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 W. 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 F. 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 W. 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

High proportions of bacteria and archaea across most biomes remain uncultured

The ISME Journal

Authors: Andrew D. Steen, Alexander Crits-Christoph, Paul Carini, Kristen M. DeAngelis, Noah Fierer, Karen G. Lloyd, J. Cameron Thrash

Published: August 6, 2019

C-DEBI Contribution Number: 482

Abstract

A recent paper by Martiny argues that “high proportions” of bacteria in diverse Earth environments have been cultured. Here we reanalyze a portion of the data in that paper, and argue that the conclusion is based on several technical errors, most notably a calculation of sequence similarity that does not account for sequence gaps, and the reliance on 16S rRNA gene amplicons that are known to be biased towards cultured organisms. We further argue that the paper is also based on a conceptual error: namely, that sequence similarity cannot be used to infer “culturability” because one cannot infer physiology from 16S rRNA gene sequences. Combined with other recent, more reliable studies, the evidence supports the conclusion that most bacterial and archaeal taxa remain uncultured.

Source: http://dx.doi.org/10.1038/s41396-019-0484-y

Subseafloor life and its biogeochemical impacts

Nature Communications

Authors: Steven D’Hondt, Robert Pockalny, Victoria M. Fulfer, Arthur J. Spivack

Published: August 6, 2019

C-DEBI Contribution Number: 454

Abstract

Subseafloor microbial activities are central to Earth’s biogeochemical cycles. They control Earth’s surface oxidation and major aspects of ocean chemistry. They affect climate on long timescales and play major roles in forming and destroying economic resources. In this review, we evaluate present understanding of subseafloor microbes and their activities, identify research gaps, and recommend approaches to filling those gaps. Our synthesis suggests that chemical diffusion rates and reaction affinities play a primary role in controlling rates of subseafloor activities. Fundamental aspects of subseafloor communities, including features that enable their persistence at low catabolic rates for millions of years, remain unknown.

Source: http://dx.doi.org/10.1038/s41467-019-11450-z

Kinetics and identities of extracellular peptidases in subsurface sediments of the White Oak River Estuary, NC

Applied and Environmental Microbiology

Published: July 19, 2019

C-DEBI Contribution Number: 485

Abstract

Anoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily slow rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities (V_max) decreased with increasing sediment depth, although V_maxexpressed on a per cell basis was approximately the same at all depths. Half-saturation constants (K_m) decreased with depth, indicating peptidases that functioned more efficiently at low substrate concentrations. Potential activities of extracellular peptidases acting on molecules that are enriched in degraded organic matter (D-phenylalanine and L-ornithine) increased relative to enzymes that act on L-phenylalanine, further suggesting microbial community adaptation to access degraded organic matter. Nineteen classes of predicted, exported peptidases were identified in genomic data from the same site, of which genes for class C25 (gingipain-like) peptidases represented more than 40% at each depth. Methionine aminopeptidases, zinc carboxypeptidases, and class S24-like peptidases, which are involved in single-stranded DNA repair, were also abundant. These results suggest a subsurface heterotrophic microbial community that primarily accesses low-quality detrital organic matter via a diverse suite of well-adapted extracellular enzymes.

Source: http://dx.doi.org/10.1128/aem.00102-19

Related Items

Awards

Characterization of subsurface extracellular enzymes and the organisms that produce them using metatranscriptomics and bottom-up metaproteomics

Award Dates: June 1, 2018 — May 31, 2019

Awardee: Taylor Royalty (University of Tennessee Knoxville)

Advisor: Andrew D. Steen (University of Tennessee Knoxville)

Novel peptidases in subsurface sediments: Activities and substrate specificities

Award Dates: March 1, 2013 — December 31, 2014

PI: Andrew D. Steen (University of Tennessee, Knoxville)

Current Placement: Assistant Professor, University of Tennessee

Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment

Frontiers in Microbiology

Authors: Zak Kerrigan, John B. Kirkpatrick, Steven D’Hondt

Published: July 16, 2019

C-DEBI Contribution Number: 484

Abstract

To assess the influence of 16S ribosomal RNA (rRNA) tag choice on estimates of microbial diversity and/or community composition in seawater and marine sediment, we examined bacterial diversity and community composition from a site in the Central North Atlantic and a site in the Equatorial Pacific. For each site, we analyzed samples from four zones in the water column, a seafloor sediment sample, and two subseafloor sediment horizons (with stratigraphic ages of 1.5 and 5.5 million years old). We amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity to analyze for diversity and community composition. OTU richness is much higher with the V6 tag than with the V4 tag, and subsequently OTU-level community composition is quite different between the two tags. Vertical patterns of relative diversity are broadly the same for both tags, with maximum taxonomic richness in seafloor sediment and lowest richness in subseafloor sediment at both geographic locations. Genetic dissimilarity between sample locations is also broadly the same for both tags. Community composition is very similar for both tags at the class level, but very different at the level of 97% similar OTUs. Class-level diversity and community composition of water-column samples are very similar at each water depth between the Atlantic and Pacific. However, sediment communities differ greatly from the Atlantic site to the Pacific site. Finally, for relative patterns of diversity and class-level community composition, deep sequencing and shallow sequencing provide similar results.

Source: http://dx.doi.org/10.3389/fmicb.2019.01640

Diversity decoupled from sulfur isotope fractionation in a sulfate‐reducing microbial community

Geobiology

Authors: Jesse Colangelo-Lillis, Claus Pelikan, Craig W. Herbold, Ianina Altshuler, Alexander Loy, Lyle G. Whyte, Boswell A. Wing

Published: July 21, 2019

C-DEBI Contribution Number: 483

Abstract

The extent of fractionation of sulfur isotopes by sulfate‐reducing microbes is dictated by genomic and environmental factors. A greater understanding of species‐specific fractionations may better inform interpretation of sulfur isotopes preserved in the rock record. To examine whether gene diversity influences net isotopic fractionation in situ, we assessed environmental chemistry, sulfate reduction rates, diversity of putative sulfur‐metabolizing organisms by 16S rRNA and dissimilatory sulfite reductase (dsrB) gene amplicon sequencing, and net fractionation of sulfur isotopes along a sediment transect of a hypersaline Arctic spring. In situ sulfate reduction rates yielded minimum cell‐specific sulfate reduction rates < 0.3 × 10⁻¹⁵ moles cell⁻¹ day⁻¹. Neither 16S rRNA nor dsrB diversity indices correlated with relatively constant (38‰–45‰) net isotope fractionation (ε³⁴S_{sulfide‐sulfate}). Measured ε³⁴S values could be reproduced in a mechanistic fractionation model if 1%–2% of the microbial community (10%–60% of Deltaproteobacteria) were engaged in sulfate respiration, indicating heterogeneous respiratory activity within sulfate‐reducing populations. This model indicated enzymatic kinetic diversity of Apr was more likely to correlate with sulfur fractionation than DsrB. We propose that, above a threshold Shannon diversity value of 0.8 for dsrB, the influence of the specific composition of the microbial community responsible for generating an isotope signal is overprinted by the control exerted by environmental variables on microbial physiology.

