paper, we characterize the resident sediment microbial communities influenced by cool hydrothermal advection, which is evident from nitrate and oxygen concentrations. 16S rRNA gene sequencing revealed that Thaumarchaea, Proteobacteria, and Planctomycetes were the most abundant phyla in all sediments across the system regardless of influence from seepage. Members of the Thaumarchaeota (Marine Group I), Alphaproteobacteria (Rhodospirillales), Nitrospirae, Nitrospina, Acidobacteria, and Gemmatimonadetes were enriched in the sediments influenced by CHS advection. Of the various geochemical parameters investigated, nitrate concentrations correlated best with microbial community structure, indicating structuring based on seepage of nitrate-rich fluids. A comparison of microbial communities from hydrothermal sediments, seafloor basalts, and local seawater at Dorado Outcrop showed differences that highlight the distinct niche space in CHS. Sediment microbial communities from Dorado Outcrop differ from those at previously characterized, warmer CHS sediment, but are similar to deep-sea sediment habitats with surficial ferromanganese nodules, such as the Clarion Clipperton Zone. We conclude that cool hydrothermal venting at seafloor outcrops can alter the local sedimentary oxidation–reduction pathways, which in turn influences the microbial communities within the fluid discharge affected sediment.

Source: http://dx.doi.org/10.3389/fmicb.2018.01249

Genome Sequence of Geothermobacter sp. Strain HR-1, an Iron Reducer from the Lō‘ihi Seamount, Hawai’i

Genome Announcements

Authors: Hillary H. Smith, Karla Abuyen, Jason Tremblay, Pratixaben Savalia, Ileana Pérez-Rodríguez, David Emerson, Benjamin J. Tully, Jan P. Amend

Published: May 24, 2018

C-DEBI Contribution Number: 424

Abstract

Geothermobacter sp. strain HR-1 was isolated from the Lō‘ihi Seamount vent system in the Pacific Ocean at a depth of 1,000 m. Reported here is its 3.84-Mb genome sequence. This research was funded as part of the 2017 NSF Community College Cultivation Cohort (C4) Research Experience for Undergraduates.

Source: http://dx.doi.org/10.1128/genomea.00339-18

Assessment of apolar lipids in subseafloor rocks and potential contaminants from the Atlantis Massif (IODP Expedition 357)

Organic Geochemistry

Authors: Katherine A. Hickok, Tran B. Nguyen, Susan Q. Lang

Published: May 1, 2018

C-DEBI Contribution Number: 428

Abstract

International Ocean Discovery Program Expedition 357 drilled 17 boreholes across the Atlantis Massif with the goals of investigating carbon cycling and the presence of life in a zone of active serpentinization. The expedition recovered multiple lithologies including gabbros, basalts, carbonate sands, and serpentinites. A subset of contrasting lithologies were analyzed for apolar lipid content to determine if non-volatile organic molecules can be detected in the oceanic subsurface. The definitive detection and identification of abiotic and biological lipids in the subsurface of an actively serpentinizing system would be a significant step towards understanding a variety of scientific processes, including the evolution of pre-biotic chemistry, microbial habitability, and the global carbon cycle. Given the high potential for contamination during drilling, a suite of materials used in sample collection and processing were also analyzed to characterize their signatures. An n-alkane series ranging from C₁₈ to C₃₀with δ¹³C isotopic values of –30.9‰ to –28.8‰ was present in lithologically diverse samples. Multiple lines of evidence point to the rock saw used to remove core exteriors during sample processing as the source of these compounds. Many of the other sample-handling procedures designed to reduce surface contamination were determined to be effective and could be implemented in future projects. This result highlights the value of careful prevention and characterization of contamination to allow for more accurate interpretations of complex and dynamic subsurface processes, and the importance that future reports of these compounds occurs in conjunction with thorough contamination assessments.

Source: http://dx.doi.org/10.1016/j.orggeochem.2018.05.003

Related Items

Awards

Direct access to the serpentinite subsurface: a biogeochemical investigation of fluids to characterize a unique habitat

Award Dates: May 1, 2016 — April 30, 2017

PI: Susan Q. Lang (University of South Carolina)

Bioenergetic influences upon carbon flow in alkaliphilic sulfate-reducing microbial populations with relevance to the subsurface biosphere at the Lost City Hydrothermal Field

Award Dates: April 1, 2015 — March 31, 2017

PI: Susan Q. Lang (University of South Carolina)

Co-I: Matthew O. Schrenk (Michigan State)

Microbial decomposition of marine dissolved organic matter in cool oceanic crust

Nature Geoscience

Authors: Sunita R. Shah Walter, Ulrike Jaekel, Helena Osterholz, Andrew T. Fisher, Julie A. Huber, Ann Pearson, Thorsten Dittmar, Peter R. Girguis

Published: April 23, 2018

C-DEBI Contribution Number: 413

Abstract

Marine dissolved organic carbon (DOC) is one of the largest active reservoirs of reduced carbon on Earth. In the deep ocean, DOC has been described as biologically recalcitrant and has a radiocarbon age of 4,000 to 6,000 years, which far exceeds the timescale of ocean overturning. However, abiotic removal mechanisms cannot account for the full magnitude of deep-ocean DOC loss. Deep-ocean water circulates at low temperatures through volcanic crust on ridge flanks, but little is known about the associated biogeochemical processes and carbon cycling. Here we present analyses of DOC in fluids from two borehole observatories installed in crustal rocks west of the Mid-Atlantic Ridge, and show that deep-ocean DOC is removed from these cool circulating fluids. The removal mechanism is isotopically selective and causes a shift in specific features of molecular composition, consistent with microbe-mediated oxidation. We suggest organic molecules with an average radiocarbon age of 3,200 years are bioavailable to crustal microbes, and that this removal mechanism may account for at least 5% of the global loss of DOC in the deep ocean. Cool crustal circulation probably contributes to maintaining the deep ocean as a reservoir of ‘aged’ and refractory DOC by discharging the surviving organic carbon constituents that are molecularly degraded and depleted in ¹⁴C and ¹³C into the deep ocean.

Source: http://dx.doi.org/10.1038/s41561-018-0109-5

Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient

PeerJ

Authors: Angus Angermeyer, Sarah C. Crosby, Julie A. Huber

Benthic octopods cluster on bare rock on Dorado Outcrop, a ~3000 m deep basalt exposure. The outcrop hosts intermittent discharge of relatively cool (up to 12.3 °C) hydrothermal fluid that carries about half as much oxygen as bottom seawater (~54 μM vs. 108 μM). We analyzed 231 hours of video footage and still images taken by sub-sea vehicles in 2013 and 2014 that documented the clustered octopods, members of the poorly-known genus Muusoctopus. The largest cluster (102 octopods) occurred in a 19 m² area of fluid discharge, where the basalt was sediment-free; individual octopods were also seen across the outcrop. The clustered octopods appeared to be brooding eggs and a total of 11 egg clutches were confirmed. None of the 186 eggs closely examined showed embryonic development. The intermittent fluid discharge may clear the basalt of sediment and attract gravid octopods which then spawn. However, the increased temperature and limited oxygen of the discharging fluids may threaten the octopods’ survival. Octopods in/near areas of discharging fluid had significantly higher estimated respiration rates (3.1–9.8 contractions/minute) than did octopods away from discharging fluid (0.8–6.0 contractions/minute). Warm fluids likely increase the octopods’ metabolic rate and thus their oxygen demand but provide only limited oxygen. The resultant physiological stress is hypothesized to eventually kill eggs near fluid discharge. We hypothesize, because these eggs do not survive, the population is sustained by a larger pool of undetectable females that brood their eggs inside cool conduits of this and perhaps other, unstudied basalt outcrops.

Source: http://dx.doi.org/10.1016/j.dsr.2018.03.011

Scientific rationale and international obligations for protection of active hydrothermal vent ecosystems from deep-sea mining

Marine Policy

Published: April 1, 2018

C-DEBI Contribution Number: 425

Abstract

There is increasing interest in mining minerals on the seabed, including seafloor massive sulfide deposits that form at hydrothermal vents. The International Seabed Authority is currently drafting a Mining Code, including environmental regulations, for polymetallic sulfides and other mineral exploitation on the seabed in the area beyond national jurisdictions. This paper summarizes 1) the ecological vulnerability of active vent ecosystems and aspects of this vulnerability that remain subject to conjecture, 2) evidence for limited mineral resource opportunity at active vents, 3) non-extractive values of active vent ecosystems, 4) precedents and international obligations for protection of hydrothermal vents, and 5) obligations of the International Seabed Authority under the UN Convention on the Law of the Sea for protection of the marine environment from the impacts of mining. Heterogeneity of active vent ecosystems makes it extremely challenging to identify “representative” systems for any regional, area-based management approach to conservation. Protection of active vent ecosystems from mining impacts (direct and indirect) would set aside only a small fraction of the international seabed and its mineral resources, would contribute to international obligations for marine conservation, would have non-extractive benefits, and would be a precautionary approach.

Source: http://dx.doi.org/10.1016/j.marpol.2018.01.020

Thioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments

International Journal of Systematic and Evolutionary Microbiology

Authors: Rachel Chang, Lina J. Bird, Casey Barr, Magdalena R. Osburn, Elizabeth Wilbanks, Kenneth H. Nealson, Annette R. Rowe

Published: March 23, 2018

C-DEBI Contribution Number: 420

Abstract

A taxonomic and physiologic characterization was carried out on Thioclava strain ElOx9T, which was isolated from a bacterial consortium enriched on electrodes poised at electron donating potentials. The isolate is Gram-negative, catalase-positive and oxidase-positive; the cells are motile short rods. The bacterium is facultatively anaerobic with the ability to utilize nitrate as an electron acceptor. Autotrophic growth with H₂ and S0 (oxidized to sulfate) was observed. The isolate also grows heterotrophically with organic acids and sugars. Growth was observed at salinities from 0 to 10% NaCl and at temperatures from 15 to 41 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs in the genus Thioclava ; it had the highest sequence similarity of 98.8 % to Thioclava atlantica 13D2W-2T, followed by Thioclava dalianensis DLFJ1-1T with 98.5 % similarity, Thioclava pacifica TL 2T with 97.7 % similarity, and then Thioclava indica DT23-4T with 96.9 %. All other sequence similarities were below 97 % to characterized strains. The digital DNA–DNA hybridization estimated when compared to T. atlantica 13D2W-2T, T. dalianensis DLFJ1-1T, T. pacifica TL 2T and T. indica DT23-4T were 15.8±2.1, 16.7+2.1, 14.3±1.9 and 18.3±2.1 %. The corresponding average nucleotide identity values between these strains were determined to be 65.1, 67.8, 68.4 and 64.4 %, respectively. The G+C content of the chromosomal DNA is 63.4 mol%. Based on these results, a novel species Thioclava electrotropha sp. nov. is proposed, with the type strain ElOx9T (=DSM 103712T=ATCC TSD-100T).

Source: http://dx.doi.org/10.1099/ijsem.0.002723

Related Items

Awards

Passing electrons through marine sediments: Cultivation and characterization of microbes that utilize extracellular electron transport

Award Dates: May 1, 2013 — April 30, 2015

Awardee: Annette R. Rowe (University of Southern California)

Current Placement: Postdoc, USC, 2012-, USC

Degree: Ph.D. Microbiology, Cornell University (2011)

Advisor: Kenneth H. Nealson (University of Southern California)

Effective Strategies for Engaging Community College Students in Research via Cutting-Edge Technology

Marine Technology Society Journal

Authors: Stephanie Schroeder, Jan P. Amend

Published: March 26, 2018

C-DEBI Contribution Number: 421

Abstract

As we train the next generation of Science, Technology, Engineering, and Math (STEM) researchers, it is imperative that we expand our recruitment to community college students. Many of these students are highly motivated and extremely talented, but they often lack exposure to cutting edge technology found at R1 institutions, much less have the opportunities to participate in original research. The Center for Dark Energy Biosphere Investigations (C-DEBI) at the University of Southern California (USC) started a community college research internship summer program in 2013. The non-residential and residential programs combined so far have trained 60 students in the biogeosciences, with 46 of them having transferred to four-year institutions and 95% remaining in STEM fields. Their introduction to and acquired competence in several advanced technologies have further prepared these students to pursue graduate degrees and rewarding careers in research-based STEM fields.

