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Graduate Fellowships

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Date Desc
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Awards > Graduate Fellowships
Award Dates: June 1, 2018 — May 31, 2019
Characterization of subsurface extracellular enzymes and the organisms that produce them using metatranscriptomics and bottom-up metaproteomics
Awardee: Taylor Royalty (University of Tennessee Knoxville)
Advisor: Andrew D. Steen (University of Tennessee Knoxville)
Awards > Graduate Fellowships
Award Dates: July 1, 2018 — June 30, 2019
Population genomics of Nitrospirae bacteria inhabiting deep
Awardee: Clarisse Sullivan (University of Hawaii, Manoa)
Advisor: Michael S. Rappé (University of Hawaii, Manoa)
Awards > Graduate Fellowships
Award Dates: June 1, 2017 — May 31, 2018
Insights into the genomics of deep subsurface vs. near surface Thermococcus isolates
Awardee: Lilja Strang (Western Washington University)
Advisor: Craig L. Moyer (Western Washington University)
Awards > Graduate Fellowships
Award Dates: May 10, 2016 — August 31, 2018
3D Spatial mapping of the energetic return of 1000 metabolisms within the compositional variation of oceanic crusts near mid-ocean ridges
Awardee: Tucker Ely (Arizona State University)
Advisor: Everett L. Shock (Arizona State University)
Awards > Graduate Fellowships
Award Dates: June 1, 2016 — May 31, 2017
Geochemical controls on organic carbon quantity and quality in the deep subsurface
Awardee: Emily R. Estes (Woods Hole Oceanographic Institution)
Current Placement: Postdoctoral Researcher, University of Delaware, 2017-
Advisor: Colleen M. Hansel (Woods Hole Oceanographic Institution)
Awards > Graduate Fellowships
Award Dates: September 1, 2014 — August 31, 2016
Analytical tools for cross metagenome comparisons
Awardee: Cara Magnabosco (Princeton University)
Current Placement: Systems Biology Group, Simons Center for Data Analysis, 2016-
Advisor: Tullis C. Onstott (Princeton University)
Awards > Graduate Fellowships
Award Dates: September 24, 2012 — December 23, 2014
Modeling rates of olivine bioweathering in ocean crust
Awardee: Amy R. Smith (Oregon State University)
Current Placement: Postdoctoral Researcher, Woods Hole Oceanographic Institution
Advisor: Frederick S. Colwell (Oregon State University)
Awards > Graduate Fellowships
Award Dates: December 1, 2012 — December 31, 2014
Ridge flank crustal fluid microbial community genomics, expression, and phylogeny
Awardee: Sean P. Jungbluth (University of Hawaii)
Current Placement: Postdoctoral Researcher, Joint Genome Institute, 2017-
Advisor: Michael S. Rappé (University of Hawaii)
Awards > Graduate Fellowships
Award Dates: May 16, 2013 — May 15, 2015
Comparative analysis of serpentinizing fluids in Turkey and the Phillippines: Insights and the "genetic legacy" of deep subsurface microbes
Awardee: Kristin M. Woycheese (University of Illinois, Chicago)
Current Placement: Scientific Editor, Accdon
Advisor: D’Arcy R. Meyer-Dombard (University of Illinois, Chicago)
Awards > Graduate Fellowships
Award Dates: July 1, 2013 — June 30, 2014
Biogeography and diversity of methane and sulfur-cycling ecotypes in deep subsurface sediments
Awardee: Melissa Adams (Harvard University)
Current Placement: Patent Agent, Lando & Anastsi 2017-
Advisor: Peter R. Girguis (Harvard University)
Awards > Graduate Fellowships
Award Dates: August 10, 2013 — August 9, 2015
Quantifying biological production of ethane and propane in deep subsurface sediments
Awardee: Ryan Sibert (University of Georgia)
Advisor: Samantha B. Joye (University of Georgia)
Awards > Graduate Fellowships
Award Dates: August 16, 2013 — August 15, 2015
Identifying the mechanisms and limits of the microbial enhancement of olivine dissolution
Awardee: Mark A. Torres (University of Southern California)
Current Placement: Assistant Professor, Rice, 2017-
Advisor: A. Joshua West (University of Southern California)
Awards > Graduate Fellowships
Award Dates: May 16, 2014 — May 15, 2016
Investigating microbial activities driving organic matter transformations in the deep subsurface
Awardee: Adrienne Hoarfrost (University of North Carolina, Chapel Hill)
Advisor: Carol Arnosti (University of North Carolina, Chapel Hill)
Awards > Graduate Fellowships
Award Dates: June 1, 2014 — May 31, 2016
An in-depth analysis of the subvent biosphere within the Okinawa backarc basin Iheya North hydrothermal field
Awardee: Leah D. Brandt (Pennsylvania State University)
Advisor: Christopher H. House (Pennsylvania State University)
Awards > Graduate Fellowships
Award Dates: August 1, 2014 — May 31, 2016
Microbial carbon cycling beneath the West Antarctic Ice Sheet
Awardee: Alexander B. Michaud (Montana State University)
Current Placement: Postdoc, Aarhus (Jørgensen), 2016-
Advisor: John C. Priscu (Montana State University)
Awards > Graduate Fellowships
Award Dates: June 15, 2011 — May 15, 2013
Metagenomic signatures in seafloor rocks and subsurface sediments
Awardee: Esther Singer (University of Southern California)
Current Placement: Project Scientist, DOI Joint Genome Institute, 2017-
Advisor: Katrina J. Edwards (University of Southern California)
Awards > Graduate Fellowships
Award Dates: August 16, 2011 — August 15, 2013
Proteomic profiling of neutrophilic, iron-oxidizing Mariprofundus ferrooxydans, strain PV-1, grown under different iron sources
Awardee: Roman A. Barco (University of Southern California)
Current Placement: Postdoctoral Researcher, University of Southern California, 2017-
Advisor: Katrina J. Edwards (University of Southern California)
Awards > Graduate Fellowships
Award Dates: August 16, 2011 — August 15, 2013
Deep phylogenetic and metagenomic analysis of microbial diversity associated with ferromanganese nodules collected from the South Pacific Gyre
Awardee: Benjamin J. Tully (University of Southern California)
Current Placement: Postdoctoral Research Associate, C-DEBI at University of Southern California, 2014-
Advisor: John F. Heidelberg (University of Southern California)
Awards > Graduate Fellowships
Award Dates: May 1, 2012 — June 30, 2014
Constraints on microbial biogeography in hydrothermally active sediments of Guaymas Basin: Energetic limits, physical stressors, and upward compression of metabolic zones
Awardee: Luke J. McKay (University of North Carolina, Chapel Hill)
Current Placement: Assistant Research Professor, Montana State University
Advisor: Andreas P. Teske (University of North Carolina, Chapel Hill)
Awards > Graduate Fellowships
Award Dates: June 1, 2012 — May 31, 2014
Working around drilling contamination in deep cores: Costa Rica Margin
Awardee: Amanda J. Martino (Pennsylvania State University)
Current Placement: Assistant Professor, Saint Francis University, 2014-
Advisor: Christopher H. House (Pennsylvania State University)
Awards > Graduate Fellowships
Award Dates: July 1, 2012 — June 30, 2014
Nature of labile and refractory phosphorus pools fueling life in deep sub-seafloor sediments
Awardee: Delphine Defforey (University of California, Santa Cruz)
Current Placement: Associate Editor, Nature Communications, 2016-
Advisor: Adina Paytan (University of California, Santa Cruz)
Awards > Graduate Fellowships
Award Dates: July 1, 2012 — June 30, 2014
Genomic analyses and microbial cultivations in unexplored sub-seafloor ridge flank and continental margin environments
Awardee: Joseph A. Russell (University of Delaware)
Current Placement: Senior Scientist, MRIGlobal
Advisor: Jennifer F. Biddle (University of Delaware)
Awards > Graduate Fellowships
Award Dates: July 1, 2012 — June 30, 2014
Key variables for modeling rates of microbially mediated sulfate reduction
Awardee: Kiana L. Frank (Harvard University)
Current Placement: Assistant Research Faculty, University of Hawaii, 2014-
Advisor: Peter R. Girguis (Harvard University)
Awards > Graduate Fellowships
Characterization of subsurface extracellular enzymes and the organisms that produce them using metatranscriptomics and bottom-up metaproteomics
Awardee: Taylor Royalty (University of Tennessee Knoxville)
Advisor: Andrew D. Steen (University of Tennessee Knoxville)
Amount: $45,360.00
Award Dates: June 1, 2018 — May 31, 2019