Source: http://dx.doi.org/10.1111/gbi.12356

Related Items

Awards

MEGA Analogue for Subsurface Sedimentary In-Vivo Evolution (MASSIVE) Plate

Award Dates: November 1, 2017 — October 31, 2018

Awardee: Jesse Colangelo-Lillis (University of Colorado, Boulder)

Degree: Ph.D. Earth & Planetary Science, McGill University (2016)

Advisor: Boswell A. Wing (University of Colorado, Boulder)

Archaea dominate oxic subseafloor communities over multimillion-year time scales

Science Advances

Published: June 1, 2019

C-DEBI Contribution Number: 463

Abstract

Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.

Source: http://dx.doi.org/10.1126/sciadv.aaw4108

Related Items

Awards

Microbial activity in oxygenated subseafloor sediment

Award Dates: September 1, 2014 — August 31, 2015

PI: William D. Orsi (Woods Hole Oceanographic Institution)

Current Placement: Assistant Professor, University of Munich (LMU)

Co-I: Tracy Mincer (Woods Hole Oceanographic Institution)

Nanocalorimetry reveals growth dynamics of Escherichia coli cells undergoing adaptive evolution during long-term stationary phase

Applied and Environmental Microbiology

Authors: Alberto Robador, Jan P. Amend, Steven E. Finkel

Published: May 31, 2019

C-DEBI Contribution Number: 480

Abstract

Bacterial populations in long-term stationary phase laboratory cultures can provide insights into physiological and genetic adaptations to low-energy conditions and population dynamics in natural environments. While overall population density remains stable, these communities are very dynamic and characterized by the rapid emergence and succession of distinct mutants expressing the Growth Advantage in Stationary Phase (GASP) phenotype, which can reflect an increased capacity to withstand energy limitations and environmental stress. Here we characterize the metabolic heat signatures and growth dynamics of GASP mutants within an evolving population using isothermal calorimetry. We aged Escherichia coli in anaerobic batch cultures over 20 days inside an isothermal nanocalorimeter and observed distinct heat events related to the emergence of three mutant populations expressing the GASP phenotype after 1.5, 3, and 7 days. Given the heat produced by each population, the maximum number of GASP mutant cells was calculated revealing abundances of ∼2.5 x 10⁷, ∼7.5 x 10⁶, and ∼9.9 x 10⁶ cells in the population, respectively. These data indicate that mutants capable of expressing the GASP phenotype can be acquired during the exponential growth phase and subsequently expressed in long-term stationary phase (LTSP) culture.

Source: http://dx.doi.org/10.1128/aem.00968-19

The effect of O₂ and pressure on thiosulfate oxidation by Thiomicrospira thermophila

Geobiology

Authors: Jennifer L. Houghton, Dionysis I. Foustoukos, David A. Fike

Published: June 10, 2019

C-DEBI Contribution Number: 477

Abstract

Microbial sulfur cycling in marine sediments often occurs in environments characterized by transient chemical gradients that affect both the availability of nutrients and the activity of microbes. High turnover rates of intermediate valence sulfur compounds and the intermittent availability of oxygen in these systems greatly impact the activity of sulfur‐oxidizing micro‐organisms in particular. In this study, the thiosulfate‐oxidizing hydrothermal vent bacterium Thiomicrospira thermophila strain EPR85 was grown in continuous culture at a range of dissolved oxygen concentrations (0.04–1.9 mM) and high pressure (5–10 MPa) in medium buffered at pH 8. Thiosulfate oxidation under these conditions produced tetrathionate, sulfate, and elemental sulfur, in contrast to previous closed‐system experiments at ambient pressure during which thiosulfate was quantitatively oxidized to sulfate. The maximum observed specific growth rate at 5 MPa pressure under unlimited O₂ was 0.25 hr⁻¹. This is comparable to the μ_max (0.28 hr⁻¹) observed at low pH (<6) at ambient pressure when T. thermophila produces the same mix of sulfur species. The half‐saturation constant for O₂ (K_O2) estimated from this study was 0.2 mM (at a cell density of 10⁵ cells/ml) and was robust at all pressures tested (0.4–10 MPa), consistent with piezotolerant behavior of this strain. The cell‐specific K_O2 was determined to be 1.5 pmol O₂/cell. The concentrations of products formed were correlated with oxygen availability, with tetrathionate production in excess of sulfate production at all pressure conditions tested. This study provides evidence for transient sulfur storage during times when substrate concentration exceeds cell‐specific K_O2 and subsequent consumption when oxygen dropped below that threshold. These results may be common among sulfur oxidizers in a variety of environments (e.g., deep marine sediments to photosynthetic microbial mats).

Source: http://dx.doi.org/10.1111/gbi.12352

Related Items

Awards

Symbiotic growth of piezophilic deep-sea vent bacteria

Award Dates: November 1, 2017 — October 31, 2018

PIs: Dionysis I. Foustoukos (Carnegie Institution for Science), Costantino Vetriani (Rutgers University)

Cytosine Methylation Within Marine Sediment Microbial Communities: Potential Epigenetic Adaptation to the Environment

Frontiers in Microbiology

Authors: Ian M. Rambo, Adam Marsh, Jennifer F. Biddle

Published: June 11, 2019

C-DEBI Contribution Number: 472

Abstract

Marine sediments harbor a vast amount of Earth’s microbial biomass, yet little is understood regarding how cells subsist in this low-energy, presumably slow-growth environment. Cells in marine sediments may require additional methods for genetic regulation, such as epigenetic modification via DNA methylation. We investigated this potential phenomenon within a shallow estuary sediment core spanning 100 years of age. Here, we provide evidence of dynamic community m5-cytosine methylation within estuarine sediment metagenomes. The methylation states of individual CpG sites were reconstructed and quantified across three depths within the sediment core. A total of 6,254 CpG sites were aligned for direct comparison of methylation states between samples, and 4,235 of these sites mapped to taxa and genes. Our results demonstrate the presence of differential methylation within environmental CpG sites across an age gradient of sediment. We show that epigenetic modification can be detected via Illumina sequencing within complex environmental communities. The change in methylation state of environmentally relevant genes across depths may indicate a dynamic role of DNA methylation in regulation of biogeochemical processes.