The Marine Technology Society is a not-for-profit, international, professional association. Founded in 1963, the Society believes that the advancement of marine technology and the productive, sustainable use of the oceans depend upon the active exchange of ideas between government, industry and academia. See www.mtsociety.org. Ⓒ 2018 Marine Technology Society. This article is for personal use only, and is not to be distributed in any format.

Source: http://www.darkenergybiosphere.org/wp-content/uploads/SchroederAmend-final.pdf

Potential for primary productivity in a globally-distributed bacterial phototroph

The ISME Journal

Authors: Elaina D. Graham, John F. Heidelberg, Benjamin J. Tully

Published: March 9, 2018

C-DEBI Contribution Number: 418

Abstract

Aerobic anoxygenic phototrophs (AAnPs) are common in marine environments and are associated with photoheterotrophic activity. To date, AAnPs that possess the potential for carbon fixation have not been identified in the surface ocean. Using the Tara Oceans metagenomic dataset, we have identified draft genomes of nine bacteria that possess the genomic potential for anoxygenic phototrophy, carbon fixation via the Calvin-Benson-Bassham cycle, and the oxidation of sulfite and thiosulfate. Forming a monophyletic clade within the Alphaproteobacteria and lacking cultured representatives, the organisms compose minor constituents of local microbial communities (0.1–1.0%), but are globally distributed, present in multiple samples from the North Pacific, Mediterranean Sea, the East Africa Coastal Province, and the Atlantic. This discovery may require re-examination of the microbial communities in the oceans to understand and constrain the role this group of organisms may play in the global carbon cycle.

Source: http://dx.doi.org/10.1038/s41396-018-0091-3

Tracking Electron Uptake from a Cathode into Shewanella Cells: Implications for Energy Acquisition from Solid-Substrate Electron Donors

mBio

Authors: Annette R. Rowe, Pournami Rajeev, Abhiney Jain, Sahand Pirbadian, Akihiro Okamoto, Jeffrey A. Gralnick, Mohamed Y. El-Naggar, Kenneth H. Nealson

Editors: Markus W. Ribbe

Published: February 27, 2018

C-DEBI Contribution Number: 417

Abstract

While typically investigated as a microorganism capable of extracellular electron transfer to minerals or anodes, Shewanella oneidensis MR-1 can also facilitate electron flow from a cathode to terminal electron acceptors, such as fumarate or oxygen, thereby providing a model system for a process that has significant environmental and technological implications. This work demonstrates that cathodic electrons enter the electron transport chain of S. oneidensis when oxygen is used as the terminal electron acceptor. The effect of electron transport chain inhibitors suggested that a proton gradient is generated during cathode oxidation, consistent with the higher cellular ATP levels measured in cathode-respiring cells than in controls. Cathode oxidation also correlated with an increase in the cellular redox (NADH/FMNH₂) pool determined with a bioluminescence assay, a proton uncoupler, and a mutant of proton-pumping NADH oxidase complex I. This work suggested that the generation of NADH/FMNH₂ under cathodic conditions was linked to reverse electron flow mediated by complex I. A decrease in cathodic electron uptake was observed in various mutant strains, including those lacking the extracellular electron transfer components necessary for anodic-current generation. While no cell growth was observed under these conditions, here we show that cathode oxidation is linked to cellular energy acquisition, resulting in a quantifiable reduction in the cellular decay rate. This work highlights a potential mechanism for cell survival and/or persistence on cathodes, which might extend to environments where growth and division are severely limited.

Source: http://dx.doi.org/10.1128/mbio.02203-17

Related Items

Awards

Passing electrons through marine sediments: Cultivation and characterization of microbes that utilize extracellular electron transport

Award Dates: May 1, 2013 — April 30, 2015

Awardee: Annette R. Rowe (University of Southern California)

Current Placement: Postdoc, USC, 2012-, USC

Degree: Ph.D. Microbiology, Cornell University (2011)

Advisor: Kenneth H. Nealson (University of Southern California)

Nitrogen Cycling of Active Bacteria within Oligotrophic Sediment of the Mid-Atlantic Ridge Flank

Geomicrobiology Journal

Published: February 15, 2018

C-DEBI Contribution Number: 378

Abstract

Microbial ecology within oligotrophic marine sediment is poorly understood, yet is critical for understanding geochemical cycles. Here, 16S rRNA sequences from RNA and DNA inform the structure of active and total microbial communities in oligotrophic sediment on the western flank of the Mid-Atlantic Ridge. Sequences identified as Bacillariophyta chloroplast were detected within DNA, but undetectable within RNA, suggesting preservation in 5.6-million-year-old sediment. Statistical analysis revealed that RNA-based microbial populations correlated significantly with nitrogen concentrations, whereas DNA-based populations did not correspond to measured geochemical analytes. Bioenergetic calculations determined which metabolisms could yield energy in situ, and found that denitrification, nitrification, and nitrogen fixation were all favorable. A metagenome was produced from one sample, and included genes mediating nitrogen redox processes. Nitrogen respiration by active bacteria is an important metabolic strategy in North Pond sediments, and could be widespread in the oligotrophic sedimentary biosphere.

Source: http://dx.doi.org/10.1080/01490451.2017.1392649

Take the Plunge: A STEM Camp Centered on Seafloor Science

Current: The Journal of Marine Education

Authors: Charles Geoffrey Wheat, Trevor Fournier, Karen Monahan, Claudia Paul

Published: February 21, 2018

C-DEBI Contribution Number: 411

Abstract

While most of the Science, Technology, Engineering, and Mathematics (STEM) efforts center on classroom programs, many lack hands-on activities that allow students to experience phenomenon-based learning and produce a complex scientific project. To meet this need, we developed week-long STEM summer day camps (ssrovcamp.org) for two age groups: rising 3^rd-5^th and 6-9^th graders. Campers learn about seafloor exploration through multiple hands-on, technology-rooted, team-based activities. At the end of the week, campers design and present research missions for an actual seafloor feature, incorporating hypotheses, methods, and operations. Current: The Journal of Marine Education, is a journal produced by NMEA, the National Marine Educators Association.

Source: http://www.darkenergybiosphere.org/wp-content/uploads/Wheat-et-al-2018-SSROV-Current.pdf

Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions

Frontiers in Microbiology

Authors: Alberto Robador, Douglas E. LaRowe, Steven E. Finkel, Jan P. Amend, Kenneth H. Nealson

Published: February 1, 2018

C-DEBI Contribution Number: 414

Marine sediments constitute one of the most energy-limited habitats on Earth, in which microorganisms persist over extraordinarily long timescales with very slow metabolisms. This habitat provides an ideal environment in which to study the energetic limits of life. However, the bioenergetic factors that can determine whether microorganisms will grow, lie dormant, or die, as well as the selective environmental pressures that determine energetic trade-offs between growth and maintenance activities, are not well understood. Numerical models will be pivotal in addressing these knowledge gaps. However, models rarely account for the variable physiological states of microorganisms and their demand for energy. Here, we review established modeling constructs for microbial growth rate, yield, maintenance, and physiological state, and then provide a new model that incorporates all of these factors. We discuss this new model in context with its future application to the marine subsurface. Understanding the factors that regulate cell death, physiological state changes, and the provenance of maintenance energy (i.e., endogenous versus exogenous metabolism), is crucial to the design of this model. Further, measurements of growth rate, growth yield, and basal metabolic activity will enable bioenergetic parameters to be better constrained. Last, biomass and biogeochemical rate measurements will enable model simulations to be validated. The insight provided from the development and application of new microbial modeling tools for marine sediments will undoubtedly advance the understanding of the minimum power required to support life, and the ecophysiological strategies that organisms utilize to cope under extreme energy limitation for extended periods of time.

Source: http://dx.doi.org/10.3389/fmicb.2018.00180

Related Items

Awards

Develop a 1D biogeochemical-evolutionary model for deep sediments

Award Dates: October 10, 2016 — October 9, 2018

Awardee: James A. Bradley (University of Southern California)

Degree: Ph.D. Geographical Sciences, University of Bristol (2016)

Advisor: Douglas E. LaRowe (University of Southern California)

Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity

Microbiome

Authors: Julie Reveillaud, Rika E. Anderson, Sintra Reves-Sohn, Colleen M. Cavanaugh, Julie A. Huber

Published: January 27, 2018

C-DEBI Contribution Number: 412

Abstract

The microbial endosymbionts of two species of vestimentiferan tubeworms (Escarpia sp. and Lamellibrachia sp.2) collected from an area of low-temperature hydrothermal diffuse vent flow at the Mid-Cayman Rise (MCR) in the Caribbean Sea were characterized using microscopy, phylogenetic analyses, and a metagenomic approach. The present study adds new evidence that tubeworm endosymbionts can potentially switch from autotrophic to heterotrophic metabolism, or may be mixotrophic, presumably while free-living, and also suggests their versatile metabolic potential may enable both the host and symbionts to exploit a wide range of environmental conditions. Together, the marked gene content and sequence dissimilarity at the rRNA operon and whole genome level between vent and seep symbionts suggest these newly described endosymbionts from the MCR belong to a novel tubeworm endosymbiont genera, introduced as Candidatus Vondammii.

Source: http://dx.doi.org/10.1186/s40168-018-0411-x

Abrupt burial imparts persistent changes to the bacterial diversity of turbidite-associated sediment profiles

Geobiology

Authors: Benjamin Kimball Harrison, A. Myrbo, B. E. Flood, Jake V. Bailey

Published: January 19, 2018

C-DEBI Contribution Number: 408

Abstract

The emplacement of subaqueous gravity-driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical and biological signatures of turbidite deposition, the response of bacteria and archaea within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and those attached to allochthonous material must respond to substantially altered environmental conditions and selective pressures. As a consequence, turbidites and underlying sediments provide an exceptional opportunity to examine (i) the microbial community response to rapid sedimentation and (ii) the preservation and identification of displaced micro-organisms. We collected Illumina MiSeq sequence libraries across turbidite boundaries at ~26 cm sediment depth in La Jolla Canyon off the coast of California, and at ~50 cm depth in meromictic Twin Lake, Hennepin County, MN. 16S rRNA gene signatures of relict and active bacterial populations exhibit persistent differences attributable to turbidite deposition. In particular, both the marine and lacustrine turbidite boundaries are sharply demarcated by the abundance and diversity of Chloroflexi, suggesting a characteristic sensitivity to sediment disturbance history or to differences in organic substrates across turbidite profiles. Variations in the abundance of putative dissimilatory sulfate-reducing Deltaproteobacteria across the buried La Jolla Canyon sediment–water interface reflect turbidite-induced changes to the geochemical environment. Species-level distinctions within the Deltaproteobacteria clearly conform to the sedimentological boundary, suggesting a continuing impact of genetic inheritance distinguishable from broader trends attributable to selective pressure. Abrupt, <1-cm scale changes in bacterial diversity across the Twin Lake turbidite contact are consistent with previous studies showing that relict DNA signatures attributable to sediment transport may be more easily preserved in low-energy, anoxic environments. This work raises the possibility that deep subsurface microbial communities may inherit variations in microbial diversity from sediment flow and deformation events.