Abstract

Approximately 150 Pg of organic carbon resides in subsurface sediments (Ciais et al. 2013). Understanding the preservation, transformation, and remineralization of this carbon is a prerequisite to understanding the global carbon cycle. Extracellular enzymes are required by subsurface heterotrophic microbes to access complex molecules from this reservoir (Arnosti 2011) and thus, influence carbon turnover. Identifying which microbes produce which extracellular enzymes and under what conditions has remained a challenge. Here, it is proposed to apply bottom-up metaproteomics, metatranscriptomics, and shotgun-metagenomics on subsurface microbe communities from the White Oak River estuary to help close this knowledge gap.
Awards > Graduate Fellowships
Population genomics of Nitrospirae bacteria inhabiting deep
Awardee: Clarisse Sullivan (University of Hawaii, Manoa)
Advisor: Michael S. Rappé (University of Hawaii, Manoa)
Amount: $51,373.00
Award Dates: July 1, 2018 — June 30, 2019

Abstract

The goals of this project are to comprehensively describe the potential metabolic attributes, evolutionary history, and population genetic/microevolutionary characteristics of members of the bacterial phylum Nitrospirae inhabiting the basalt-hosted deep subseafloor of the Juan de Fuca Ridge flank in the Northeast Pacific Ocean. This will be accomplished by leveraging an existing suite of crustal fluid samples from research cruises spanning 2008-2014 (including existing geochemical and physical metadata), and high throughput DNA sequencing from metagenomes and genome sequences generated from single microbial cells by the Department of Energy’s Joint Genome Institute through a Community Sequencing Program Award.
Awards > Graduate Fellowships
Insights into the genomics of deep subsurface vs. near surface Thermococcus isolates
Awardee: Lilja Strang (Western Washington University)
Advisor: Craig L. Moyer (Western Washington University)
Amount: $29,662.00
Award Dates: June 1, 2017 — May 31, 2018

Abstract

Gleaning access to microorganisms deep below the ocean floor is usually limited to deep-sea drilling: however, after the sudden release of a megaplume into the water column, such as at Gorda Ridge in 1996, access to these microbes was possible. Thermococcus isolates have been identified and isolated from this megaplume. These Thermococcus isolates were found to be genetically distinct from their relatives, indicating that they have a distinct biogeography and evolutionary history. This project will use genome sequencing to explore the genetic features specific to deep subsurface Thermococcus lineages from the Gorda Ridge as compared to other "shallow" subsurface isolates.
Awards > Graduate Fellowships
3D Spatial mapping of the energetic return of 1000 metabolisms within the compositional variation of oceanic crusts near mid-ocean ridges
Awardee: Tucker Ely (Arizona State University)
Advisor: Everett L. Shock (Arizona State University)
Amount: $150,005.00
Award Dates: May 10, 2016 — August 31, 2018

Abstract

The oceanic crust near mid-ocean ridge spreading centers is a rich source of reducing chemistries and biologically relevant energy sources. It is here that countless microbial metabolic strategies crowd the hydrothermal emissions billowing into the sea, having reacted with the mantle-derived rock deep within. The relative energetic payoff of disparate strategies—a function of electron donor/acceptor availability—changes as a function of host rock composition, temperature, and water-to-rock ratio. This project has constructed chemical maps of these subsurface environments to all realistic extents of these variables, depicting how subtle changes in each generates changes in solute flux and energetic payoffs.