Source: http://dx.doi.org/10.3389/fmicb.2019.01291

Related Items

Awards

Investigating subsurface genomic signatures for features of evolution, adaptation and quiescence

Award Dates: September 1, 2013 — February 28, 2015

PI: Adam Marsh (University of Delaware)

Co-I: Jennifer F. Biddle (University of Delaware)

Evidence for Low‐Temperature Diffuse Venting at North Pond, Western Flank of the Mid‐Atlantic Ridge

Geochemistry, Geophysics, Geosystems

Authors: Heinrich W. Villinger, P. Müller, Wolfgang Bach, Keir Becker, Beth N. Orcutt, N. Kaul, Charles Geoffrey Wheat

Published: June 5, 2019

C-DEBI Contribution Number: 479

Abstract

During expedition MSM37 on the German RV Maria S. Merian, bottom water temperature and sediment temperature profiles were measured in the vicinity of North Pond (western flank of Mid‐Atlantic Ridge) during exploratory dives with Remotely Operated Vehicle Jason II. In addition, push cores were taken at locations with high sediment temperature gradients. We could identify two locations where sediment temperature gradients exceed 1 K/m and bottom water temperatures showed an anomaly of up to 0.04 °C above background. We interpret these observations as clear indication of low‐temperature diffuse venting of fluids that have traveled through the uppermost crust. We can safely assume that the observed phenomena are widespread at ridge flank settings where sediment cover is thin or absent, and hence, we can explain the efficient heat mining on ridge flanks. Due to the difficulties of locating diffuse low‐temperature discharge sites and due to the fact that discharge can occur through thin sediment cover as well as through sediment‐free basement outcrops, it will be very difficult to quantify fluxes of energy and mass from low‐temperature diffuse venting in ridge flank settings; however, thermal anomalies may be used to locate sites of discharge for geochemical, microbial, and hydrologic characterization.

Source: http://dx.doi.org/10.1029/2018gc008113

Being open about my multiple sclerosis helps me be a better advocate

Science

Authors: Stephanie Schroeder

Published: May 23, 2019

C-DEBI Contribution Number: 478

Abstract

This site visit would determine whether the funding for the center where I worked would be renewed. It was critical that we do well—for the center and for my job as education director. But as the panelists asked their questions, all I could think was, “I have multiple sclerosis.” I had been diagnosed a couple weeks prior and was in a state of shock. For months I had noticed my body behaving strangely, for example when my ankle stopped working after I walked a few kilometers. I had known what the symptoms might mean—my mother was diagnosed with multiple sclerosis (MS) in the ’90s. But I had ignored them. I was not prepared to deal with my own battle.

Source: http://dx.doi.org/10.1126/science.caredit.aay1345

Complex microbial communities drive iron and sulfur cycling in Arctic fjord sediments

Applied and Environmental Microbiology

Authors: Joy Buongiorno, L. C. Herbert, Laura M. Wehrmann, Alexander B. Michaud, K. Laufer, Hans Røy, Bo Barker Jørgensen, A. Szynkiewicz, A. Faiia, K. M. Yeager, K. Schindler, Karen G. Lloyd

Published: May 10, 2019

C-DEBI Contribution Number: 476

Abstract

Glacial retreat is changing biogeochemical cycling in the Arctic, where glacial runoff contributes iron for oceanic shelf primary production. In Svalbard fjords, we hypothesize that microbes catalyze intense iron and sulfur cycling in low organic matter sediments. This is because low organic matter limits sulfide generation, allowing iron mobility to the water column instead of precipitation as iron monosulfides. Here, we tested this with high-depth-resolution 16S rRNA gene libraries in the upper 20 cm at two sites in Van Keulenfjorden, Svalbard. At the site closer to the glaciers, iron-reducing Desulfuromonadales, iron-oxidizing Gallionella and Mariprofundus, and sulfur-oxidizing Thiotrichales and Epsilonproteobacteria were abundant above 12 cm depth. Below this depth, the relative abundances of sequences for sulfate-reducing Desulfobacteraceae and Desulfobulbaceae increased. At the outer station, the switch from iron-cycling clades to sulfate reducers occurred at shallower depths (∼5 cm), corresponding to higher sulfate reduction rates. Relatively labile organic matter (shown by δ¹³C and C/N ratios) was more abundant at this outer site and ordination analysis suggested that this affected microbial community structure in surface sediments. Network analysis revealed more correlations between predicted iron- and sulfur-cycling taxa, and with uncultured clades proximal to the glacier. Together, these results suggest that complex microbial communities catalyze redox cycling of iron and sulfur, especially closer to the glacier, where sulfate reduction is limited due to low organic matter availability. Diminished sulfate reduction in upper sediments enables iron to flux into the overlying water, where it may be transported to the shelf.

Source: http://dx.doi.org/10.1128/aem.00949-19

Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa

The ISME Journal

Authors: Elizabeth Trembath-Reichert, David A. Butterfield, Julie A. Huber

Published: May 9, 2019

C-DEBI Contribution Number: 470

Abstract

There are many unknowns regarding the distribution, activity, community composition, and metabolic repertoire of microbial communities in the subseafloor of deep-sea hydrothermal vents. Here we provide the first characterization of subseafloor microbial communities from venting fluids along the central Mariana back-arc basin (15.5–18°N), where the slow-spreading rate, depth, and variable geochemistry along the back-arc distinguish it from other spreading centers. Results indicated that diverse Epsilonbacteraeota were abundant across all sites, with a population of high temperature Aquificae restricted to the northern segment. This suggests that differences in subseafloor populations along the back-arc are associated with local geologic setting and resultant geochemistry. Metatranscriptomics coupled to stable isotope probing revealed bacterial carbon fixation linked to hydrogen oxidation, denitrification, and sulfide or thiosulfate oxidation at all sites, regardless of community composition. NanoSIMS (nanoscale secondary ion mass spectrometry) incubations at 80 °C show only a small portion of the microbial community took up bicarbonate, but those autotrophs had the highest overall rates of activity detected across all experiments. By comparison, acetate was more universally utilized to sustain growth, but within a smaller range of activity. Together, results indicate that microbial communities in venting fluids from the Mariana back-arc contain active subseafloor communities reflective of their local conditions with metabolisms commonly shared across geologically disparate spreading centers throughout the ocean.