Source: http://dx.doi.org/10.1111/gbi.12271

Related Items

Awards

Buried alive: Microbial responses to sediment flux with implications for the deep biosphere

Award Dates: April 1, 2012 — April 30, 2014

Awardee: Benjamin Kimball Harrison (University of Minnesota)

Current Placement: Environmental Science Research Specialist, Central Michigan University

Degree: Ph.D. Geochemistry, California Institute of Technology (2011)

Advisor: Jake V. Bailey (University of Minnesota)

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

Scientific Data

Authors: Benjamin J. Tully, Elaina D. Graham, John F. Heidelberg

At deep-sea hydrothermal vents, microbial communities thrive across geochemical gradients above, at, and below the seafloor. In this study, we determined the gene content and transcription patterns of microbial communities and specific populations to understand the taxonomy and metabolism both spatially and temporally across geochemically different diffuse fluid hydrothermal vents. Vent fluids were examined via metagenomic, metatranscriptomic, genomic binning, and geochemical analyses from Axial Seamount, an active submarine volcano on the Juan de Fuca Ridge in the NE Pacific Ocean, from 2013 to 2015 at three different vents: Anemone, Marker 33, and Marker 113. Results showed that individual vent sites maintained microbial communities and specific populations over time, but with spatially distinct taxonomic, metabolic potential, and gene transcription profiles. The geochemistry and physical structure of each vent both played important roles in shaping the dominant organisms and metabolisms present at each site. Genomic binning identified key populations of SUP05, Aquificales and methanogenic archaea carrying out important transformations of carbon, sulfur, hydrogen, and nitrogen, with groups that appear unique to individual sites. This work highlights the connection between microbial metabolic processes, fluid chemistry, and microbial population dynamics at and below the seafloor and increases understanding of the role of hydrothermal vent microbial communities in deep ocean biogeochemical cycles.

Source: http://dx.doi.org/10.1111/1462-2920.14011

Contamination tracer testing with seabed drills: IODP Expedition 357

Scientific Drilling

Authors: Beth N. Orcutt, Markus Bergenthal, Tim Freudenthal, David C. Smith, Marvin D. Lilley, Luzie Schnieders, Sophie Green, Gretchen L. Früh-Green

Published: November 30, 2017

C-DEBI Contribution Number: 398

Weathered crude oil sank to the seafloor following the Deepwater Horizon disaster in 2010, removing this oil from further physical and photo-chemical degradation processes and leaving benthic processes as the mechanisms for altering and remediating this hydrocarbon source. To quantify potential microbial oil degradation rates at the seafloor, and associated changes in sediment microbial community structure and pore fluid composition, we used a benthic lander system to deploy novel sediment flow-through chambers at a natural hydrocarbon seep in the Gulf of Mexico (at a depth of 1226 m in lease block GC600) roughly 265 km southwest of the Deepwater Horizon wellhead (at 1500 m depth). Sediment amended with 20% unweathered crude oil had elevated rates of sulfate reduction over the course of the 5-month-long experiment as compared to an unamended control, yielding potential rates of sulfate reduction (600–800 mmol m^–2d^–1) among the highest measured in hydrocarbon-influenced seafloor sediment. Oil amendment also stimulated methane production towards the end of the experiment, and led to slightly higher cell densities without significant changes in microbial community structure, based on 16S rRNA gene sequence libraries and fatty acid profiles. Assuming a link between sulfate reduction and hydrocarbon degradation, these results suggest that electron acceptor availability may become limiting in heavily oiled deep-sea environments, resulting in minimal degradation of deposited oil. This study provides unique data on seafloor sediment responses to oil deposition, and reveals the value of using observatories to fill the gap in understanding deep-sea microbial processes, especially for ephemeral and stochastic events such as oil spills.

Source: http://dx.doi.org/10.1525/elementa.129

Genome Sequence of Geothermobacter sp. Strain EPR-M, a Deep-Sea Hydrothermal Vent Iron Reducer

Genome Announcements

Published: June 8, 2017

C-DEBI Contribution Number: 402

Abstract

Geothermobacter sp. strain EPR-M was isolated from a hydrothermal vent on the East Pacific Rise and has been shown to participate in the reduction of Fe(III) oxides. Here, we report its 3.73-Mb draft genome sequence.

Source: http://dx.doi.org/10.1128/genomea.00424-17

Structure, Function and Evolution of the Hsp60 Chaperonins

Heat Shock Proteins

Authors: Sara E. Rowland, Frank T. Robb

Published: January 1, 2017

C-DEBI Contribution Number: 401

Abstract

In 1973, Christian Anfinsen and coworkers noted that accelerated protein folding in intact cells and cell extracts suggested that a “disulfide interchange enzyme” might be present in vivo. This concept of catalyzed folding foreshadowed the discovery of ubiquitous protein chaperones. The chaperonin GroEL/GroES was identified serendipitously when GroE mutants of E. coli failed to grow bacteriophage λ and were also temperature sensitive. The GroEL/GroES proved to be a ubiquitous chaperone and heat shock protein in bacteria and eukaryotic organelles, with two back-to-back rings of seven subunits each, forming a cavity that enclosed nonnative proteins, capped by the separate GroES lid complex. Group II chaperonins were subsequently discovered in all of the Archaea and in the Eukaryote cytoplasm with a similar cage-like shape, only with a “built-in” lid instead of the GroES module of Group I chaperonins. These chaperones have been intensely studied for three decades and have provided deep insights into protein-folding mechanisms. Despite this, some aspects of chaperonin-induced protein folding remain controversial.

The shared architecture and sequence similarity of two classes of chaperonins implies that they share a common ancestor. A recently identified, deeply branching clade of archaeal-like chaperonins encoded in bacteria may shed light on the early history of chaperonins. This clade shares many molecular properties with Group II chaperones; however, their phylogeny suggests that they arose early in prokaryotic evolution and may represent a vestige of the common ancestor of Group I and Group II chaperonins.

Source: http://dx.doi.org/10.1007/978-981-10-4651-3_1

290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology

PeerJ

Authors: Benjamin J. Tully, Rohan Sachdeva, Elaina D. Graham, John F. Heidelberg

Published: July 10, 2017

C-DEBI Contribution Number: 333

Abstract

The Tara Oceans Expedition has provided large, publicly-accessible microbial metagenomic datasets from a circumnavigation of the globe. Utilizing several size fractions from the samples originating in the Mediterranean Sea, we have used current assembly and binning techniques to reconstruct 290 putative draft metagenome-assembled bacterial and archaeal genomes, with an estimated completion of ≥50%, and an additional 2,786 bins, with estimated completion of 0–50%. We have submitted our results, including initial taxonomic and phylogenetic assignments, for the putative draft genomes to open-access repositories for the scientific community to use in ongoing research.

Source: http://dx.doi.org/10.7717/peerj.3558

Editorial: Deep Carbon in Earth: Early Career Scientist Contributions to the Deep Carbon Observatory

Frontiers in Earth Science

Authors: Donato Giovannelli, Benjamin A. Black, Alysia D. Cox, Cody S. Sheik

Published: November 3, 2017

C-DEBI Contribution Number: 396

Abstract

Since its inception, the Deep Carbon Observatory (DCO) has coalesced a multidisciplinary and international group of researchers focused on understanding and quantifying Earth's deep carbon budget. Carbon is the fourth most abundant element in the universe, and understanding carbon chemistry under a variety of environmental conditions impacts all aspects of planetary sciences. DCO recognizes that contributions of early career scientists are integral to the advancement of knowledge regarding the quantities, movements, origins, and forms of Earth's deep carbon. This research topic highlights the contributions of the DCO Early Career Scientist community.

Source: http://dx.doi.org/10.3389/feart.2017.00089

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

The ISME Journal

Authors: Benjamin J. Tully, Charles Geoffrey Wheat, Brian T. Glazer, Julie A. Huber

Published: November 3, 2017

C-DEBI Contribution Number: 395

Abstract

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb₃- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.

Source: http://dx.doi.org/10.1038/ismej.2017.187

Influences of the Tonga Subduction Zone on seafloor massive sulfide deposits along the Eastern Lau Spreading Center and Valu Fa Ridge

Geochimica et Cosmochimica Acta

Authors: Guy N. Evans, Margaret K. Tivey, Jeffrey S. Seewald, Charles Geoffrey Wheat

Published: October 1, 2017

C-DEBI Contribution Number: 403

Abstract

This study investigates the morphology, mineralogy, and geochemistry of seafloor massive sulfide (SMS) deposits from six back-arc hydrothermal vent fields along the Eastern Lau Spreading Center (ELSC) and Valu Fa Ridge (VFR) in the context of endmember vent fluid chemistry and proximity to the Tonga Subduction Zone. To complement deposit geochemistry, vent fluid analyses of Cu, Zn, Ba, Pb and H_2,(aq)were completed to supplement existing data and enable thermodynamic calculations of mineral saturation states at in situ conditions. Results document southward increases in the abundance of mantle-incompatible elements in hydrothermal fluids (Ba and Pb) and SMS deposits (Ba, Pb, As, and Sb), which is also expressed in the abundance of barite (BaSO₄) and galena (PbS) in SMS deposits. These increases correspond to a decrease in distance between the ELSC/VFR and the Tonga Subduction Zone that correlates with a change in crustal lithology from back-arc basin basalt in the north to mixed andesite, rhyolite, and dacite in the south. Barite influences deposit morphology, contributing to the formation of horizontal flanges and squat terraces. Results are also consistent with a regional-scale lowering of hydrothermal reaction zone temperatures from north to south (except at the southernmost Mariner vent field) that leads to lower-temperature, higher-pH vent fluids relative to mid-ocean ridges of similar spreading rates (Mottl et al., 2011). These fluids are Cu- and Zn-poor and the deposits formed from these fluids are Cu-poor but Zn-rich. In contrast, at the Mariner vent field, higher-temperature and lower pH vent fluids are hypothesized to result from higher reaction zone temperatures and the localized addition of acidic magmatic volatiles (Mottl et al., 2011). The Mariner fluids are Cu- and Zn-rich and vent from SMS deposits that are rich in Cu but poor in Zn with moderate amounts of Pb. Thermodynamic calculations indicate that the contrasting metal contents of vent fluids and SMS deposits can be accounted for by vent fluid pH. Wurtzite/sphalerite ((Zn, Fe)S) and galena (PbS) are saturated at higher temperatures in higher-pH, Zn-, Cu-, and Pb-poor ELSC/VFR vent fluids, but are undersaturated at similar temperatures in low-pH, Zn-, Cu-, and Pb-rich vent fluids from the Mariner vent field.

Indicators of pH in the ELSC and VFR SMS deposits include the presence of co-precipitated wurtzite and chalcopyrite along conduit linings in deposits formed from higher pH fluids, and different correlations between concentrations of Zn and Ag in bulk geochemical analyses. Significant positive bulk geochemical Zn:Ag correlations occur for deposits at vent fields where hydrothermal fluids have a minimum pH (at 25 °C) < 3.3, while correlations of Zn:Ag are weak or negative for deposits at vent fields where the minimum vent fluid pH (at 25 °C) > 3.6. Data show that the compositions of the mineral linings of open conduit chimneys (minerals present, mol% FeS in (Zn,Fe)S) that precipitate directly from hydrothermal fluids closely reflect the temperature and sulfur fugacity of sampled hydrothermal fluids. These mineral lining compositions thus can be used as indicators of hydrothermal fluid temperature and composition (pH, metal content, sulfur fugacity).

Source: http://dx.doi.org/10.1016/j.gca.2017.08.010

Estimating population turnover rates from relative quantification methods reveals microbial dynamics in marine sediment

Applied and Environmental Microbiology

Authors: Richard T. Kevorkian, Jordan T. Bird, Alexander K. Shumaker, Karen G. Lloyd

Published: October 20, 2017

C-DEBI Contribution Number: 400

Abstract

Difficulty quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentration consistent with predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, for fraction of read abundance times cells), to estimate population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply-branching uncultured groups and ∼ 98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from quantitative PCR (qPCR) at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate reducing bacteria, Desulfovibrio sp., Desulfobacter sp., and Desulfobacterium sp. increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions only stimulates growth in a few clades directly involved in methanogenesis, rather than the whole microbial community.

Source: http://dx.doi.org/10.1128/aem.01443-17

Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds

Proceedings of the National Academy of Sciences

Authors: Elizabeth Trembath-Reichert, Yuki Morono, Akira Ijiri, Tatsuhiko Hoshino, Katherine S. Dawson, Fumio Inagaki, Victoria J. Orphan

Published: October 3, 2017

C-DEBI Contribution Number: 389

Abstract

The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be “hot spots” for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C). The 30-month SIP incubations were amended with deuterated water as a passive tracer for growth and different combinations of ¹³C- or ¹⁵N-labeled methanol, methylamine, and ammonium added at low (micromolar) concentrations to investigate methylotrophy in the deep subseafloor biosphere. Although the cell densities were low (50–2,000 cells per cubic centimeter), bulk geochemical measurements and single-cell–targeted nanometer-scale secondary ion mass spectrometry demonstrated active metabolism of methylated substrates by the thermally adapted microbial assemblage, with differing substrate utilization profiles between coal and shale incubations. The conversion of labeled methylamine and methanol was predominantly through heterotrophic processes, with only minor stimulation of methanogenesis. These findings were consistent with in situ and incubation 16S rRNA gene surveys. Microbial growth estimates in the incubations ranged from several months to over 100 y, representing some of the slowest direct measurements of environmental microbial biosynthesis rates. Collectively, these data highlight a small, but viable, deep coal bed biosphere characterized by extremely slow-growing heterotrophs that can utilize a diverse range of carbon and nitrogen substrates.