Related Items

Project Data
Project Data
Last Modified: December 19, 2018
3D Spatial mapping of the energetic return of 1000 metabolisms within the compositional variation of oceanic crusts near mid-ocean ridges
Project Maintainers: Tucker Ely
Awards > Graduate Fellowships
Geochemical controls on organic carbon quantity and quality in the deep subsurface
Awardee: Emily R. Estes (Woods Hole Oceanographic Institution)
Current Placement: Postdoctoral Researcher, University of Delaware, 2017-
Advisor: Colleen M. Hansel (Woods Hole Oceanographic Institution)
Amount: $33,000.00
Award Dates: June 1, 2016 — May 31, 2017

Abstract

Sediment underlying ocean gyres receives minimal input of fresh organic matter yet sustains a small but active heterotrophic microbial community. The concentration and composition of the organic carbon (OC) available to this deep biosphere however is unknown. We analyzed the content and composition of OC in pelagic sediment in order to identify mechanism(s) that dictate the balance between OC preservation and utilization by microorganisms. Sediment cores from the North Atlantic gyre (KN223), South Pacific Gyre (Knox02-RR), and Peru Basin (IODP site 1231) allowed for a global comparison and a test of how sediment lithology and redox state affect OC preservation. OC was present in low concentrations in all samples (0.01—0.61%), at depths up to 112 meters below seafloor and estimated sediment ages of up to 50 million years. Synchrotron-based near edge X-ray absorption fine structure (NEXAFS) spectroscopy was conducted on over 100 samples, one of the first applications of NEXAFS to sedimentary environments. NEXAFS revealed an OC reservoir dominated by amide and carboxylic functionalities in a scaffolding of O-alkyl and aliphatic carbons. Detection of extractable, extracellular proteins supports this composition and suggests that sedimentary OC is protein-derived. This composition was common across all sites and depths, implicating physical rather than chemical mechanisms in OC preservation on long timescales. This study thereby points to physical access rather than energy or metabolic potential as a key constraint on subsurface heterotrophic life.

Related Items

Publications
Publications > Monograph
Published: February 1, 2017
Ph.D. Thesis
Geochemical controls on the distribution and composition of biogenic and sedimentary carbon
Authors: Emily R. Estes
C-DEBI Contribution Number: 359
Publications > Journal Article
Published: January 21, 2019
Nature Geoscience
Persistent organic matter in oxic subseafloor sediment
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
C-DEBI Contribution Number: 450
Awards > Graduate Fellowships
Analytical tools for cross metagenome comparisons
Awardee: Cara Magnabosco (Princeton University)
Current Placement: Systems Biology Group, Simons Center for Data Analysis, 2016-
Advisor: Tullis C. Onstott (Princeton University)
Amount: $64,000.00
Award Dates: September 1, 2014 — August 31, 2016

Abstract

The subsurface biosphere represents one of the final frontiers on Earth and may provide a model for how life can survive on other planets. While focusing on terrestrial subsurface and depths of over 3,000 meters underground, we present and apply a variety of computational tools and techniques for exploring the deep biosphere. Life at this depth is scarce and nutrients are often limited to hydrogen, sulfate, and single carbon compounds such as methane, carbon monoxide and carbon dioxide. Metagenomics and other sequencing techniques shed light onto how subsurface microorganisms transform these limited nutrients into energy and survive underground. When appropriate, such methods are combined with geochemical measurements and thermodynamic predictions to provide the most accurate picture of life underground. In that direction, we find that the South African subsurface fluids exhibit a spectrum of redox conditions (influenced by the origin and age of the subsurface fluids) that directly affect the microbial community composition and function. Although these large-scale community shifts are believed to occur over long periods underground, we also present evidence for an adaptive methane oxidizing community that responds to changes in geochemistry over relatively short periods. Combined, these results provide a picture of how microbial communities function in the terrestrial subsurface as well as a theoretical framework for understanding the selective pressures these organisms face.

Related Items

Publications
Publications > Journal Article
Published: November 21, 2016
Proceedings of the National Academy of Sciences
An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
Authors: Maggie C. Y. Lau, Thomas L. Kieft, Olukayode Kuloyo, Borja Linage-Alvarez, Esta van Heerden, Melody R. Lindsay, Cara Magnabosco, Wei Wang, Jessica B. Wiggins, Ling Guo, David H. Perlman, Saw Kyin, Henry H. Shwe, Rachel L. Harris, Youmi Oh, Min Joo Yi, Roland Purtschert, Greg F. Slater, Shuhei Ono, Siwen Wei, Long Li, Barbara Sherwood Lollar, Tullis C. Onstott
C-DEBI Contribution Number: 340
Awards > Graduate Fellowships
Modeling rates of olivine bioweathering in ocean crust
Awardee: Amy R. Smith (Oregon State University)
Current Placement: Postdoctoral Researcher, Woods Hole Oceanographic Institution
Advisor: Frederick S. Colwell (Oregon State University)
Amount: $63,766.00
Award Dates: September 24, 2012 — December 23, 2014

Abstract

Igneous oceanic crust contains the largest aquifer on earth (Johnson & Pruis, 2003). The basaltic layer contains ~2300 m2 kg-1 of surface area that supports an extensive subsurface microbial ecosystem (Heberling et al., 2010; Nielsen & Fisk, 2010; Santelli et al., 2008).  Biological activities in this ecosystem can impact global carbon cycling and increase productivity in the ocean (Edwards et al., 2011; McCarthy et al., 2010). Previous studies of surface layer rocks and mineral deposits have suggested that mineralogy dictates microbial community structure in the upper oceanic crust (Flores et al., 2011; Sylvan et al., 2013; Toner et al., 2013) and subseafloor planktonic communities have been previously investigated (Cowen et al., 2003; Jungbluth et al., 2014, 2013); however, the role of mineralogy and composition in the attached community that comprises the bulk of the habitable zone in the subseafloor has not been previously determined. Planktonic and mineral-attached microbial communities in aquifers are distinct from one another (Lehman, 2007), and investigating the attached community will lead to a more holistic view of this largest crustal aquifer. As a C-DEBI graduate fellow, I analyzed microbial communities attached to igneous minerals and glasses incubated in IODP Hole 1301A of the Juan de Fuca Ridge. I found that Archaeal communities on olivine (a Fe-bearing silicate mineral common in the crust) were distinct from those on other common minerals and glasses, while bacterial communities were influenced by mineral composition. Using olivine bioreactors in the laboratory, I found that isolated subseafloor microbes increased the dissolution of olivine and promoted mineralization of secondary phases, potentially influencing biogeochemical cycles in the ocean. Finally, preliminary metagenomic analysis of attached communities from the JFR indicate that genes for fermentation, one-carbon metabolism, protein synthesis, aromatic compound metabolism, respiration, and fatty acid metabolism are more abundant in the subseafloor than other subsurface or marine environments. These new insights into the attached subseafloor biosphere, through support from C-DEBI, are helping to propel the field of deep biosphere research into a new era and challenging our view of this extensive subseafloor biosphere.