Source: http://dx.doi.org/10.1038/s41396-019-0431-y

Microbial Diversity in Sub-Seafloor Sediments from the Costa Rica Margin

Geosciences

Authors: Amanda J. Martino, Matthew E. Rhodes, Rosa León-Zayas, Isabella E. Valente, Jennifer F. Biddle, Christopher H. House

Published: May 13, 2019

C-DEBI Contribution Number: 473

Abstract

The exploration of the deep biosphere continues to reveal a great diversity of microorganisms, many of which remain poorly understood. This study provides a first look at the microbial community composition of the Costa Rica Margin sub-seafloor from two sites on the upper plate of the subduction zone, between the Cocos and Caribbean plates. Despite being in close geographical proximity, with similar lithologies, both sites show distinctions in the relative abundance of the archaeal domain and major microbial phyla, assessed using a pair of universal primers and supported by the sequencing of six metagenomes. Elusimicrobia, Chloroflexi, Aerophobetes, Actinobacteria, Lokiarchaeota, and Atribacteria were dominant phyla at Site 1378, and Bathyarchaeota, Chloroflexi, Hadesarchaeota, Aerophobetes, Elusimicrobia, and Lokiarchaeota were dominant at Site 1379. Correlations of microbial taxa with geochemistry were examined and notable relationships were seen with ammonia, sulfate, and depth. With deep sediments, there is always a concern that drilling technologies impact analyses due to contamination of the sediments via drilling fluid. Here, we use analysis of the drilling fluid in conjunction with the sediment analysis, to assess the level of contamination and remove any problematic sequences. In the majority of samples, we find the level of drilling fluid contamination, negligible.

Source: http://dx.doi.org/10.3390/geosciences9050218

Related Items

Awards

Working around drilling contamination in deep cores: Costa Rica Margin

Award Dates: June 1, 2012 — May 31, 2014

Awardee: Amanda J. Martino (Pennsylvania State University)

Current Placement: Assistant Professor, Saint Francis University

Advisor: Christopher H. House (Pennsylvania State University)

Microbial Selection and Survival in Subseafloor Sediment

Frontiers in Microbiology

Authors: John B. Kirkpatrick, Emily A. Walsh, Steven D’Hondt

Published: May 14, 2019

C-DEBI Contribution Number: 474

Abstract

Many studies have examined relationships of microorganisms to geochemical zones in subseafloor sediment. However, responses to selective pressure and patterns of community succession with sediment depth have rarely been examined. Here we use 16S rDNA sequencing to examine the succession of microbial communities at sites in the Indian Ocean and the Bering Sea. The sediment ranges in depth from 0.16 to 332 m below seafloor and in age from 660 to 1,300,000 years. The majority of subseafloor taxonomic diversity is present in the shallowest depth sampled. The best predictor of sequence presence or absence in the oldest sediment is relative abundance in the near-seafloor sediment. This relationship suggests that perseverance of specific taxa into deep, old sediment is primarily controlled by the taxonomic abundance that existed when the sediment was near the seafloor. The operational taxonomic units that dominate at depth comprise a subset of the local seafloor community at each site, rather than a grown-in group of geographically widespread subseafloor specialists. At both sites, most taxa classified as abundant decrease in relative frequency with increasing sediment depth and age. Comparison of community composition to cell counts at the Bering Sea site indicates that the rise of the few dominant taxa in the deep subseafloor community does not require net replication, but might simply result from lower mortality relative to competing taxa on the long timescale of community burial.

Source: http://dx.doi.org/10.3389/fmicb.2019.00956

Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments

mBio

Editors: Nicole Dubilier

Published: April 16, 2019

C-DEBI Contribution Number: 471

Abstract

Energy-starved microbes in deep marine sediments subsist at near-zero growth for thousands of years, yet the mechanisms for their subsistence are unknown because no model strains have been cultivated from most of these groups. We investigated Baltic Sea sediments with single-cell genomics, metabolomics, metatranscriptomics, and enzyme assays to identify possible subsistence mechanisms employed by uncultured Atribacteria, Aminicenantes, Actinobacteria group OPB41, Aerophobetes, Chloroflexi, Deltaproteobacteria, Desulfatiglans, Bathyarchaeota, and Euryarchaeota marine group II lineages. Some functions appeared to be shared by multiple lineages, such as trehalose production and NAD⁺-consuming deacetylation, both of which have been shown to increase cellular life spans in other organisms by stabilizing proteins and nucleic acids, respectively. Other possible subsistence mechanisms differed between lineages, possibly providing them different physiological niches. Enzyme assays and transcripts suggested that Atribacteria and Actinobacteria group OPB41 catabolized sugars, whereas Aminicenantes and Atribacteria catabolized peptides. Metabolite and transcript data suggested that Atribacteria utilized allantoin, possibly as an energetic substrate or chemical protectant, and also possessed energy-efficient sodium pumps. Atribacteria single-cell amplified genomes (SAGs) recruited transcripts for full pathways for the production of all 20 canonical amino acids, and the gene for amino acid exporter YddG was one of their most highly transcribed genes, suggesting that they may benefit from metabolic interdependence with other cells. Subsistence of uncultured phyla in deep subsurface sediments may occur through shared strategies of using chemical protectants for biomolecular stabilization, but also by differentiating into physiological niches and metabolic interdependencies.

Source: http://dx.doi.org/10.1128/mbio.02376-18

Publications > Thesis

MS Thesis

Three-dimensional simulations of fluid and heat flow associated with faults in volcanic ocean crust