Source: http://dx.doi.org/10.1073/pnas.1707525114

Related Items

Awards

Awards > Research Exchange Grants

Award Dates: March 17, 2015 — April 10, 2015

Determination of deep biosphere cell activity and identity utilizing the state of the art low-biomass, single cell techniques developed at JAMSTEC in their class 10,000 clean room

PI: Elizabeth Trembath-Reichert (California Institute of Technology)

Current Placement: Postdoctoral Researcher, Woods Hole Oceanographic Institution

Advisor: Victoria J. Orphan (California Institute of Technology)

Host: Fumio Inagaki (JAMSTEC)

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents

Nature Communications

Authors: Rika E. Anderson, Julie Reveillaud, Emily Reddington, Tom O. Delmont, A. Murat Eren, Jill McDermott, Jeffrey S. Seewald, Julie A. Huber

Published: October 24, 2017

C-DEBI Contribution Number: 387

Abstract

Little is known about evolutionary drivers of microbial populations in the warm subseafloor of deep-sea hydrothermal vents. Here we reconstruct 73 metagenome-assembled genomes (MAGs) from two geochemically distinct vent fields in the Mid-Cayman Rise to investigate patterns of genomic variation within subseafloor populations. Low-abundance populations with high intra-population diversity coexist alongside high-abundance populations with low genomic diversity, with taxonomic differences in patterns of genomic variation between the mafic Piccard and ultramafic Von Damm vent fields. Populations from Piccard are significantly enriched in nonsynonymous mutations, suggesting stronger purifying selection in Von Damm relative to Piccard. Comparison of nine Sulfurovum MAGs reveals two high-coverage, low-diversity MAGs from Piccard enriched in unique genes related to the cellular membrane, suggesting these populations were subject to distinct evolutionary pressures that may correlate with genes related to nutrient uptake, biofilm formation, or viral invasion. These results are consistent with distinct evolutionary histories between geochemically different vent fields, with implications for understanding evolutionary processes in subseafloor microbial populations.

Source: http://dx.doi.org/10.1038/s41467-017-01228-6

Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments

The ISME Journal

Authors: Stephanie A. Carr, Florence Schubotz, Robert B. Dunbar, Christopher T. Mills, Robert Dias, Roger E. Summons, Kevin W. Mandernack

Published: October 17, 2017

C-DEBI Contribution Number: 390

Abstract

Despite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica’s Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment. Based on structural and isotopic measurements, glycerol dialkyl glycerol tetraethers with diglycosyl phosphatidylglycerol head groups were classified as biomarkers for active methanogens. The stable carbon isotope (δ¹³C) values of these biomarkers and the Methanosaeta partial genome suggest that these organisms are acetoclastic methanogens and represent a relatively small (0.2%) but active population. Metagenomic and lipid analyses suggest that Thaumarchaeota and heterotrophic bacteria co-exist with Methanosaeta and together contribute to increasing concentrations and δ¹³C values of dissolved inorganic carbon with depth. This study presents the first functional insights of deep subsurface Methanosaeta organisms and highlights their role in methane production and overall carbon cycling within sedimentary environments.

Source: http://dx.doi.org/10.1038/ismej.2017.150

Alkaline vents and steep Na+ gradients from ridge-flank basalts—Implications for the origin and evolution of life

Geology

Authors: Roy E. Price, Eric Boyd, Tori M. Hoehler, Laura M. Wehrmann, Erlendur Bogason, Hreiðar Þór Valtýsson, Jóhann Örlygsson, Bjarni Gautason, Jan P. Amend

Published: October 19, 2017

C-DEBI Contribution Number: 393

Abstract

Life may have emerged on early Earth in serpentinizing systems, where ultramafic rocks react with aqueous solutions to generate high levels of dissolved H₂ and CH₄ and, on meeting seawater, steep redox, ionic, and pH gradients. Most extant life harnesses energy as ion (e.g., H⁺, Na⁺) gradients across membranes, and it seems reasonable to suggest that environments with steep ion gradients would have also been important for early life forms. The Strytan Hydrothermal Field (SHF) is a mid-ocean ridge–flank submarine hydrothermal (~70 °C) vent in Iceland that produces steep Na⁺ (<3–468 mM) and pH (8.1–10.2) gradients, concomitant with enrichments in methane (0.5–1.4 μM) and hydrogen (0.1–5.2 μM), relative to seawater. Large (up to 55 m) saponite towers create ideal "incubators" similar to other proposed origin-of-life analogs (e.g., Lost City hydrothermal field in the mid-Atlantic). However, the SHF is basalt hosted. We suggest that the observed conditions are generated by (1) plagioclase hydrolysis, coupled with calcite precipitation, and (2) hydration of Mg in pyroxene and olivine in basalt. Along with microbial activity, aqueous reactions of Fe in olivine and pyroxene are possible sources of the observed H₂. Although the δ¹³C-CH₄ values were highly variable (–53‰ to –8‰), isotopically heavy CH₄ suggests possible abiotic formation or the imprint of methane oxidation. If environments similar to SHF occurred on the early Earth, they should be considered as potential origin-of-life environments.

Source: http://dx.doi.org/10.1130/g39474.1

Related Items

Awards

A Lost City-type hydrothermal system in readily accessible, shallow water

Award Dates: December 1, 2012 — November 30, 2014

PI: Jan P. Amend (University of Southern California)

Co-I: Roy E. Price (University of Southern California)

Spatially variable geothermal heat flux in West Antarctica: evidence and implications

Geophysical Research Letters

Authors: Carolyn Branecky Begeman, Slawek M. Tulaczyk, Andrew T. Fisher

Published: September 26, 2017

C-DEBI Contribution Number: 391

Abstract

Geothermal heat flux (GHF) is an important part of the basal heat budget of continental ice sheets. The difficulty of measuring GHF below ice sheets has directly hindered progress in understanding of ice sheet dynamics. We present a new GHF measurement from below the West Antarctic Ice Sheet, made in subglacial sediment near the grounding zone of the Whillans Ice Stream. The measured GHF is 88 ± 7 mW m^-2, a relatively high value compared to other continental settings and to other GHF measurements along the eastern Ross Sea of 55 mW m^-2 and 69 ± 21 mW m^-2, but within the range of regional values indicated by geophysical estimates. The new GHF measurement was made ~100 km from the only other direct GHF measurement below the ice sheet, which was considerably higher at 285 ± 80 mW m^-2, suggesting spatial variability that could be explained by shallow magmatic intrusions or the advection of heat by crustal fluids. Analytical calculations suggest that spatial variability in GHF exceeds spatial variability in the conductive heat flux through ice along the Siple Coast. Accurate GHF measurements and high-resolution GHF models may be necessary to reliably predict ice sheet evolution, including responses to ongoing and future climate change.

Source: http://dx.doi.org/10.1002/2017gl075579

Hydrothermal circulation and the thermal structure of shallow subduction zones

Geosphere

Authors: Robert N. Harris, Glenn A. Spinelli, Andrew T. Fisher

Published: September 1, 2017

C-DEBI Contribution Number: 373

Abstract

Hydrothermal circulation within oceanic basement can have a profound influence on temperatures in the upper crust, including those close to the subduction thrust and in the overlying plate. Heat flow evidence for hydrothermal circulation in the volcanic basement of incoming plates includes: (1) values that are well below conductive predictions due to the advection of heat into the ocean, and (2) variability about conductive predictions that cannot be explained by variations in seafloor relief or thermal conductivity. In this review we summarize evidence for hydrothermal circulation in subducting oceanic basement from the Nankai, Costa Rica, south-central Chile, Haida Gwaii, and Cascadia margins and explore its influence on plate boundary temperatures. Models of these systems using a high Nusselt number proxy for hydrothermal circulation are used to illustrate the influence of this process on seafloor observations and thermal conditions at depth. We show that at these subduction zones, patterns of seafloor heat flow are best explained by thermal models that include the influence of hydrothermal circulation.

Source: http://dx.doi.org/10.1130/ges01498.1

Thriving or Surviving? Evaluating active microbial guilds in Baltic Sea sediment

Environmental Microbiology Reports

Authors: Laura A. Zinke, Megan M. Mullis, Jordan T. Bird, Ian P.G. Marshall, Bo Barker Jørgensen, Karen G. Lloyd, Jan P. Amend, Brandi Kiel Reese

Published: August 24, 2017

C-DEBI Contribution Number: 380

Abstract

Microbial life in the deep subsurface biosphere is taxonomically and metabolically diverse, but it is vigorously debated whether the resident organisms are thriving (metabolizing, maintaining cellular integrity, and expressing division genes) or just surviving. As part of Integrated Ocean Drilling Program (IODP) Expedition 347: Baltic Sea Paleoenvironment, we extracted and sequenced RNA from organic carbon-rich, nutrient-replete, and permanently anoxic sediment. In stark contrast to the oligotrophic subsurface biosphere, Baltic Sea Basin samples provided a unique opportunity to understand the balance between metabolism and other cellular processes. Targeted sequencing of 16S rRNA transcripts showed Atribacteria (an uncultured phylum) and Chloroflexi to be among the dominant and the active members of the community. Metatranscriptomic analysis identified methane cycling, sulfur cycling, and halogenated compound utilization as active in situ respiratory metabolisms. Genes for cellular maintenance, cellular division, motility, and antimicrobial production were also transcribed. This indicates that microbial life in deep subsurface Baltic Sea Basin sediments was not only alive, but thriving.

Source: http://dx.doi.org/10.1111/1758-2229.12578

Cool seafloor hydrothermal springs reveal global geochemical fluxes

Earth and Planetary Science Letters

Authors: Charles Geoffrey Wheat, Andrew T. Fisher, James McManus, Samuel M. Hulme, Beth N. Orcutt

Published: October 1, 2017

C-DEBI Contribution Number: 377

Abstract

We present geochemical data from the first samples of spring fluids from Dorado Outcrop, a basaltic edifice on 23 M.y. old seafloor of the Cocos Plate, eastern Pacific Ocean. These samples were collected from the discharge of a cool hydrothermal system (CHS) on a ridge flank, where typical reaction temperatures in the volcanic crust are low (2–20 °C) and fluid residence times are short. Ridge-flank hydrothermal systems extract 25% of Earth's lithospheric heat, with a global discharge rate equivalent to that of Earth's river discharge to the ocean; CHSs comprise a significant fraction of this global flow. Upper crustal temperatures around Dorado Outcrop are ∼15 °C, the calculated residence time is <3 y, and the composition of discharging fluids is only slightly altered from bottom seawater. Many of the major ions concentrations in spring fluids are indistinguishable from those of bottom seawater; however, concentrations of Rb, Mo, V, U, Mg, phosphate, Si and Li are different. Applying these observed differences to calculated global CHS fluxes results in chemical fluxes for these ions that are ≥15% of riverine fluxes. Fluxes of K and B also may be significant, but better analytical resolution is required to confirm this result. Spring fluids also have ∼50% less dissolved oxygen (DO) than bottom seawater. Calculations of an analytical model suggest that the loss of DO occurs primarily (>80%) within the upper basaltic crust by biotic and/or abiotic consumption. This calculation demonstrates that permeable pathways within the upper crust can support oxic water–rock interactions for millions of years.

Source: http://dx.doi.org/10.1016/j.epsl.2017.07.049

Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov.