Related Items

Publications
Publications > Journal Article
Published: January 1, 2012
Astrobiology
Olivine-Respiring Bacteria Isolated from the Rock-Ice Interface in a Lava-Tube Cave, a Mars Analog Environment
Authors: Radu Popa, Amy R. Smith, Rodica Popa, Jane Boone, Martin R. Fisk
C-DEBI Contribution Number: 155
Publications > Journal Article
Published: March 10, 2016
Geomicrobiology Journal
Deep Crustal Communities of the Juan de Fuca Ridge Are Governed by Mineralogy
Authors: Amy R. Smith, Martin R. Fisk, Andrew R. Thurber, Gilberto E. Flores, Olivia U. Mason, Radu Popa, Frederick S. Colwell
C-DEBI Contribution Number: 320
Project Data
Project Data
Last Modified: January 25, 2016
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
Project Maintainers: Radu Popa, Martin R. Fisk, Gilberto E. Flores, Amy R. Smith
Awards > Graduate Fellowships
Ridge flank crustal fluid microbial community genomics, expression, and phylogeny
Awardee: Sean P. Jungbluth (University of Hawaii)
Current Placement: Postdoctoral Researcher, Joint Genome Institute, 2017-
Advisor: Michael S. Rappé (University of Hawaii)
Amount: $65,850.00
Award Dates: December 1, 2012 — December 31, 2014

Abstract

Our understanding of microbial life within the seafloor of the dark ocean is still in its infancy; particularly, with respect to the largely inaccessible sediment-covered ocean crust. Despite our profound lack of access, some experts argue that the upper ocean basement is among the most suitable subseafloor environment for microbial life. During my tenure as a C-DEBI Graduate Fellowship, I explored the deep biosphere of the subseafloor crust on the eastern flank of the Juan de Fuca Ridge by retrieving pristine crustal fluids via seafloor sampling and instrumentation platforms. Analysis of the microbial life was highly successful and resulted in several publications including one that describes a novel microbial assemblage within the basement fluid environment that is distinct from sediment and seawater, and another that reveals temporally dynamic microbial communities in the deep subsurface. Investigations are ongoing using metagenomic and metatranscriptomic approaches and, though in the preliminary stages, indicate that sulfate-reduction, methanogenesis, and fermentation are popular themes in the anoxic basaltic biosphere. The phylogenetic and implied physiological diversity in the oceanic crust is of broad interest due to the contribution to global biomass, elemental cycling, and astrobiology topics related to subsurface chemosynthetic-based ecosystems. The C-DEBI Graduate Fellowship allowed me to pursue this exciting work and facilitated many opportunities that helped to establish my professional scientific network.

Related Items

Publications
Publications > Journal Article
Published: July 12, 2012
The ISME Journal
Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank
Authors: Sean P. Jungbluth, Jana Grote, Huei-Ting Lin, James P. Cowen, Michael S. Rappé
C-DEBI Contribution Number: 134
Publications > Proceedings
Published: September 5, 2011
Proceedings of the IODP
Data report: microbial diversity in sediment near Grizzly Bare Seamount in Holes U1363B and U1363G
Authors: Sean P. Jungbluth, L. G. H. Johnson, James P. Cowen, Michael S. Rappé
C-DEBI Contribution Number: 181
Project Data
Project Data
Last Modified: December 15, 2016
Microbiology and biogeochemistry of Juan de Fuca Ridge flank borehole fluids
Project Maintainers: Michael S. Rappé
Awards > Graduate Fellowships
Comparative analysis of serpentinizing fluids in Turkey and the Phillippines: Insights and the "genetic legacy" of deep subsurface microbes
Awardee: Kristin M. Woycheese (University of Illinois, Chicago)
Current Placement: Scientific Editor, Accdon
Advisor: D’Arcy R. Meyer-Dombard (University of Illinois, Chicago)
Amount: $64,000.00
Award Dates: May 16, 2013 — May 15, 2015

This study assessed deep subsurface-to-surface transitional microbial communities in two serpentinizing ecosystems: a flaming gas/fluid seep in Yanartaş, Turkey and a bubbling fluid seep in Manleluag Spring National Park, the Philippines. These systems exhibited some similar geochemical and taxonomic attributes, but different physical properties that help demonstrate the effect surface conditions have on the subsurface. 16S rRNA gene sequencing, coupled with metagenomic and geochemical analysis, reveal dynamic microbial ecosystems supported partly by the products of active serpentinization. At Yanartaş, the fluid seeps may be ephemeral. Large travertine deposits are visible on the mountain slope as relicts of former fluid seeps. At Manleluag, the tropical climate causes monsoon and “dry” seasons, which influence dissolved inorganic and organic carbon input in the system. The 16S rRNA gene sequencing and metagenomic shotgun sequencing data suggest that, despite differences in regional climate and vegetation cover, Manleluag and Yanartaş exhibit taxonomic and functional similarities. Metabolisms involving methane, nitrogen, iron, and sulfur cycling, hydrogen oxidation, and respiration were detected in both 16S rRNA amplicon and metagenomic sequence datasets. Metagenomic analysis detected genes involved with osmotic and oxidative stress at both sites, and sporulation and dormancy genes at Manleluag. Several transposable elements were also reported at both Manleluag and Yanartaş. These mechanisms may allow subsurface microbial communities to adapt to surface conditions. In general, the surface and subsurface environment appear to be inherently connected at Yanartaş and Manleluag; the surface and subsurface both shape the microbial community in these ecosystems, and the microbial community alters the biogeochemistry.