Authors: Esther Adelstein

Published: January 1, 2017

C-DEBI Contribution Number: 394

Abstract

Hydrothermal circulation extracts a significant fraction of lithospheric heat from the ocean crust, with most of this advective heat loss occurring on ridge flanks, far from mid-ocean ridges. Faults in ocean crust are common in many settings, and may serve as high-transmissivity structures that facilitate advective transport and focus discharge of fluid, heat, and solutes below and at the seafloor. Coupled flow along fault zones has been invoked in a variety of settings, but circulation patterns are not well constrained by observational data or earlier models. We present results from three-dimensional, fully coupled numerical simulations of fluid and heat flow in sediment-covered ridge-flank ocean crust cut by a fault. We explore a range of fault and surrounding crustal characteristics, including crust and fault permeability, fault dip angle, thickness, and depth. We are particularly interested in resolving relations between fault and crustal characteristics and seafloor heat flux patterns. Simulation results show variability in patterns of fluid circulation and seafloor heat flux as a function of fault geometry and crustal properties. The seafloor heat flux pattern above fault traces tends to show variability along strike (in response to underlying regions of rapid upward and downward flow along the fault trace), and asymmetry in seafloor heat flux anomalies, with higher values above the fault trace and lower values in the immediately surrounding seafloor, especially above the hanging wall. The negative anomaly is generally greater when the fault dip angle is lower. Higher permeability in the crustal rocks adjacent to the fault zone tend result in small-scale convection and small-amplitude variations in seafloor heat flux, and more diffuse convection cells in the fault zone itself. Convection in the surrounding crust decreases the importance of the fault zone in extracting lithospheric heat. Simulations also show that faults that penetrate deeper into the crust produce a significantly larger seafloor heat flux anomaly than do shallower faults, indicating that deeper faults extract lithospheric heat more efficiently. Patterns of seafloor heat flux from these simulations indicate that fault-zone hydrothermal circulation should produce thermal anomalies that are detectable in field measurements. Linking field observations directly to numerical simulations can provide better understanding of the geometry and properties of faults and fluid flow patterns in the volcanic ocean crust.

Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context

Frontiers in Microbiology

Authors: Nancy Merino, Heidi Aronson, Diana P. Bojanova, Jayme Feyhl-Buska, Michael L. Wong, Shu Zhang, Donato Giovannelli

Published: April 15, 2019

C-DEBI Contribution Number: 468

Abstract

Prokaryotic life has dominated most of the evolutionary history of our planet, evolving to occupy virtually all available environmental niches. Extremophiles, especially those thriving under multiple extremes, represent a key area of research for multiple disciplines, spanning from the study of adaptations to harsh conditions, to the biogeochemical cycling of elements. Extremophile research also has implications for origin of life studies and the search for life on other planetary and celestial bodies. In this article, we will review the current state of knowledge for the biospace in which life operates on Earth and will discuss it in a planetary context, highlighting knowledge gaps and areas of opportunity.

Source: http://dx.doi.org/10.3389/fmicb.2019.00780

Elemental Uptake by Calcite Slowly Grown From Seawater Solution: An in-situ Study via Depth Profiling

Frontiers in Earth Science

Authors: Rinat Gabitov, Aleksey Sadekov, Vasiliy Yapaskurt, Chiara Borrelli, Andrey Bychkov, Kaitlyn Sabourin, Alberto Perez-Huerta

Published: March 28, 2019

C-DEBI Contribution Number: 469

Abstract

Crystal growth rate has not been sufficiently explored to understand element partitioning between calcite and seawater solutions. We investigated the uptake of Li, B, Mg, Sr, and Ba by Mg-bearing calcite slowly grown on a calcite cleavage fragment. Experiments were conducted by elevating the alkalinity of an artificial seawater solution. Growth rates were evaluated by addition of lanthanum spike. At the end of each experiment, cleavage fragments were extracted and examined with micro-Raman spectroscopy, scanning electron microscopy (SEM), electron backscattered diffraction (EBSD), and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) using depth profiling technique. Distribution of Li, B, Mg, Sr, and Ba in calcite overgrowth as well as partition coefficients of those elements were evaluated.

Source: http://dx.doi.org/10.3389/feart.2019.00051

Related Items

Awards

Awards > Research Exchange Grants

Award Dates: May 15, 2014 — September 15, 2014

Biologically induced methane oxidation and precipitation of carbonate minerals: An experimental study

PI: Rinat Gabitov (Mississippi State University)

Host: Karyn L. Rogers (Rensselaer Polytechnic Institute)

IODP Advances in the Understanding of Subseafloor Life

Oceanography

Authors: Steven L. D’Hondt, Fumio Inagaki, Beth Orcutt, Kai-Uwe Hinrichs

Published: March 1, 2019

C-DEBI Contribution Number: 461

Abstract

The most recent decadal phase of scientific ocean drilling through the International Ocean Discovery Program (IODP) has resulted in paradigm-shifting understanding of life below the seafloor. Enabled by new drilling and coring approaches, cutting-edge methodologies, and novel observatory science, IODP expeditions have significantly advanced understanding of the amount and diversity of subseafloor life, the metabolic strategies that this life uses to survive under extreme energy limitation, and consequences of this life for the Earth system. Here, we summarize highlights from recent IODP expeditions focused on life beneath the seafloor and emphasize remaining major science challenges in investigating the form and function of life in this environment.

Source: http://dx.doi.org/10.5670/oceanog.2019.146

Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents

The ISME Journal

Authors: Lucy C. Stewart, Christopher K. Algar, Caroline S. Fortunato, Benjamin I. Larson, Joseph J. Vallino, Julie A. Huber, David A. Butterfield, James F. Holden

Published: March 6, 2019

C-DEBI Contribution Number: 464

Abstract

The size and biogeochemical impact of the subseafloor biosphere in oceanic crust remain largely unknown due to sampling limitations. We used reactive transport modeling to estimate the size of the subseafloor methanogen population, volume of crust occupied, fluid residence time, and nature of the subsurface mixing zone for two low-temperature hydrothermal vents at Axial Seamount. Monod CH₄ production kinetics based on chemostat H₂ availability and batch-culture Arrhenius growth kinetics for the hyperthermophile Methanocaldococcus jannaschii and thermophile Methanothermococcus thermolithotrophicus were used to develop and parameterize a reactive transport model, which was constrained by field measurements of H₂, CH₄, and metagenome methanogen concentration estimates in 20–40 °C hydrothermal fluids. Model results showed that hyperthermophilic methanogens dominate in systems where a narrow flow path geometry is maintained, while thermophilic methanogens dominate in systems where the flow geometry expands. At Axial Seamount, the residence time of fluid below the surface was 29–33 h. Only 10¹¹ methanogenic cells occupying 1.8–18 m³ of ocean crust per m² of vent seafloor area were needed to produce the observed CH₄ anomalies. We show that variations in local geology at diffuse vents can create fluid flow paths that are stable over space and time, harboring persistent and distinct microbial communities.