The ISME Journal

Authors: Jiro F. Mori, Jarrod J. Scott, Kevin W. Hager, Craig L. Moyer, Kirsten Küsel, David Emerson

Published: August 18, 2017

C-DEBI Contribution Number: 379

Abstract

Chemosynthetic Fe-oxidizing communities are common at diffuse-flow hydrothermal vents throughout the world’s oceans. The foundational members of these communities are the Zetaproteobacteria, a class of Proteobacteria that is primarily associated with ecosystems fueled by ferrous iron, Fe(II). We report here the discovery of two new isolates of Zetaproteobacteria isolated from the Mid-Atlantic Ridge (TAG-1), and the Mariana back-arc (SV-108), that are unique in that they can utilize either Fe(II) or molecular hydrogen (H2) as sole electron donor and oxygen as terminal electron acceptor for growth. Both strains precipitated Fe-oxyhydroxides as amorphous particulates. The cell doubling time on H2 vs Fe(II) for TAG-1 was 14.1 vs 21.8 h, and for SV-108 it was 16.3 vs 20 h, and it appeared both strains could use either H2 or Fe(II) simultaneously. The strains were close relatives, based on genomic analysis, and both possessed genes for the uptake NiFe-hydrogenase required for growth on H2. These two strains belong to Zetaproteobacteria operational taxonomic unit 9 (ZetaOTU9). A meta-analysis of public databases found ZetaOTU9 was only associated with Fe(II)-rich habitats, and not in other environments where known H2-oxidizers exist. These results expand the metabolic repertoire of the Zetaproteobacteria, yet confirm that Fe(II) metabolism is the primary driver of their physiology and ecology.

Source: http://dx.doi.org/10.1038/ismej.2017.132

Related Items

Awards

Combining omics approaches to gain a comprehensive understanding of microbial diversity and activity in subsurface igneous basement along the Louisville Seamount Trail (IODP Expedition 330)

Award Dates: October 1, 2013 — September 30, 2015

PI: Jason B. Sylvan (University of Southern California)

Current Placement: Assistant Professor, Texas A&M University

Co-Is: David Emerson (Bigelow Laboratory for Ocean Science),
Erin Field (Bigelow Laboratory for Ocean Science; University of Delaware)

Current Placement: Assistant Professor, ECU, 2015-

International Journal of Systematic and Evolutionary Microbiology

Authors: Donato Giovannelli, Matthew Chung, Justin Staley, Costantino Vetriani, Valentin Starovoytov, Nadine Le Bris

Published: July 1, 2016

C-DEBI Contribution Number: 382

Abstract

An anaerobic, nitrate-reducing, sulfur- and thiosulfate-oxidizing bacterium, designated strain 1812ET, was isolated from the vent polychaete Riftia pachyptila, which was collected from a deep-sea hydrothermal vent on the East Pacific Rise. Cells were Gram-stain-negative rods, measuring approximately 1.05±0.11 µm by 0.40±0.05 µm. Strain 1812ET grew at 25 – –45 °C (optimum 35 °C), with 1.5–4.0 % (w/v) NaCl (optimum 3.0 %) and at pH 5.0–8.0 (optimum pH 6.0). The generation time under optimal conditions was 3 h. Strain 1812ET was an anaerobic chemolithotroph that grew with either sulfur or thiosulfate as the energy source and carbon dioxide as the sole carbon source. Nitrate was used as a sole terminal electron acceptor. The predominant fatty acids were C_16 : 1 ω7c, C_18 : 1 ω7c and C_16 : 0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was menaquinone MK-6 and the G+C content of the genomic DNA was 47.4 mol%. Phylogenetic analysis of the 16S rRNA gene of strain 1812ET showed that the isolate belonged to the Epsilonproteobacteria , and its closest relatives were Sulfurovum lithotrophicum 42BKTT and Sulfurovum aggregans Monchim 33T (98.3 and 95.7 % sequence similarity, respectively). DNA–DNA relatedness between strain 1812ET and the type strain of S. lithotrophicum was 29.7 %, demonstrating that the two strains are not members of the same species. Based on the phylogenetic, molecular, chemotaxonomic and physiological evidence, strain 1812ET represents a novel species within the genus Sulfurovum , for which the name Sulfurovum riftiae sp. nov. is proposed. The type strain is 1812ET (=DSM 101780T=JCM 30810T).

Source: http://dx.doi.org/10.1099/ijsem.0.001106

Identification of organic compounds in ocean basement fluids

Organic Geochemistry

Authors: Douglas E. LaRowe, Boris P. Koch, Alberto Robador, Matthias Witt, Kerstin Ksionzek, Jan P. Amend

Published: August 1, 2017

C-DEBI Contribution Number: 376

Abstract

We have analyzed the dissolved organic carbon, OC, in ocean basement fluids using Fourier Transform-Ion Cyclotron Resonance-Mass Spectrometry (FT-ICR-MS). The compounds identified at the two sites, near the Juan de Fuca and Mid-Atlantic Ridges (North Pond), differ substantially from each other and from seawater. Compared to Juan de Fuca, North Pond organics had a lower average molecular weight (349 vs. 372 g/mol), 50% more identifiable compounds (2181 vs. 1482), and demonstrably lower average nominal oxidation state of carbon (-0.70 vs. -0.57). The North Pond fluids were also found to have many more N- and S-bearing compounds. Based on our data, the marine subsurface can alter the types of dissolved OC, DOC, compounds in seawater.

Source: http://dx.doi.org/10.1016/j.orggeochem.2017.07.017

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea

mBio

Authors: Connor T. Skennerton, Karuna Chourey, Ramsunder Iyer, Robert L. Hettich, Gene W. Tyson, Victoria J. Orphan

Editors: Nicole Dubilier

Published: August 1, 2017

C-DEBI Contribution Number: 374

Abstract

The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANME partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors.

Source: http://dx.doi.org/10.1128/mbio.00530-17

Microbial biofilms associated with fluid chemistry and megafaunal colonization at post-eruptive deep-sea hydrothermal vents

Deep Sea Research Part II: Topical Studies in Oceanography

Authors: Charles E. O’Brien, Donato Giovannelli, Breea Govenar, George W. Luther, Richard A. Lutz, Timothy M. Shank, Costantino Vetriani

Published: November 1, 2015

C-DEBI Contribution Number: 386

Abstract

At deep-sea hydrothermal vents, reduced, super-heated hydrothermal fluids mix with cold, oxygenated seawater. This creates temperature and chemical gradients that support chemosynthetic primary production and a biomass-rich community of invertebrates. In late 2005/early 2006 an eruption occurred on the East Pacific Rise at 9°50′N, 104°17′W. Direct observations of the post-eruptive diffuse-flow vents indicated that the earliest colonizers were microbial biofilms. Two cruises in 2006 and 2007 allowed us to monitor and sample the early steps of ecosystem recovery. The main objective of this work was to characterize the composition of microbial biofilms in relation to the temperature and chemistry of the hydrothermal fluids and the observed patterns of megafaunal colonization. The area selected for this study had local seafloor habitats of active diffuse flow (in-flow) interrupted by adjacent habitats with no apparent expulsion of hydrothermal fluids (no-flow). The in-flow habitats were characterized by higher temperatures (1.6–25.2 °C) and H₂S concentrations (up to 67.3 µM) than the no-flow habitats, and the microbial biofilms were dominated by chemosynthetic Epsilonproteobacteria. The no-flow habitats had much lower temperatures (1.2–5.2 °C) and H₂S concentrations (0.3–2.9 µM), and Gammaproteobacteria dominated the biofilms. Siboglinid tubeworms colonized only in-flow habitats, while they were absent at the no-flow areas, suggesting a correlation between siboglinid tubeworm colonization, active hydrothermal flow, and the composition of chemosynthetic microbial biofilms.

Source: http://dx.doi.org/10.1016/j.dsr2.2015.07.020

High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment

Standards in Genomic Sciences

Published: September 8, 2016

C-DEBI Contribution Number: 385

Abstract

Sedimenticola selenatireducens strain AK4OH1^T (= DSM 17993^T = ATCC BAA-1233^T) is a microaerophilic bacterium isolated from sediment from the Arthur Kill intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1^T was the first representative of its genus to be isolated for its unique coupling of the oxidation of aromatic acids to the respiration of selenate. It is a versatile heterotroph and can use a variety of carbon compounds, but can also grow lithoautotrophically under hypoxic and anaerobic conditions. The draft genome comprises 4,588,530 bp and 4276 predicted protein-coding genes including genes for the anaerobic degradation of 4-hydroxybenzoate and benzoate. Here we report the main features of the genome of S. selenatireducensstrain AK4OH1^T.

Source: http://dx.doi.org/10.1186/s40793-016-0191-5

The Role of Microbial Electron Transfer in the Coevolution of the Biosphere and Geosphere

Annual Review of Microbiology

Authors: Benjamin I. Jelen, Donato Giovannelli, Paul G. Falkowski

Published: September 8, 2016

C-DEBI Contribution Number: 384

Aquatic habitats beneath ice masses contain active microbial ecosystems capable of cycling important greenhouse gases, such as methane (CH₄). A large methane reservoir is thought to exist beneath the West Antarctic Ice Sheet, but its quantity, source and ultimate fate are poorly understood. For instance, O₂ supplied by basal melting should result in conditions favourable for aerobic methane oxidation. Here we use measurements of methane concentrations and stable isotope compositions along with genomic analyses to assess the sources and cycling of methane in Subglacial Lake Whillans (SLW) in West Antarctica. We show that sub-ice-sheet methane is produced through the biological reduction of CO₂ using H₂. This methane pool is subsequently consumed by aerobic, bacterial methane oxidation at the SLW sediment–water interface. Bacterial oxidation consumes >99% of the methane and represents a significant methane sink, and source of biomass carbon and metabolic energy to the surficial SLW sediments. We conclude that aerobic methanotrophy may mitigate the release of methane to the atmosphere upon subglacial water drainage to ice sheet margins and during periods of deglaciation.

Source: http://dx.doi.org/10.1038/ngeo2992

Related Items

Awards

Microbial carbon cycling beneath the West Antarctic Ice Sheet

Award Dates: August 1, 2014 — May 31, 2016

Awardee: Alexander B. Michaud (Montana State University)

Current Placement: Postdoc, Aarhus (Jørgensen), 2016-

Advisor: John C. Priscu (Montana State University)

Climate oscillations reflected within the microbiome of Arabian Sea sediments

Scientific Reports

Authors: William D. Orsi, Marco J. L. Coolen, Cornelia Wuchter, Lijun He, Kuldeep D. More, Xabier Irigoien, Guillem Chust, Carl Johnson, Jordon D. Hemingway, Mitchell Lee, Valier Galy, Liviu Giosan

Published: July 20, 2017

C-DEBI Contribution Number: 358

Abstract

Selection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5–15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.

Source: http://dx.doi.org/10.1038/s41598-017-05590-9

Editorial: Recent Advances in Geomicrobiology of the Ocean Crust

Frontiers in Microbiology

Authors: Beth N. Orcutt, Jason B. Sylvan, Cara M. Santelli

Published: July 21, 2017

C-DEBI Contribution Number: 375

Abstract

Editorial on the Research Topic Recent Advances in Geomicrobiology of the Ocean Crust. Igneous oceanic crust is one of the largest potential habitats for life on earth (Orcutt et al., 2011), and microbial activity supported by rock-water-microbe reactions in this environment can impact global biogeochemical cycles (Bach and Edwards, 2003). However, our understanding of the microbiology of this system, especially the subsurface “deep biosphere” component of it, has traditionally been limited by sample availability and quality. Over the past decade, several major international programs (such as the Center for Dark Energy Biosphere Investigations, the current International Ocean Discovery Program, and its predecessor Integrated Ocean Drilling Program, and the Deep Carbon Observatory) have focused on advancing our understanding of life in this cryptic, yet globally relevant, biosphere. Additionally, many field and laboratory research programs are examining hydrothermal vent systems—a seafloor expression of seawater that has been thermally and chemically altered in subseafloor crust—and the microbial communities supported by these mineral-rich fluids. The papers in this special issue bring together recent discoveries of microbial presence, diversity, and activity in these dynamic ocean environments.