Related Items

Publications
Publications > Journal Article
Published: February 19, 2015
Frontiers in Microbiology
Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines)
Authors: Kristin M. Woycheese, D’Arcy R. Meyer-Dombard, Dawn Cardace, Anacleto M. Argayosa, Carlo A. Arcilla
C-DEBI Contribution Number: 288
Awards > Graduate Fellowships
Biogeography and diversity of methane and sulfur-cycling ecotypes in deep subsurface sediments
Awardee: Melissa Adams (Harvard University)
Current Placement: Patent Agent, Lando & Anastsi 2017-
Advisor: Peter R. Girguis (Harvard University)
Amount: $32,000.00
Award Dates: July 1, 2013 — June 30, 2014

The microbially mediated anaerobic oxidation of methane (AOM) is critical for regulating the flux of methane from the ocean. AOM is coupled to sulfate reduction (SR) in many anoxic marine environments, which has been extensively studied at cold seeps, hydrothermal vents, and the sulfate-methane transition zone at the seafloor. Sulfate-dependent AOM is performed by specialized groups of anaerobic methane-oxidizing (ANME) archaea, which are thought to form consortial relationships with sulfate-reducing bacteria (SRB). Certain ANME and SRB groups have been shown to occupy different ecological niches in both hydrocarbon seep and hydrothermal vent sediments. However, the environmental parameters that select for certain phylogenetic variants across these hydrocarbon-rich marine ecosystems are still unknown. In this study, we generated the largest dataset to date of 16S rRNA gene sequences for these uncultivable deep sea microorganisms using Illumina sequencing. Sediment strata were collected from the cold seeps of Hydrate Ridge, metalliferous sediments of Juan de Fuca Ridge, and organic-rich hydrothermal sediments of Guaymas Basin. We then used the Illumina MiSeq platform to assess archaeal and bacterial richness, diversity, and taxonomic composition followed by phylogenetic analyses of ANME and SRB phylotypes across environmental gradients and geographic ranges. Environmental metadata were used to establish the relationships between ANME and SRB phylotype distribution and environmental gradients as well as the extent of these functional groups in different hydrocarbon-rich ecosystems. Our results indicate that physicochemical constraints, particularly temperature and substrate availability, drive the distribution of different ANME and SRB ecotypes and the associated communities in spatially separated sites.

Awards > Graduate Fellowships
Quantifying biological production of ethane and propane in deep subsurface sediments
Awardee: Ryan Sibert (University of Georgia)
Advisor: Samantha B. Joye (University of Georgia)
Amount: $59,062.00
Award Dates: August 10, 2013 — August 9, 2015

Light hydrocarbon gas mixtures are commonly found in organic-rich marine sediments. Methane (C1) is typically the dominant constituent in these mixtures, but ethane (C2) and propane (C3) are nearly always present in trace amounts. C1 dynamics are typically associated with either thermal cracking of deeply buried organic matter or the metabolic end-product of organic matter degradation. Ethane and propane production had typically been associated with thermocatalytic processes in deeply buried sediments, but limited studies suggested C2/C3 production in biogenic C1 gas mixtures was likely attributable to the activity of methanogenic archaea. However, very few of these studies looked at C1/C2 production in deep-sea sediments, and quantification of rates had either not been attempted, or were absent from the literature. We attempted to use organic-rich, cold seep sediments from the Green Canyon area of the Gulf of Mexico (GC600) to determine C2/C3 dynamics in the first ten meters of sediment (i.e. 0 – 10 m). We found C2/C3 production in near surface cold-seep sediments to be indistinguishable from the background degassing signatures of clay minerals. Surface sediments (i.e. < 4 m) are hypothesized to be dominated by communities of organisms that oxidize C2/C3 compounds, rather than communities that produce them. Experiments determining the controls and magnitude of C2/C3 oxidation in surface sediments in cold-seep environments are ongoing. We hypothesized that C2/C3 production likely occurs deeper in the sediment column (i.e. > 4 m), based primarily on ethane and propane profiles of similar environments. Such material proved difficult to acquire; efforts are ongoing to obtain deep piston cores (i.e. >10 m) for environmental profiling and experimental manipulation in the deeper sediment layers where C2/C3 production likely occurs.

Awards > Graduate Fellowships
Identifying the mechanisms and limits of the microbial enhancement of olivine dissolution
Awardee: Mark A. Torres (University of Southern California)
Current Placement: Assistant Professor, Rice, 2017-
Advisor: A. Joshua West (University of Southern California)
Amount: $64,000.00
Award Dates: August 16, 2013 — August 15, 2015

Abstract

The project focused on the efficacy by which microorganisms can obtain nutrient Fe from silicate minerals. Silicate minerals are a particularly abundant mineral phase in the oceanic crust and thus the bio-availability of silicate-bound nutrients has important implications for microbial activity in the deep subseafloor (C-DEBI theme 1) and the limits to microbial life (C-DEBI theme 3). The specific goal of this project was to quantitatively determine how metal-binding organic compounds (siderophores) produced by microorganisms under Fe-limited conditions affect the rate of Fe-silicate mineral dissolution using laboratory experiments. The exact effect of microbial activity on Fe-silicate mineral dissolution has previously been hard to discern due to the complicating effects of feedbacks associated with microbial growth, siderophore production, and mineral dissolution rates. To limit the effects of these feedbacks, my experimental design used purified microbial siderophores and a silicate mineral (olivine) that dissolves at a rate that is relatively insensitive to the accumulation of its constituent ions in solution. My results showed that sub-millimolar siderophore concentrations lead to an order of magnitude increase in olivine dissolution rates. The accelerating effect of siderophores was linked to the removal of an inhibiting surface Fe-oxide coating that forms during the reaction of olivine at circum-neutral pH in the presence of O2. By combining the experimental results with a numerical model of the relevant biological feedbacks, this work further constrained the maximum extent to which microbial activity may affect silicate mineral dissolution rates under conditions of Fe-limitation. The results of this study are presently under review for publication in Geobiology.