Source: http://dx.doi.org/10.1038/s41396-019-0382-3

Dissolved organic carbon in basalt-hosted deep subseafloor fluids of the Juan de Fuca Ridge flank

Earth and Planetary Science Letters

Authors: Huei-Ting Lin, Daniel J. Repeta, Li Xu, Michael S. Rappé

Published: May 1, 2019

C-DEBI Contribution Number: 462

Abstract

Marine dissolved organic carbon (DOC) is highly depleted in radiocarbon and thus inferred to be largely refractory to removal processes that operate on less than millennial timescales. However, a growing number of reports have shown that a large fraction of marine DOC can be effectively removed during circulation through submarine hydrothermal systems. What is not clear, however, is whether the DOC that remains in hydrothermal fluids is remnant non-reactive DOC from recharged seawater, or DOC that has been largely produced in the subsurface. We collected and characterized warm (∼65 °C) hydrothermal fluids from deep (18, 40, 73, 200 m) within the basalt-hosted basement of the Juan de Fuca Ridge flank in the Northeast Pacific Ocean. DOC concentrations in hydrothermal fluids were 9 to 18 μM, much lower than measured in local deep seawater (37.5 μM). DOCΔ¹⁴C values of −683‰ to −856‰ were much lower than the Δ¹⁴C-dissolved inorganic carbon (DIC) values of −880‰ to −918‰, while DOC δ¹³C values of −23.6‰ to −27.0‰ were much heavier than that of the particulate organic carbon (POC) pool (∼−34‰), suggesting that biological production in the subsurface is not a primary source of DOC. Rather, our data suggest that isotopically enriched DOC are selectively removed from recharged seawater, leaving DOC that is very isotopically depleted in the basaltic basement fluids. Despite the removal of 50–75% of DOC in the subsurface, nuclear magnetic resonance (NMR) functional group analyses indicate that aromatic compounds were added to basaltic basement fluids during passage through the deep subseafloor and may partly contribute to the depleted ¹⁴C DOC in the ridge-flank basement fluids.

Source: http://dx.doi.org/10.1016/j.epsl.2019.02.008

The Energetics of Fermentation in Natural Settings

Geomicrobiology Journal

Authors: Douglas E. LaRowe, Jan P. Amend

Published: March 14, 2019

C-DEBI Contribution Number: 459

Abstract

Fermentation plays a fundamental role in organic carbon degradation on a global scale. However, little is known about how environmental variables influence this process. In a step towards quantifying how temperature and composition influence fermentation, we have calculated the Gibbs energies of 47 fermentation reaction, ΔG_r, from 0–150 °C for a broad range of compositions representing microbial habitats as variable as sediments, estuaries, soils, and crustal rocks. The organic compounds in these reactions include amino acids, nucleic acid bases, monosaccharides, carboxylates, methanogenic compounds and more. The amount of energy available varies considerably, from +54 kJ (mol C)⁻¹ for palmitate fermentation, to −184 kJ (mol C)⁻¹ for methylamine disproportionation. For some reactions, there is little difference in ΔG_r between low and high energy systems (e.g., the monosaccharide reactions) while others span a much broader range (e.g., the nucleic acid bases). There is no clear-cut trend between exergonicity and temperature, and the values of standard state Gibbs energies of reactions, ΔG⁰_r, for nearly half of the reactions lie outside the range of ΔG_r values. To carry out some of these calculations, the thermodynamic properties for six organic compounds were estimated: dimethylamine, trimethylamine, resorcinol, phloroglucinol and cyclohexane carboxylate and its conjugate acid.

Source: http://dx.doi.org/10.1080/01490451.2019.1573278

Carbon fixation and energy metabolisms of a subseafloor olivine biofilm

The ISME Journal

Authors: Amy R. Smith, Brandon Kieft, Ryan Mueller, Martin R. Fisk, Olivia U. Mason, Radu Popa, Frederick S. Colwell

Published: March 12, 2019

C-DEBI Contribution Number: 467

Abstract

Earth’s largest aquifer ecosystem resides in igneous oceanic crust, where chemosynthesis and water-rock reactions provide the carbon and energy that support an active deep biosphere. The Calvin Cycle is the predominant carbon fixation pathway in cool, oxic, crust; however, the energy and carbon metabolisms in the deep thermal basaltic aquifer are poorly understood. Anaerobic carbon fixation pathways such as the Wood-Ljungdahl pathway, which uses hydrogen (H₂) and CO₂, may be common in thermal aquifers since water-rock reactions can produce H₂in hydrothermal environments and bicarbonate is abundant in seawater. To test this, we reconstructed the metabolisms of eleven bacterial and archaeal metagenome-assembled genomes from an olivine biofilm obtained from a Juan de Fuca Ridge basaltic aquifer. We found that the dominant carbon fixation pathway was the Wood-Ljungdahl pathway, which was present in seven of the eight bacterial genomes. Anaerobic respiration appears to be driven by sulfate reduction, and one bacterial genome contained a complete nitrogen fixation pathway. This study reveals the potential pathways for carbon and energy flux in the deep anoxic thermal aquifer ecosystem, and suggests that ancient H₂-based chemolithoautotrophy, which once dominated Earth’s early biosphere, may thus remain one of the dominant metabolisms in the suboceanic aquifer today.

Source: http://dx.doi.org/10.1038/s41396-019-0385-0

Related Items

Awards

Genetic diversity and distribution of microbes colonizing igneous minerals and glasses incubated in IODP Hole 1301A on the eastern flank of the Juan de Fuca Ridge

Award Dates: June 1, 2011 — May 31, 2013

PI: Radu Popa (Portland State University)

Co-Is: Amy R. Smith (Portland State University),

Current Placement: Postdoctoral Researcher, Woods Hole Oceanographic Institution

Gilberto E. Flores (Portland State University), Martin R. Fisk (Portland State University)

Characterization of Carbonate Crust from a Recently Discovered Methane Seep on the North Atlantic Continental Margin of the USA

Minerals

Published: February 26, 2019

C-DEBI Contribution Number: 466

Abstract

This study is focused on mineralogical and chemical characterization of an authigenic carbonate rock (crust) collected at a recently discovered cold seep on the US North Atlantic continental margin. X-ray diffraction (XRD) and scanning electron microscopy (SEM) indicate that the carbonate rock is composed of microcrystalline aragonite cement, white acicular aragonite crystals (AcAr), equant quartz crystals, small microcrystalline aluminosilicates, and trace amounts of iron sulfide microcrystals. Element/calcium ratios were measured with laser ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS) using a calcite standard, which was prepared by annealing USGS certified carbonate powder (MACS-3). The occurrence of microscopic, non-carbonate inclusions precluded evaluation of trace elements in the aragonite cement, but allowed for in situ analysis of AcAr crystals. Carbon and oxygen isotopes were analyzed via isotope ratio mass spectrometry (IRMS) and expressed as δ¹³C and δ¹⁸O. Low δ¹³C values suggest that aragonite grew as a result of anaerobic oxidation of methane and observed δ¹⁸O values indicate that the temperature of aragonite crystallization was 1.7–1.9 °C.