Source: http://dx.doi.org/10.3389/fmicb.2017.01368

A Review of the Geochemistry and Microbiology of Marine Shallow-Water Hydrothermal Vents

Reference Module in Earth Systems and Environmental Sciences

Authors: Roy E. Price, Donato Giovannelli

Published: May 30, 2017

C-DEBI Contribution Number: 367

Abstract

Marine shallow-water vents are ubiquitous but poorly studied geothermal environments located worldwide between the intertidal zone and 212 m depth. Important factors differentiating them from their deep-sea counterparts include sunlight, tidal/wave pumping, meteoric water sources, terrigenous inputs, elevated metal concentrations, and abundant free gas. Mixing of vent fluids with oxidized seawater generates multiple redox disequilibria readily exploited by microbes. Although highly diverse, two major groups include an Epsilonprotebacteria-dominated community sharing similarities with deep-sea analogs, and a community dominated by Gammaproteobacteria/Firmicutes. The distribution of different microbial taxa within each vent is primarily controlled by temperature and availability of suitable electron donors and acceptors. However, the coexistence of phototrophs, chemolithoautotrophs, and a high abundance of aerobic and anaerobic heterotrophs, suggests the presence of sunlight and high organic carbon loads define unique microbial habitats that are transitionary between terrestrial and deep-sea vents. We summarize here the current knowledge of shallow-sea vents worldwide, highlighting gaps on our understanding of these unique environments.

Source: http://dx.doi.org/10.1016/b978-0-12-409548-9.09523-3

Incorporating Deep Sea Science and Underwater Robotics in Low-Income Schools

Current: The Journal of Marine Education

Authors: Dieuwertje Kast

Published: June 1, 2017

C-DEBI Contribution Number: 372

Abstract

Excerpt: The USC Young Scientists Program (YSP) Director, and the National Marine Educators Association (NMEA) Expanded Audience Committee Chair Dieuwertje Kast, hosted a deep sea science workshop for 50 fourth and fifth grade students at Vermont Elementary on November 15, 2016. The event was a collaboration between YSP, Ocean Exploration Trust/Nautilus, Deezmaker, OpenROV, and the Center for Dark Energy Biosphere Investigations (C-DEBI, a National Science Foundation Science and Technology Center) and NMEA. C-DEBI provided YSP with an Educator Small Grant to make the event possible. C-DEBI research focuses on the discovery of the microbial life below the ocean floor, in rocks, and sediments (the deep biosphere). C-DEBI welcomed the proposal that engaged diverse and underserved populations and brought in scientists from ethnic minority backgrounds. Current: The Journal of Marine Education, is a journal produced by NMEA, the National Marine Educators Association.

Source: http://www.darkenergybiosphere.org/wp-content/uploads/C-DEBI-article_Current.pdf

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the Candidate Superphylum Parcubacteria (OD1)

Environmental Microbiology

Authors: Rosa León-Zayas, Logan Peoples, Jennifer F. Biddle, Sheila Podell, Mark Novotny, James Cameron, Roger S. Lasken, Douglas H. Bartlett

Published: May 1, 2017

C-DEBI Contribution Number: 369

Abstract

Candidate phyla (CP) are broad phylogenetic clusters of organisms that lack cultured representatives. Included in this fraction is the candidate Parcubacteria superphylum. Specific characteristics that have been ascribed to the Parcubacteria include reduced genome size, limited metabolic potential, and exclusive reliance on fermentation for energy acquisition. The study of new environmental niches, such as the marine versus terrestrial subsurface, often expands the understanding of the genetic potential of taxonomic groups. For this reason we analyzed twelve Parcubacteria single amplified genomes (SAGs) from sediment samples collected within the Challenger Deep of the Mariana Trench, obtained during the Deepsea Challenge (DSC) Expedition. Many of these SAGs are closely related to environmental sequences obtained from deep-sea environments based on 16S rRNA gene similarity and BLAST matches to predicted proteins. DSC SAGs encode features not previously identified in Parcubacteria obtained from other habitats. These include adaptation to oxidative stress, polysaccharide modification, and genes associated with respiratory nitrate reduction. The DSC SAGs are also distinguished by relative greater abundance of genes for nucleotide and amino acid biosynthesis, repair of alkylated DNA and the synthesis of mechanosensitive ion channels. These results present an expanded view of the Parcubacteria, among members residing in an ultra-deep hadal environment.

Source: http://dx.doi.org/10.1111/1462-2920.13789

Biogeochemical N signatures from rate-yield trade-offs during in vitro chemosynthetic NO 3 - reduction by deep-sea vent ε-Proteobacteria and Aquificae growing at different temperatures

Geochimica et Cosmochimica Acta

Authors: Ileana Pérez-Rodríguez, Stefan M. Sievert, Marilyn L. Fogel, Dionysis I. Foustoukos

Published: May 1, 2017

C-DEBI Contribution Number: 238

Abstract

NO₃^- reduction is a metabolism that is widespread among ε-Proteobacteria and Aquificae, two abundant classes of microorganisms found at deep-sea vents. In this study, we used Sulfurovum lithotrophicum, Caminibacter mediatlanticus and Thermovibrio ammonificans as representatives of these groups to study ecophysiological, metabolic and biogeochemical parameters associated with chemolithoautotrophic NO₃^- reduction under different temperature regimes. We observed that while S. lithotrophicum and C. mediatlanticus achieved higher cell densities than T. ammonificans, the overall NO₃^- consumption by the latter was on average ∼ 9 and ∼ 5 times faster on a per cell basis, respectively. Comparison with previously published data from other cultured vent ε-Proteobacteria and Aquificae suggests that the rate-yield trade-offs observed in our experiments are generally conserved between these two groups in line with their ecophysiologies. Kinetic isotope effects of N from NO₃^- reduction were 9.6 ± 2.7 ‰ for S. lithotrophicum, 6.4 ± 0.7 ‰ for C. mediatlanticus and 8.8 ± 0.6 ‰ for T. ammonificans. Our results help evaluate how metabolic partitioning between growth efficiency and reaction kinetics during chemolithoautotrophic NO₃^- reduction affect the concentration and isotope composition of N compounds at deep-sea hydrothermal vents.

Source: http://dx.doi.org/10.1016/j.gca.2017.05.014

Related Items

Awards

Dissimilatory Fe(III) reduction metabolisms in high-pressure ocean crustal environments: An experimental case study of the archeaon Geoglobus acetivorans

Award Dates: May 1, 2013 — April 30, 2015

Awardee: Ileana Pérez-Rodríguez (Carnegie Institute of Washington)

Current Placement: Asst Prof, U Penn, 2017-

Degree: Ph.D. Microbial Ecology, Rutgers University (2011)

Advisors: Dionysis I. Foustoukos (Carnegie Institute of Washington), Andrew Steele (Carnegie Institute of Washington)

Publications >

eLife

Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans

Authors: Donato Giovannelli, Stefan M. Sievert, Michael Hügler, Stephanie Markert, Dörte Becher, Thomas Schweder, Costantino Vetriani

Published: April 24, 2017

C-DEBI Contribution Number: 368

Abstract

Anaerobic thermophiles inhabit relic environments that resemble the early Earth. However, the lineage of these modern organisms co-evolved with our planet. Hence, these organisms carry both ancestral and acquired genes and serve as models to reconstruct early metabolism. Based on comparative genomic and proteomic analyses, we identified two distinct groups of genes in Thermovibrio ammonificans: the first codes for enzymes that do not require oxygen and use substrates of geothermal origin; the second appears to be a more recent acquisition, and may reflect adaptations to cope with the rise of oxygen on Earth. We propose that the ancestor of the Aquificae was originally a hydrogen oxidizing, sulfur reducing bacterium that used a hybrid carbon fixation pathway for CO₂fixation. With the gradual rise of oxygen in the atmosphere, more efficient terminal electron acceptors became available and this lineage acquired genes that increased its metabolic flexibility while retaining ancestral metabolic traits.

Source: http://dx.doi.org/10.7554/elife.18990

Related Items

Awards

Alternative carbon fixation strategies in the model organism Thermovibrio ammonificans: A model system to study energy limitation in the deep biosphere

Award Dates: June 1, 2014 — May 31, 2016

Awardee: Donato Giovannelli (Rutgers University)

Current Placement: Research Fellow, National Research Council, Institute for Marine Science CNR-ISMAR Ancona

Degree: Ph.D. Applied Biology, Ecology and Microbiology, University of Naples (2013)

Advisor: Costantino Vetriani (Rutgers University)

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

PeerJ

Authors: Sean P. Jungbluth, Tijana Glavina del Rio, Susannah G. Tringe, Ramunas Stepanauskas, Michael S. Rappé

Published: April 6, 2017

C-DEBI Contribution Number: 356

Abstract

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.

Source: http://dx.doi.org/10.7717/peerj.3134

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations

Geobiology

Published: April 17, 2017

C-DEBI Contribution Number: 365

Abstract

Reactive Fe(III) minerals can influence methane (CH₄) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH₄ oxidation. The balance between Fe(III) reduction, methanogenesis, and CH₄oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH₄ fluxes to the atmosphere, thereby regulating the capacity for CH₄ to warm the early Earth under the Faint Young Sun. We studied CH₄ and Fe cycling in anoxic incubations of ferruginous sediment from the ancient ocean analogue Lake Matano, Indonesia, over three successive transfers (500 days in total). Iron reduction, methanogenesis, CH₄ oxidation, and microbial taxonomy were monitored in treatments amended with ferrihydrite or goethite. After three dilutions, Fe(III) reduction persisted only in bottles with ferrihydrite. Enhanced CH₄ production was observed in the presence of goethite, highlighting the potential for reactive Fe(III) oxides to inhibit methanogenesis. Supplementing the media with hydrogen, nickel and selenium did not stimulate methanogenesis. There was limited evidence for Fe(III)-dependent CH₄ oxidation, although some incubations displayed CH₄-stimulated Fe(III) reduction. 16S rRNA profiles continuously changed over the course of enrichment, with ultimate dominance of unclassified members of the order Desulfuromonadales in all treatments. Microbial diversity decreased markedly over the course of incubation, with subtle differences between ferrihydrite and goethite amendments. These results suggest that Fe(III) oxide mineralogy and availability of electron donors could have led to spatial separation of Fe(III)-reducing and methanogenic microbial communities in ferruginous marine sediments, potentially explaining the persistence of CH₄ as a greenhouse gas throughout the first half of Earth history.

Source: http://dx.doi.org/10.1111/gbi.12239

Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria

Environmental Microbiology

Authors: Nagissa Mahmoudi, Steven R. Beaupré, Andrew D. Steen, Ann Pearson

Published: March 1, 2017

C-DEBI Contribution Number: 366

Abstract

Aquatic sediments harbor diverse microbial communities that mediate organic matter degradation and influence biogeochemical cycles. The pool of bioavailable carbon continuously changes as a result of abiotic processes and microbial activity. It remains unclear how microbial communities respond to heterogeneous organic matrices and how this ultimately affects heterotrophic respiration. To explore the relationships between the degradation of mixed carbon substrates and microbial activity, we incubated batches of organic-rich sediments in a novel bioreactor (IsoCaRB) that permitted continuous observations of CO₂ production rates, as well as sequential sampling of isotopic signatures (δ¹³C, Δ¹⁴C), microbial community structure and diversity, and extracellular enzyme activity. Our results indicated that lower molecular weight (MW), labile, phytoplankton-derived compounds were degraded first, followed by petroleum-derived exogenous pollutants, and finally by higher MW polymeric plant material. This shift in utilization coincided with a community succession and increased extracellular enzyme activities. Thus, sequential utilization of different carbon pools induced changes at both the community and cellular level, shifting community composition, enzyme activity, respiration rates, and residual organic matter reactivity. Our results provide novel insight into the accessibility of sedimentary organic matter and demonstrate how bioavailability of natural organic substrates may affect the function and composition of heterotrophic bacterial populations. This article is protected by copyright. All rights reserved.