Related Items

Publications
Publications > Journal Article
Published: March 19, 2014
Nature
Sulphide oxidation and carbonate dissolution as a source of CO2 over geological timescales
Authors: Mark A. Torres, A. Joshua West, Gaojun Li
C-DEBI Contribution Number: 197
Publications > Journal Article
Published: October 1, 2015
Geochimica et Cosmochimica Acta
Geomorphic regime modulates hydrologic control of chemical weathering in the Andes–Amazon
Authors: Mark A. Torres, A. Joshua West, Kathryn E. Clark
C-DEBI Contribution Number: 273
Publications > Thesis
Published: January 1, 2015
PhD Thesis
Chemical Weathering Across Spatial and Temporal Scales
Authors: Mark A. Torres
C-DEBI Contribution Number: 299
Publications > Journal Article
Published: February 7, 2019
Geobiology
The kinetics of siderophore-mediated olivine dissolution
Authors: Mark A. Torres, Sijia Dong, Kenneth H. Nealson, A. Joshua West
C-DEBI Contribution Number: 460
Project Data
Project Data
Last Modified: August 18, 2017
Identifying the Mechanisms and Limits of the Microbial Enhancement of Olivine Dissolution
Project Maintainers: Mark A. Torres, A. Joshua West
Awards > Graduate Fellowships
Investigating microbial activities driving organic matter transformations in the deep subsurface
Awardee: Adrienne Hoarfrost (University of North Carolina, Chapel Hill)
Advisor: Carol Arnosti (University of North Carolina, Chapel Hill)
Amount: $64,000.00
Award Dates: May 16, 2014 — May 15, 2016

Abstract

Heterotrophic organisms are central to subsurface microbial communities and play an important role in carbon cycling. Most approaches to measuring enzymatic activities rely on the addition of a fluorescently labeled substrate to a sediment incubation. However, quantifying rates of extracellular enzymatic hydrolysis of organic matter is often problematic due to the tendency for a fluorescently labeled organic substrate to sorb to the sediment matrix. This results in lower fluorescence intensities and distorted, inaccurate hydrolysis rate calculations. In this project, a desorption treatment was developed to counteract the adverse effects of sorption on enzymatic activity measurements. Upon subsampling a sediment incubation amended with a fluorescently labeled substrate, the subsample is treated with a concentrated solution of unlabeled substrate, along with 0.2% sodium dodecyl sulfate (SDS), in order to competitively desorb the adsorbed, fluorescent substrate target. This treatment improves measured fluorescence intensities by a median of 62.5%, and is particularly effective at desorbing high molecular weight substrate products, resulting in debiased hydrolysis rates that are 14.75 nM/hr lower on average. Competitive desorption treatment was demonstrated to be effective for multiple substrates and in a broad range of sediments from diverse geological and geochemical contexts. Future applications of this method will result in more quantitative and comparable hydrolysis rates in subsurface sediments, will enable enzymatic activity measurements in problematic sediments that were previously infeasible, and will facilitate physiological characterization of microbial communities and model organisms in order to better understand heterotrophic carbon cycling in the subsurface environment.

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Publications
Publications > Journal Article
Published: February 16, 2017
Frontiers in Earth Science
Improved Measurement of Extracellular Enzymatic Activities in Subsurface Sediments Using Competitive Desorption Treatment
Authors: Adrienne Hoarfrost, Rachel Snider, Carol Arnosti
C-DEBI Contribution Number: 355
Project Data
Project Data
Last Modified: October 20, 2016
Investigating microbial activities driving organic matter transformations in the deep subsurface
Project Maintainers: Adrienne Hoarfrost, Carol Arnosti
Awards > Graduate Fellowships
An in-depth analysis of the subvent biosphere within the Okinawa backarc basin Iheya North hydrothermal field
Awardee: Leah D. Brandt (Pennsylvania State University)
Advisor: Christopher H. House (Pennsylvania State University)
Amount: $64,000.00
Award Dates: June 1, 2014 — May 31, 2016

Abstract

The Iheya North Hydrothermal Field in the Okinawa Backarc Basin represents an ideal environment in which to investigate the biotic temperature fringe of microbial life at depth because of its subsurface hydrothermal activity within its continental margin-type sediment profile. Geographically, the Okinawa Backarc Basin is situated along a continental margin, which is a sediment profile type commonly sampled and studied across the seafloor (e.g. Peru Margin, Costa Rica Margin, Cascadia Margin). The hydrothermal network within the subsurface here supplies an additional temperature obstacle to microbial life existing in the sediments. In particular, the sediment profile at Site C0014 exhibits a transition from hemipelagic ooze with pumiceous volcaniclastic sediments and low temperature (4°C) to a hydrothermally altered sequence of clays within the top ~10 mbsf of sediment. Temperature measurements indicate a gradient of approximately 3°C/m, which is roughly an order of magnitude greater than continental margin sites (e.g. Cascadia Margin, IODP 311 and Costa Rica Margin, IODP 344), but is more gradual than intense, centimeter-scale gradients from other hot, surface sediments. We have focused on the application of culture-independent, molecular methods to understand taxonomic and functional characteristics through this hydrothermal gradient. Confidence in DNA recovery suggests a microbial biosphere extent of approximately 15 mbsf (55°C). Results from both 16S rRNA gene surveys and metagenomics analyses suggest a temperature-dependent stratigraphy of taxonomic and functional adaptations between the shallowest and deepest sample horizons. Cosmopolitan marine subsurface bacterial and archaeal taxa are present throughout the top 10 mbsf, whereas, hyperthermophilic heterotrophic as well as thermophilic anaerobic methanotrophic archaea appear in varying local abundances in deeper, hydrothermal clay horizons.