Source: http://dx.doi.org/10.3390/min9030138

Related Items

Awards

Awards > Research Exchange Grants

Award Dates: May 15, 2014 — September 15, 2014

Biologically induced methane oxidation and precipitation of carbonate minerals: An experimental study

PI: Rinat Gabitov (Mississippi State University)

Host: Karyn L. Rogers (Rensselaer Polytechnic Institute)

Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile Methanocaldococcus jannaschii during Hydrogen-Limited Growth and Interspecies Hydrogen Transfer

Applied and Environmental Microbiology

Authors: Begüm D. Topçuoğlu, Cem Meydan, Tran B. Nguyen, Susan Q. Lang, James F. Holden

Published: March 1, 2019

C-DEBI Contribution Number: 465

Abstract

Hyperthermophilic methanogens are often H₂ limited in hot subseafloor environments and their survival may be due in part to physiological adaptations to low H₂ conditions and interspecies H₂ transfer. The hyperthermophilic methanogen Methanocaldococcus jannaschii was grown in monoculture at high (80-83 μM) and low (15-27 μM) aqueous H₂ concentrations and in co-culture with the hyperthermophilic H₂ producer Thermococcus paralvinellae. The purpose was to measure changes in growth and CH₄ production kinetics, CH₄ fractionation, and gene expression in M. jannaschii with changes in H₂ flux. Growth and cell-specific CH₄ production rates of M. jannaschii decreased with decreasing H₂ availability and decreased further in co-culture. However, cell yield (cells produced per mole of CH₄ produced) increased six-fold when M. jannaschii was grown in co-culture relative to monoculture. Relative to high H₂concentrations, isotopic fractionation of CO₂ to CH₄ (ϵ_CO2-CH4) was 16‰ larger for cultures grown at low H₂ concentrations and 45‰ and 56‰ larger for M. jannaschii growth in co-culture on maltose and formate, respectively. Gene expression analyses showed H₂-dependent methylene-tetrahydromethanopterin (H₄MPT) dehydrogenase expression decreased and coenzyme F₄₂₀-dependent methylene-H₄MPT dehydrogenase expression increased with decreasing H₂ availability and in co-culture growth. In co-culture, gene expression decreased for membrane-bound ATP synthase and hydrogenase. The results suggest that H₂ availability significantly affects the CH₄ and biomass production and CH₄ fractionation by hyperthermophilic methanogens in their native habitats.

Source: http://dx.doi.org/10.1128/aem.00180-19

The kinetics of siderophore-mediated olivine dissolution

Geobiology

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

Published: February 7, 2019

C-DEBI Contribution Number: 460

Abstract

Silicate minerals represent an important reservoir of nutrients at Earth's surface and a source of alkalinity that modulates long‐term geochemical cycles. Due to the slow kinetics of primary silicate mineral dissolution and the potential for nutrient immobilization by secondary mineral precipitation, the bioavailability of many silicate‐bound nutrients may be limited by the ability of micro‐organisms to actively scavenge these nutrients via redox alteration and/or organic ligand production. In this study, we use targeted laboratory experiments with olivine and the siderophore deferoxamine B to explore how microbial ligands affect nutrient (Fe) release and the overall rate of mineral dissolution. Our results show that olivine dissolution rates are accelerated in the presence of micromolar concentrations of deferoxamine B. Based on the non‐linear decrease in rates with time and formation of a Fe³⁺‐ligand complex, we attribute this acceleration in dissolution rates to the removal of an oxidized surface coating that forms during the dissolution of olivine at circum‐neutral pH in the presence of O₂ and the absence of organic ligands. While increases in dissolution rates are observed with micromolar concentrations of siderophores, it remains unclear whether such conditions could be realized in natural environments due to the strong physiological control on microbial siderophore production. So, to contextualize our experimental results, we also developed a feedback model, which considers how microbial physiology and ligand‐promoted mineral dissolution kinetics interact to control the extent of biotic enhancement of dissolution rates expected for different environments. The model predicts that physiological feedbacks severely limit the extent to which dissolution rates may be enhanced by microbial activity, though the rate of physical transport modulates this limitation.

Source: http://dx.doi.org/10.1111/gbi.12332

Related Items

Awards

Identifying the mechanisms and limits of the microbial enhancement of olivine dissolution

Award Dates: August 16, 2013 — August 15, 2015

Awardee: Mark A. Torres (University of Southern California)

Current Placement: Assistant Professor, Rice University

Advisor: A. Joshua West (University of Southern California)

Draft Genome Sequences of Penicillium spp. from Deeply Buried Oligotrophic Marine Sediments

Microbiology Resource Announcements

Authors: Morgan S. Sobol, Tatsuhiko Hoshino, Taiki Futagami, Fumio Inagaki, Brandi Kiel Reese

Published: February 7, 2019

C-DEBI Contribution Number: 458

Abstract

Here, we report genome sequences of two Penicillium isolates from below the seafloor of the oligotrophic South Pacific Gyre. These genomes are the first reported for fungi from deeply buried marine sediment. Both genomes will provide valuable information regarding the role of fungi and carbon cycling in the energy-limited subsurface biosphere.

Source: http://dx.doi.org/10.1128/mra.01613-18

Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere

The ISME Journal

Authors: Stephanie A. Carr, Sean P. Jungbluth, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Tanja Woyke, Michael S. Rappé, Beth N. Orcutt

Published: February 7, 2019

C-DEBI Contribution Number: 451

Abstract

The exploration of Earth’s terrestrial subsurface biosphere has led to the discovery of several new archaeal lineages of evolutionary significance. Similarly, the deep subseafloor crustal biosphere also harbors many unique, uncultured archaeal taxa, including those belonging to Candidatus Hydrothermarchaeota, formerly known as Marine Benthic Group-E. Recently, Hydrothermarchaeota was identified as an abundant lineage of Juan de Fuca Ridge flank crustal fluids, suggesting its adaptation to this extreme environment. Through the investigation of single-cell and metagenome-assembled genomes, we provide insight into the lineage’s evolutionary history and metabolic potential. Phylogenomic analysis reveals the Hydrothermarchaeota to be an early-branching archaeal phylum, branching between the superphylum DPANN, Euryarchaeota, and Asgard lineages. Hydrothermarchaeota genomes suggest a potential for dissimilative and assimilative carbon monoxide oxidation (carboxydotrophy), as well as sulfate and nitrate reduction. There is also a prevalence of chemotaxis and motility genes, indicating adaptive strategies for this nutrient-limited fluid-rock environment. These findings provide the first genomic interpretations of the Hydrothermarchaeota phylum and highlight the anoxic, hot, deep marine crustal biosphere as an important habitat for understanding the evolution of early life.