Source: http://dx.doi.org/10.1111/1462-2920.13745

Related Items

Awards

Investigating the bioavailability and degradation of sedimentary organic matter

Award Dates: September 1, 2016 — August 31, 2018

Awardee: Nagissa Mahmoudi (Harvard University)

Current Placement: Assistant Professor, McGill University

Advisor: Ann Pearson (Harvard University)

Microbial and Biogeochemical Dynamics in Glacier Forefields Are Sensitive to Century-Scale Climate and Anthropogenic Change

Frontiers in Earth Science

Authors: James A. Bradley, Alexandre M. Anesio, Sandra Arndt

Published: April 3, 2017

C-DEBI Contribution Number: 363

Abstract

The recent retreat of glaciers and ice sheets as a result of global warming exposes forefield soils that are rapidly colonized by microbes. These ecosystems are dominant in high-latitude carbon and nutrient cycles as microbial activity drives biogeochemical transformations within these newly exposed soils. Despite this, little is known about the response of these emerging ecosystems and associated biogeochemical cycles to projected changes in environmental factors due to human impacts. Here, we applied the model SHIMMER to quantitatively explore the sensitivity of biogeochemical dynamics in the forefield of Midtre Lovénbreen, Svalbard, to future changes in climate and anthropogenic forcings including soil temperature, snow cover, and nutrient and organic substrate deposition. Model results indicated that the rapid warming of the Arctic, as well as an increased deposition of organic carbon and nutrients, may impact primary microbial colonizers in Arctic soils. Warming and increased snow-free conditions resulted in enhanced bacterial production and an accumulation of biomass that was sustained throughout 200 years of soil development. Nitrogen deposition stimulated growth during the first 50 years of soil development following exposure. Increased deposition of organic carbon sustained higher rates of bacterial production and heterotrophic respiration leading to decreases in net ecosystem production and thus net CO₂ efflux from soils. Pioneer microbial communities were particularly susceptible to future changes. All future climate simulations encouraged a switch from allochthonously-dominated young soils (<40 years) to microbially-dominated older soils, due to enhanced heterotrophic degradation of organic matter. Critically, this drove remineralisation and increased nutrient availability. Overall, we show that human activity, especially the burning of fossil fuels and the enhanced deposition of nitrogen and organic carbon, has the potential to considerably affect the biogeochemical development of recently exposed Arctic soils in the present day and for centuries into the future. These effects must be acknowledged when attempting to make accurate predictions of the future fate of Arctic soils that are exposed over large expanses of presently ice-covered regions.

Source: http://journal.frontiersin.org/article/10.3389/feart.2017.00026/full

In situ electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring

Environmental Microbiology

Authors: Annette R. Rowe, Miho Yoshimura, Douglas E. LaRowe, Lina J. Bird, Jan P. Amend, Kazuhito Hashimoto, Kenneth H. Nealson, Akihiro Okamoto

Published: March 1, 2017

C-DEBI Contribution Number: 364

Abstract

Serpentinization is a geologic process that produces highly reduced, hydrogen-rich fluids that support microbial communities under high pH conditions. We investigated the activity of microbes capable of extracellular electron transfer in a terrestrial serpentinizing system known as “The Cedars”. Measuring current generation with an on-site two-electrode system, we observed daily oscillations in current with the current maxima and minima occurring during daylight hours. Distinct members of the microbial community were enriched. Current generation in lab-scale electrochemical reactors did not oscillate, but was correlated with carbohydrate amendment in Cedars-specific minimal media. Gammaproteobacteria and Firmicutes were consistently enriched from lab electrochemical systems on δ-MnO₂ and amorphous Fe(OH)₃ at pH 11. However, isolation of an electrogenic strain proved difficult as transfer cultures failed to grow after multiple rounds of media transfer. Lowering the bulk pH in the media allowed us to isolate a Firmicutes strain (Paenibacillus sp.). This strain was capable of electrode and mineral reduction (including magnetite) at pH 9. This report provides evidence of the in situ activity of microbes using extracellular substrates as sinks for electrons at The Cedars, but also highlights the potential importance of community dynamics for supporting microbial life through either carbon fixation and/or moderating pH stress.

Source: http://dx.doi.org/10.1111/1462-2920.13723

Related Items

Awards

Passing electrons through marine sediments: Cultivation and characterization of microbes that utilize extracellular electron transport

Award Dates: May 1, 2013 — April 30, 2015

Awardee: Annette R. Rowe (University of Southern California)

Current Placement: Postdoc, USC, 2012-, USC

Degree: Ph.D. Microbiology, Cornell University (2011)

Advisor: Kenneth H. Nealson (University of Southern California)

Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea

Nature Microbiology

Authors: Blair Paul, David Burstein, Cindy J. Castelle, Sumit Handa, Diego Arambula, Elizabeth Czornyj, Brian C. Thomas, Partho Ghosh, Jeff F. Miller, Jillian F. Banfield, David Valentine

Published: April 3, 2017

C-DEBI Contribution Number: 361

Abstract

Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability, are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum. From reconstructed genomes we have defined monophyletic bacterial and archaeal DGR lineages that expand the known DGR range by 120% and reveal a history of horizontal retroelement transfer. Retroelement-guided diversification is further shown to be active in current CPR and DPANN populations, with an assortment of protein targets potentially involved in attachment, defence and regulation. Based on observations of DGR abundance, function and evolutionary history, we find that targeted protein diversification is a pronounced trait of CPR and DPANN phyla compared to other bacterial and archaeal phyla. This diversification mechanism may provide CPR and DPANN organisms with a versatile tool that could be used for adaptation to a dynamic, host-dependent existence.

Source: http://dx.doi.org/10.1038/nmicrobiol.2017.45

Related Items

Awards

Using a targeted metagenomic approach to examine adaptive protein diversification by microorganisms and their viruses in subseafloor sediments

Award Dates: April 1, 2016 — June 30, 2018

Awardee: Blair Paul (University of California Santa Barbara)

Degree: Ph.D. Marine Science, University of California Santa Barbara (2013)

Advisor: David Valentine (University of California Santa Barbara)

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

Scientific Data

Authors: Sean P. Jungbluth, Jan P. Amend, Michael S. Rappé

Published: March 28, 2017

C-DEBI Contribution Number: 357

Abstract

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Source: http://dx.doi.org/10.1038/sdata.2017.37

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

PeerJ

Authors: Elaina D. Graham, John F. Heidelberg, Benjamin J. Tully

Published: March 8, 2017

C-DEBI Contribution Number: 360

Abstract

Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes.

Source: http://dx.doi.org/10.7717/peerj.3035

Publications > Monograph

Ph.D. Thesis

Geochemical controls on the distribution and composition of biogenic and sedimentary carbon

Authors: Emily R. Estes

Published: February 1, 2017

C-DEBI Contribution Number: 359

Abstract

Organic carbon (OC) preserved in marine sediments acts as a reduced carbon sink that balances the global carbon cycle. Understanding the biogeochemical mechanisms underpinning the balance between OC preservation and degradation is thus critical both to quantifying this carbon reservoir and to estimating the extent of life in the deep subsurface biosphere. This work utilizes bulk and spatially-resolved X-ray absorption spectroscopy to characterize the OC content and composition of various environmental systems in order to identify the role of minerals and surrounding geochemistry in organic carbon preservation in sediments. Biogenic manganese (Mn) oxides formed either in pure cultures of Mn-oxidizing microorganisms, in incubations of brackish estuarine waters, or as ferromanganese deposits in karstic cave systems rapidly associate with OC following precipitation. This association is stable despite Mn oxide structural ripening, suggesting that mineral-associated OC could persist during early diagenetic reactions. OC associated with bacteriogenic Mn oxides is primarily proteinaceous, including intact proteins involved in Mn oxidation and likely oxide nucleation and aggregation. Pelagic sediments from 16 sites underlying the South Pacific and North Atlantic gyres and spanning a gradient of sediment age and redox state were analyzed in order to contrast the roles of oxygen exposure, OC recalcitrance, and mineral-based protection of OC as preservation mechanisms. OC and nitrogen concentrations measured at these sites are among the lowest globally (<0.1%) and, to a first order, scale with sediment oxygenation. In the deep subsurface, however, molecular recalcitrance becomes more important than oxygen exposure time in protecting OC against remineralization. Deep OC consists of primarily amide and carboxylic carbon in a scaffolding of aliphatic and O-alkyl moieties, corroborating the extremely low C/N values observed. These findings suggest that microbes in oxic pelagic sediments are carbon-limited and may preferentially remove carbon relative to nitrogen from the organic matter pool. As a whole, this work documents how interactions with mineral surfaces and exposure to oxygen generate a reservoir of OC stabilized in sediments on at least 25-million year time scales.

Source: http://dx.doi.org/10.1575/1912/8762

Related Items

Awards

Geochemical controls on organic carbon quantity and quality in the deep subsurface

Award Dates: June 1, 2016 — May 31, 2017

Awardee: Emily R. Estes (Woods Hole Oceanographic Institution)

Current Placement: Postdoctoral Researcher, University of Delaware, 2017-

Advisor: Colleen M. Hansel (Woods Hole Oceanographic Institution)

Elucidating the extent and composition of mineral-hosted carbon in the deep biosphere

Award Dates: April 1, 2015 — March 31, 2016

PI: Colleen M. Hansel (Woods Hole Oceanographic Institution)

Co-Is: Emily R. Estes (Woods Hole Oceanographic Institution), Gariela Farfan (Woods Hole Oceanographic Institution)

A new solution 31P NMR sample preparation scheme for marine sediments

Limnology and Oceanography: Methods

Authors: Delphine Defforey, Barbara J. Cade-Menun, Adina Paytan

Published: February 1, 2017

C-DEBI Contribution Number: 353

Abstract

A new approach for the preparation of marine sediment samples for solution ³¹P nuclear magnetic resonance spectroscopy (³¹P NMR) has been developed and tested. This approach addresses important aspects associated with sample pretreatments for marine sediments, including the effects of sample pretreatment on sedimentary P composition. The method increases the signals of low abundance P species in ³¹P NMR spectra by quantitatively and precisely removing up to 80% of inorganic P (orthophosphate) from sediment samples while causing minimal alteration of the chemical structure of organic P compounds. This method uses a reductive step to solubilize P bound to iron oxyhydroxides, followed by a low pH digestion to extract P from authigenic and biogenic apatite, as well as P bound to calcium carbonate. These P forms combined represent the most abundant inorganic P reservoir in marine sediments. The sample residue is then extracted in an alkaline solvent, 0.25 M NaOH with 0.05 M Na₂EDTA, and processed for ³¹P NMR spectroscopy. The method was tested on natural marine sediment samples from different localities with high inorganic P content (>85% molybdate reactive P), and allowed for the detection of orthophosphate monoesters and pyrophosphate in samples for which only an orthophosphate signal could be resolved with an NaOH-EDTA extraction alone. This new approach will allow the use of ³¹P NMR on samples for which low organic P concentrations previously hindered the use of this tool, and will help answer longstanding question regarding the fate of organic P in marine sediments.