Related Items

Publications
Publications > Journal Article
Published: October 23, 2016
Archaea
Marine Subsurface Microbial Community Shifts Across a Hydrothermal Gradient in Okinawa Trough Sediments
Authors: Leah D. Brandt, Christopher H. House
C-DEBI Contribution Number: 352
Project Data
Project Data
Last Modified: September 1, 2017
An in-depth analysis of the subvent biosphere within the Okinawa backarc basin Iheya North hydrothermal field
Project Maintainers: Christopher H. House, Jennifer F. Biddle
Awards > Graduate Fellowships
Microbial carbon cycling beneath the West Antarctic Ice Sheet
Awardee: Alexander B. Michaud (Montana State University)
Current Placement: Postdoc, Aarhus (Jørgensen), 2016-
Advisor: John C. Priscu (Montana State University)
Amount: $62,000.00
Award Dates: August 1, 2014 — May 31, 2016

Abstract

Subglacial lakes were discovered beneath the Antarctic Ice Sheet in the 1970’s and, given the presence of liquid water and saturated sediments, it has been debated whether or not these deep, cold biosphere habitats harbor active microbial communities. Subglacial Lake Whillans (SLW) was cleanly sampled in January 2013 with the goal of establishing the habitability and presence of life beneath the Antarctic Ice Sheet. The aim of this graduate fellowship project was to further characterize the SLW carbon cycle, in particular, chemolithoautotrophic microbial processes through geochemical and microbiological methods. Geochemical analyses showed that sulfide oxidizing bacteria were active and contribute to mineral weathering in the surficial sediments of SLW. Long water residence times beneath the West Antarctic Ice Sheet (WAIS) create a mineral weathering regime in SLW that is distinctly different from subglacial habitats of mountain glaciers. Concentration and stable isotope measurements of methane confirm a reservoir of methane formed by methanogenic archaea beneath the WAIS. The modeling results show that this biological methane provides a source of energy to an active methane oxidizing population at the sediment-water interface. The methane also is modeled to be an important source of carbon for biomass synthesis in the methane oxidizing population, with rates of biomass incorporation similar to that of ammonia oxidizing archaea in the SLW water column. These results provide evidence that the sub ice sheet environment provides favorable conditions and substrates to support an active microbial ecosystem, thus expanding the extent of the biosphere to include the area beneath the WAIS and, possibly, the entire Antarctic Ice Sheet.

Related Items

Publications
Publications > Journal Article
Published: May 19, 2015
Frontiers in Microbiology
A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types
Authors: Mark A. Lever, Andrea Torti, Philip Eickenbusch, Alexander B. Michaud, Tina Šantl-Temkiv, Bo Barker Jørgensen
C-DEBI Contribution Number: 263
Publications > Journal Article
Published: March 30, 2016
Geology
Solute sources and geochemical processes in Subglacial Lake Whillans, West Antarctica
Authors: Alexander B. Michaud, Mark L. Skidmore, Andrew C. Mitchell, Trista J. Vick-Majors, Carlo Barbante, Clara Turetta, Will vanGelder, John C. Priscu
C-DEBI Contribution Number: 321
Publications > Journal Article
Published: October 27, 2016
Frontiers in Microbiology
Physiological Ecology of Microorganisms in Subglacial Lake Whillans
Authors: Trista J. Vick-Majors, Andrew C. Mitchell, Amanda M. Achberger, Brent C. Christner, John E. Dore, Alexander B. Michaud, Jill A. Mikucki, Alicia M. Purcell, Mark L. Skidmore, John C. Priscu
C-DEBI Contribution Number: 337
Publications > Journal Article
Published: July 31, 2017
Nature Geoscience
Microbial oxidation as a methane sink beneath the West Antarctic Ice Sheet
Authors: Alexander B. Michaud, John E. Dore, Amanda M. Achberger, Brent C. Christner, Andrew C. Mitchell, Mark L. Skidmore, Trista J. Vick-Majors, John C. Priscu
C-DEBI Contribution Number: 371
Awards > Graduate Fellowships
Metagenomic signatures in seafloor rocks and subsurface sediments
Awardee: Esther Singer (University of Southern California)
Current Placement: Project Scientist, DOI Joint Genome Institute, 2017-
Advisor: Katrina J. Edwards (University of Southern California)
Amount: $61,333.00
Award Dates: June 15, 2011 — May 15, 2013

The seafloor and subsurface microbial world represents a significant portion of life on our planet. The influence on its proximate ambience and global processes, such as element cycles, has potentially been largely underestimated and not always been precisely evaluated. I am interested in the nature of deep biosphere microorganisms in rocks from the Loihi seamount, Hawai’i, the East Pacific Rise, and the Juan de Fuca Ridge, as well as in sediments from North Pond (Mid-Atlantic). In order to assess microbial diversity, metabolic activity, adaptation strategies and biogeographical signatures in the deep subseafloor biosphere, metagenomics by pyrosequencing will be used to complement previous research efforts with the most in-depth and precise data that is available to date.

Related Items

Publications
Publications > Journal Article
Published: September 23, 2011
PLoS ONE
Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium
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
Publications > Journal Article
Published: February 18, 2011
Applied and Environmental Microbiology
Genomic Potential of Marinobacter aquaeolei, a Biogeochemical "Opportunitroph"
Authors: Esther Singer, Eric A. Webb, William C. Nelson, John F. Heidelberg, N. Ivanova, A. Pati, Katrina J. Edwards
C-DEBI Contribution Number: 121
Publications > Journal Article
Published: January 1, 2013
Frontiers in Microbiology
Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l
Authors: Esther Singer, John F. Heidelberg, Ashita Dhillon, Katrina J. Edwards
C-DEBI Contribution Number: 144
Project Data
Project Data
Last Modified: November 6, 2015
Metagenomic signatures in seafloor rocks and subsurface sediments: East Pacific Rise and Loihi Seamount
Project Maintainers: Esther Singer
Awards > Graduate Fellowships
Proteomic profiling of neutrophilic, iron-oxidizing Mariprofundus ferrooxydans, strain PV-1, grown under different iron sources
Awardee: Roman A. Barco (University of Southern California)
Current Placement: Postdoctoral Researcher, University of Southern California, 2017-
Advisor: Katrina J. Edwards (University of Southern California)
Amount: $64,000.00
Award Dates: August 16, 2011 — August 15, 2013

Abstract

The aim of this proposal is to gain a better understanding of what subsets of proteins are actually being expressed during neutrophilic, microbial iron (Fe)-oxidation. The recently isolated Mariprofundus ferrooxydans, strain PV-1, will be used as a marine model organism to investigate proteomic differences under different Fe substrates: aqueous Fe2+ and solid Fe0. Two-dimensional gel electrophoresis (2D-GE) and shotgun proteomic methods (LC-MS/MS) will be employed to obtain results from the cultures grown under different conditions. The research being proposed would constitute the foundation for the development of diagnostic tools for the accordance, distribution, and activity level of Fe-oxidation, a globally important biogeochemical process at and below the ocean floor.