Source: http://dx.doi.org/10.1038/s41396-019-0352-9

Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns

Nature Communications

Authors: Benjamin J. Tully

Published: January 17, 2019

C-DEBI Contribution Number: 452

Abstract

Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) remain a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world, and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present a comparative genomic analysis of 250 MGII genomes, providing a comprehensive investigation of these mesophilic archaea. This analysis identifies 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera reveals distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins, common in all other subclades.

Source: http://dx.doi.org/10.1038/s41467-018-07840-4

Persistent organic matter in oxic subseafloor sediment

Nature Geoscience

Authors: Emily R. Estes, Robert Pockalny, Steven D’Hondt, Fumio Inagaki, Yuki Morono, Richard W. Murray, Dennis Nordlund, Arthur J. Spivack, Scott D. Wankel, Nan Xiao, Colleen M. Hansel

Published: January 21, 2019

C-DEBI Contribution Number: 450

Abstract

Nearly half of the global seafloor is overlain by sediment oxygenated to the basement. Yet, despite the availability of oxygen to fuel aerobic respiration, organic carbon persists over million-year timescales. Identifying the controls on organic carbon preservation requires an improved understanding of the composition and distribution of organic carbon within deep oligotrophic marine sediments. Here we show that organic carbon in sediment from the oligotrophic North Atlantic and South Pacific is low (<0.1%), yet stable to depths of 25 m and ages of 24 million years. This organic carbon is not bound in biomass and has a low carbon/nitrogen ratio. X-ray imaging and spectroscopic analyses reveal that the chemical composition of this old, deep organic carbon is dominated (40–60%) by amide and carboxylic carbon with a proteinaceous nature. We posit that organic carbon persists in oxic oligotrophic sediment through a combination of protective processes that involve adsorption to mineral surfaces and physical inaccessibility to the heterotrophic community. We estimate that up to 1.6 × 10²² g of organic carbon are sequestered on million-year timescales in oxic pelagic sediment, which exceeds current estimates of the total global sediment organic carbon and constitutes an important, previously overlooked carbon reservoir.

Source: http://dx.doi.org/10.1038/s41561-018-0291-5

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: Staff Scientist, International Ocean Discovery Program, Texas A&M University

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)

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)

Current Placement: Postdoctoral Researcher, University of North Carolina

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 — March 31, 2019

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

Current Placement: Assistant Professor, Queen Mary University of London

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: Assistant Professor, University of Cincinnati

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: Assistant Professor, University of Cincinnati

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: Assistant Professor, University of Cincinnati

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

Abstract

Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic reactions, but this is a complex, composite signal that is difficult to interpret. Here we show that nanocalorimetry can be used in combination with enumeration of viable cell counts, oxygen consumption rates, cellular protein content, and thermodynamic calculations to assess catabolic rates of an isolate of Shewanella oneidensis MR-1 and infer what fraction of the chemical energy is assimilated by the culture into biomass and what fraction is dissipated in the form of heat under different limiting conditions. In particular, our results demonstrate that catabolic rates are not necessarily coupled to rates of cell division, but rather, to physiological rearrangements of S. oneidensis MR-1 upon growth phase transitions. In addition, we conclude that the heat released by growing microorganisms can be measured in order to understand the physiochemical nature of the energy transformation and dissipation associated with microbial metabolic activity in conditions approaching those found in natural systems.

Source: http://dx.doi.org/10.3389/fmicb.2018.00109

Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer

Genome Announcements

Published: February 1, 2018

C-DEBI Contribution Number: 409

Abstract

Hydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite incubated in situ in the marine surface sediment of Catalina Island, CA. Strain SC-1 has demonstrated autotrophic growth through the oxidation of thiosulfate and iron. Here, we present the 2.45-Mb genome sequence of SC-1, which contains 2,262 protein-coding genes.

Source: http://dx.doi.org/10.1128/genomea.01581-17

Necromass as a limited source of energy for microorganisms in marine sediments

Journal of Geophysical Research: Biogeosciences

Authors: James A. Bradley, Jan P. Amend, Douglas E. LaRowe

Published: February 12, 2018

C-DEBI Contribution Number: 416

Abstract

The in situ production of necromass and its role as a power source in sustaining heterotrophic microorganisms in natural settings has never been quantified. Here, we quantify the power availability from necromass oxidation to living microorganisms buried in marine sediments over millions of years, first in the oligotrophic South Pacific Gyre (SPG), and second on a global scale. We calculate that power from autochthonously produced necromass in the upper meter of sediment at SPG provides only a small fraction (~0.02%) of the maintenance power demand of the living community (1.9×10^-19 W cell^-1). Power from necromass oxidation diminishes considerably with increasing sediment depth (and thus sediment age). Alternatively, the oxidation of allochthonous organic matter, and of radiolytic H₂, provides power equivalent to or in excess of the maintenance demands of living microorganisms at SPG. On a global scale, necromass may support the maintenance power demand of 2 to 13% of the microbial community in relatively young sediments (<10,000 years) when it is oxidized with SO₄^2- and O₂ respectively. However, in older sediments, the power supplied by necromass is negligible (<0.01%). Nevertheless, the oxidation of a single dead cell per year provides sufficient power to support the maintenance demands of dozens to thousands of cells in low-energy marine sediments. This raises the possibility that the production and oxidation of necromass may provide a mechanism for non-growing microorganisms to endure unfavorable, low-energy settings over geological timescales.

Source: http://dx.doi.org/10.1002/2017jg004186

Related Items

Awards

Develop a 1D biogeochemical-evolutionary model for deep sediments

Award Dates: October 10, 2016 — March 31, 2019

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

Current Placement: Assistant Professor, Queen Mary University of London

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

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

Bioenergetic Controls on Microbial Ecophysiology in Marine Sediments

Frontiers in Microbiology

Authors: James A. Bradley, Jan P. Amend, Douglas E. LaRowe

Published: February 13, 2018

C-DEBI Contribution Number: 415

Abstract

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 — March 31, 2019

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

Current Placement: Assistant Professor, Queen Mary University of London

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)