Source: http://dx.doi.org/10.1002/lom3.10166

Related Items

Awards

Awards > Research Exchange Grants

Award Dates: March 23, 2015 — April 6, 2015

Phosphorus uptake mechanisms in the deep sedimentary biosphere

PI: Delphine Defforey (University of California, Santa Cruz)

Current Placement: Associate Editor, Nature Communications

Advisor: Adina Paytan (University of California, Santa Cruz)

Host: Brandi Kiel Reese (Texas A&M University, Corpus Christi)

Nature of labile and refractory phosphorus pools fueling life in deep sub-seafloor sediments

Award Dates: July 1, 2012 — June 30, 2014

Awardee: Delphine Defforey (University of California, Santa Cruz)

Current Placement: Associate Editor, Nature Communications, 2016-

Advisor: Adina Paytan (University of California, Santa Cruz)

Phosphorus sources and cycling in the deep biosphere fueling: life in the dark

Award Dates: October 1, 2011 — September 30, 2014

PI: Adina Paytan (University of California, Santa Cruz)

Viruses in the Oceanic Basement

mBio

Authors: Olivia Nigro, Sean P. Jungbluth, Huei-Ting Lin, Chih-Chiang Hsieh, Jaclyn A. Miranda, Christopher R. Schvarcz, Michael S. Rappé, Grieg Steward

Editors: Stephen J. Giovannoni

Published: March 7, 2017

C-DEBI Contribution Number: 354

Abstract

Microbial life has been detected well into the igneous crust of the seafloor (i.e., the oceanic basement), but there have been no reports confirming the presence of viruses in this habitat. To detect and characterize an ocean basement virome, geothermally heated fluid samples (ca. 60 to 65°C) were collected from 117 to 292 m deep into the ocean basement using seafloor observatories installed in two boreholes (Integrated Ocean Drilling Program [IODP] U1362A and U1362B) drilled in the eastern sediment-covered flank of the Juan de Fuca Ridge. Concentrations of virus-like particles in the fluid samples were on the order of 0.2 × 10⁵ to 2 × 10⁵ ml⁻¹ (n = 8), higher than prokaryote-like cells in the same samples by a factor of 9 on average (range, 1.5 to 27). Electron microscopy revealed diverse viral morphotypes similar to those of viruses known to infect bacteria and thermophilic archaea. An analysis of virus-like sequences in basement microbial metagenomes suggests that those from archaeon-infecting viruses were the most common (63 to 80%). Complete genomes of a putative archaeon-infecting virus and a prophage within an archaeal scaffold were identified among the assembled sequences, and sequence analysis suggests that they represent lineages divergent from known thermophilic viruses. Of the clustered regularly interspaced short palindromic repeat (CRISPR)-containing scaffolds in the metagenomes for which a taxonomy could be inferred (163 out of 737), 51 to 55% appeared to be archaeal and 45 to 49% appeared to be bacterial. These results imply that the warmed, highly altered fluids in deeply buried ocean basement harbor a distinct assemblage of novel viruses, including many that infect archaea, and that these viruses are active participants in the ecology of the basement microbiome.

IMPORTANCE The hydrothermally active ocean basement is voluminous and likely provided conditions critical to the origins of life, but the microbiology of this vast habitat is not well understood. Viruses in particular, although integral to the origins, evolution, and ecology of all life on earth, have never been documented in basement fluids. This report provides the first estimate of free virus particles (virions) within fluids circulating through the extrusive basalt of the seafloor and describes the morphological and genetic signatures of basement viruses. These data push the known geographical limits of the virosphere deep into the ocean basement and point to a wealth of novel viral diversity, exploration of which could shed light on the early evolution of viruses.

This paper is dedicated to the late James P. Cowen, whose collegiality, infectious enthusiasm for science, and pioneering studies of the ocean basement microbiome inspired the work.

Source: http://dx.doi.org/10.1128/mbio.02129-16

Related Items

Awards

Characterizing viruses and their influence on the microbial community within the basement fluids of the Juan de Fuca Ridge flank

Award Dates: April 1, 2014 — March 31, 2016

Awardee: Olivia Nigro (University of Hawaii)

Degree: Assistant Professor, Hawaii Pacific University

Advisor: Grieg Steward (University of Hawaii)

Metagenomic and electron microscopic investigation of viruses and viral infections of prokaryotes in oceanic basement fluids

Award Dates: July 1, 2013 — June 30, 2015

PI: Grieg Steward (University of Hawaii)

Genomic and proteomic characterization of uncultivated viruses from large-volume samples of crustal fluids from the Juan de Fuca Ridge Flank

Award Dates: April 1, 2015 — March 31, 2016

PI: Grieg Steward (University of Hawaii)

Co-I: Olivia Nigro (University of Hawaii)

Current Placement: Assistant Professor, Hawaii Pacific University

The relative abundances of resolved ^l2CH₂D₂ and ^13CH₃D and mechanisms controlling isotopic bond ordering in abiotic and biotic methane gases

Geochimica et Cosmochimica Acta

Published: April 1, 2017

C-DEBI Contribution Number: 362

Abstract

We report measurements of resolved ¹²CH₂D₂ and ¹³CH₃D at natural abundances in a variety of methane gases produced naturally and in the laboratory. The ability to resolve ¹²CH₂D₂ from ¹³CH₃D provides unprecedented insights into the origin and evolution of CH₄. The results identify conditions under which either isotopic bond order disequilibrium or equilibrium are expected. Where equilibrium obtains, concordant Δ¹²CH₂D₂ and Δ¹³CH₃D temperatures can be used reliably for thermometry. We find that concordant temperatures do not always match previous hypotheses based on indirect estimates of temperature of formation nor temperatures derived from CH₄/H₂ D/H exchange, underscoring the importance of reliable thermometry based on the CH₄ molecules themselves. Where Δ¹²CH₂D₂ and Δ¹³CH₃D values are inconsistent with thermodynamic equilibrium, temperatures of formation derived from these species are spurious. In such situations, while formation temperatures are unavailable, disequilibrium isotopologue ratios nonetheless provide novel information about the formation mechanism of the gas and the presence or absence of multiple sources or sinks. In particular, disequilibrium isotopologue ratios may provide the means for differentiating between methane produced by abiotic synthesis vs. biological processes. Deficits in ¹²CH₂D₂ compared with equilibrium values in CH₄ gas made by surface-catalyzed abiotic reactions are so large as to point towards a quantum tunneling origin. Tunneling also accounts for the more moderate depletions in ¹³CH₃D that accompany the low ¹²CH₂D₂ abundances produced by abiotic reactions. The tunneling signature may prove to be an important tracer of abiotic methane formation, especially where it is preserved by dissolution of gas in cool hydrothermal systems (e.g., Mars). Isotopologue signatures of abiotic methane production can be erased by infiltration of microbial communities, and Δ¹²CH₂D₂ values are a key tracer of microbial recycling.

Source: http://dx.doi.org/10.1016/j.gca.2016.12.041

Improved Measurement of Extracellular Enzymatic Activities in Subsurface Sediments Using Competitive Desorption Treatment

Frontiers in Earth Science

Authors: Adrienne Hoarfrost, Rachel Snider, Carol Arnosti

Published: February 16, 2017

C-DEBI Contribution Number: 355

Abstract

Extracellular enzymatic activities initiate microbially-driven heterotrophic carbon cycling in subsurface sediments. While measurement of hydrolytic activities in sediments is fundamental to our understanding of carbon cycling, these measurements are often technically difficult due to sorption of organic substrates to the sediment matrix. Most methods that measure hydrolysis of organic substrates in sediments rely on recovery of a fluorophore or fluorescently-labeled target substrate from a sediment incubation. The tendency for substrates to sorb to sediments results in lower recovery of an added substrate, and can result in data that are unusable or difficult to interpret. We developed a treatment using competitive desorption of a fluorescently-labeled, high molecular weight organic substrate that improves recovery of the labeled substrate from sediment subsamples. Competitive desorption treatment improved recovery of the fluorescent substrate by a median of 66%, expanded the range of sediments for which activity measurements could be made, and was effective in sediments from a broad range of geochemical contexts. More reliable measurements of hydrolytic activities in sediments will yield usable and more easily interpretable data from a wider range of sedimentary environments, enabling better understanding of microbially-catalyzed carbon cycling in subsurface environments.

Source: http://dx.doi.org/10.3389/feart.2017.00013

Related Items

Awards

Investigating microbial activities driving organic matter transformations in the deep subsurface

Award Dates: May 16, 2014 — May 15, 2016

Awardee: Adrienne Hoarfrost (University of North Carolina, Chapel Hill)

Advisor: Carol Arnosti (University of North Carolina, Chapel Hill)

Inter-laboratory quantification of Bacteria and Archaea in deeply buried sediments of the Baltic Sea (IODP Expedition 347)

FEMS Microbiology Ecology

Authors: Joy Buongiorno, Stephanie Turner, Gordon Webster, Masanori Asai, Alexander K. Shumaker, Taylor Roy, Andrew Weightman, Axel Schippers, Karen G. Lloyd

Published: January 18, 2017

C-DEBI Contribution Number: 341

Abstract

Two common quantification methods for subseafloor microorganisms are catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and quantitative PCR (qPCR). Using these methods, we quantified Bacteria and Archaea in Baltic Sea basin sediments (IODP Exp. 347) down to 90 mbsf, testing the following hypotheses in an inter-laboratory comparison: 1) proteinase K permeabilization of Archaeal cell walls increases CARD-FISH accuracy, and 2) qPCR varies by more than an order of magnitude between laboratories using similar protocols. CARD-FISH counts did not differ between permeabilization treatments, demonstrating that proteinase K did not increase accuracy of CARD-FISH counts. However, 91% of these counts were below the quantification limit of 1.3 × 10⁷ cells cm⁻³. For qPCR, data varied between laboratories, but were largely within the same order of magnitude if the same primers were used, with 88% of samples being above the quantification limit. Copy number values were elevated by preparing a sediment slurry before DNA extraction: 3.88 ×10⁶ to 2.34 ×10⁹ 16S rRNA gene copies cm⁻³ vs. 1.39 × 10⁷ to 1.87 × 10⁹ total cells cm⁻³. By qPCR, Bacteria were more abundant than Archaea, although they usually were within the same order of magnitude. Overall, qPCR is more sensitive than CARD-FISH, but both require optimization to consistently achieve both precision and accuracy.

Source: http://dx.doi.org/10.1093/femsec/fix007

Related Items

Awards

Using single cell genomics to determine the roles of uncultured microbes in the deep subsurface carbon cycle

Award Dates: February 1, 2012 — January 31, 2015

PI: Karen G. Lloyd (University of Tennessee, Knoxville)

Data report: quantification of potential drilling contamination using perfluorocarbon tracer at IODP Expedition 329 sites

Proceedings of the IODP

Authors: Justine Sauvage, Leah Lewis, Dennis Graham, Arthur J. Spivack, Steven L. D’Hondt

Published: January 30, 2017

C-DEBI Contribution Number: 335

Abstract

To quantify the potential for biological contamination associated with the coring process, we conducted perfluorocarbon tracer (PFT) analysis on 556 sediment samples from Integrated Ocean Drilling Program (IODP) Expedition 329. The expedition cored deep-sea sediment at seven sites in the South Pacific Gyre (Sites U1365–U1371). We analyzed two types of sediment samples: (1) samples taken in the central part of the core (i.e., interior samples) and (2) samples taken near the core edge (i.e., exterior samples). We calculated the amount of potential drilling fluid intrusion from the mass of PFT that we measured in each sample. For the seven Expedition 329 sites (15 holes analyzed), PFT content ranges from below detection to levels where contamination is extremely apparent. The centers of the sediment cores (interior samples) contained generally less PFT than the core margins (exterior samples) and thus have lower potential drilling fluid (DF) contamination. The majority of sediment samples (interior) at Sites U1370 and U1371 have a contamination potential close to or below detection levels (i.e., 1.19 × 10^–4 ng_PFT/g_sediment or 1.78 × 10^–3 µL_DF/g_sediment on average). We observed higher contamination values (i.e., 7.28 × 10^–3 ng_PFT/g_sediment or 6.98 × 10^–2 µL_DF/g_sediment on average) at Sites U1365, U1366, and U1367. Finally, we measured much higher PFT concentrations throughout the sediment of Sites U1368 and U1369 (i.e., 5.48 × 10^–2 ng_PFT/g_sediment or 6.60 × 10^–1µL_DF/g_sediment on average). We observe no apparent correlation of sample PFT content to sediment lithology, degree of sediment disturbance, core section number, or porosity.

Source: http://dx.doi.org/10.2204/iodp.proc.329.204.2017

Ocean Sediments—an Enormous but Underappreciated Microbial Habitat

Microbe Magazine

Authors: Jan P. Amend, Douglas E. LaRowe

Published: December 1, 2016

C-DEBI Contribution Number: 346

Abstract

Summary

The oceans that cover 70% of the Earth's surface lie above 3×10⁸ km³ of sediment containing an estimated 3×10²⁹ microbial cells.
The role played by spores in low-energy sedimentary ecosystems remains an enigma.
Despite conflicting results from earlier analyses, archaea and bacteria apparently exist in similar abundances within deep-sea sediments.
Within these sediments, anaerobic metabolisms dominate, especially those in which sulfate reduction and oxidation of organic matter are coupled.
Modeling proves crucial when trying to connect sedimentary microorganisms to their appropriate geochemical environments.

Source: http://dx.doi.org/10.1128/microbe.11.427.1