Related Items

Publications
Publications > Journal Article
Published: September 23, 2011
PLoS ONE
Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium
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
Publications > Proceedings
Published: November 16, 2012
Proceedings of the IODP
Summary of carbon, nitrogen, and iron leaching characteristics and fluorescence properties of materials considered for subseafloor observatory assembly
Authors: Beth N. Orcutt, Roman A. Barco, Samantha B. Joye, Katrina J. Edwards
C-DEBI Contribution Number: 133
Publications > Journal Article
Published: January 16, 2014
Geobiology
Carbon adsorption onto Fe oxyhydroxide stalks produced by a lithotrophic iron-oxidizing bacteria
Authors: Sarah A. Bennett, Brandy M. Toner, Roman A. Barco, Katrina J. Edwards
C-DEBI Contribution Number: 201
Project Data
Project Data
Last Modified: January 13, 2016
Proteomic profiling of neutrophilic, iron-oxidizing Mariprofundus ferrooxydans, strain PV-1
Project Maintainers: Roman A. Barco, Katrina J. Edwards
Awards > Graduate Fellowships
Deep phylogenetic and metagenomic analysis of microbial diversity associated with ferromanganese nodules collected from the South Pacific Gyre
Awardee: Benjamin J. Tully (University of Southern California)
Current Placement: Postdoctoral Research Associate, C-DEBI at University of Southern California, 2014-
Advisor: John F. Heidelberg (University of Southern California)
Amount: $64,000.00
Award Dates: August 16, 2011 — August 15, 2013

The importance of microbial mediation in the biogeochemical cycles of the ocean is well documented. A major source of marine metallic minerals exists as ferromanganese (polymetallic) nodules in the deep ocean (4,000-5,000 m deep). Composed predominantly of iron, manganese, copper, nickel, and zinc, these nodules play a key role in governing the biogeochemical availability of many of these metals in the global ocean. While it is assumed that microorganisms mediate some of the processes that form nodules, it is poorly constrained as to which organisms mediate these processes or how these processes in turn may support microbial metabolisms. We propose using fingerprinting and sequencing methods to examine the microbial community diversity of organism associated with ferromanganese nodule collected from the South Pacific Gyre. Further, because many of the microbial organisms present in the deep-sea are novel and uncultivated, we plan to perform metagenomic analysis to link phylogenetic identity with physiology, with the goal of generating (near-)complete environmental genomes. The proposed research will be the first attempt to determine how the microbiology of deep oceanic nodules shape and are shaped by the environment.

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Publications
Publications > Journal Article
Published: January 1, 2012
Frontiers in Microbiology
Prospects for the study of evolution in the deep biosphere
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
Publications > Journal Article
Published: January 1, 2013
Frontiers in Microbiology
Microbial communities associated with ferromanganese nodules and the surrounding sediments
Authors: Benjamin J. Tully, John F. Heidelberg
C-DEBI Contribution Number: 167
Project Data
Project Data
Last Modified: November 10, 2015
Deep phylogenetic and metagenomic analysis of microbial diversity associated with ferromanganese nodules collected from the South Pacific Gyre
Project Maintainers: John F. Heidelberg, Benjamin J. Tully
Awards > Graduate Fellowships
Constraints on microbial biogeography in hydrothermally active sediments of Guaymas Basin: Energetic limits, physical stressors, and upward compression of metabolic zones
Awardee: Luke J. McKay (University of North Carolina, Chapel Hill)
Current Placement: Assistant Research Professor, Montana State University
Advisor: Andreas P. Teske (University of North Carolina, Chapel Hill)
Amount: $64,000.00
Award Dates: May 1, 2012 — June 30, 2014

Abstract

Shallow subsurface temperatures can reach extreme levels in just 40 cm depth in Guaymas Basin sediments, limiting microbial colonization to thermally tolerable surface sediments. At temperatures beyond approximately 80°C and 100°C, respectively, the 13C-isotopic signatures of microbial anaerobic oxidation of methane and organic matter remineralization appear to be thermally restricted. Putative methane consuming archaea dominate the archaeal clone library while sulfur cycling bacteria and Chloroflexi-related sequences dominate the bacterial clone library. Archaeal clone library data suggest that the ANME-1 Guaymas archaea tolerate high in situ temperatures up to approximately 80°C, thereby gaining an advantage in access to the geothermal methane pool in hot Guaymas Basin sediments. Lastly, the results indicate that in situ thermal and/or geochemical gradients structure archaeal community composition and biogeography more than bacterial biogeography. While the average upper thermal temperature for detectable microbial life by RNA recovery in Guaymas Basin sediments appears to be around 80°C, temperatures may fluctuate by 25°C in as little as a day. Isotopic evidence for microbially mediated methane oxidation is only slight, yet putative methanotrophic archaea are commonly recovered in nearly all samples suggesting they may perform other physiological modes or isotopic signatures are not detectable because of high methane concentrations. High temperature associated archaea appear to be represented by OTUs related to uncultured MCG and ANME-1 Guaymas groups. For bacteria the dominant high temperature associated OTU was phylogenetically associated with the Thermodesulfobacteriaceae. Two of the four main themes of C-DEBI research are “Extent of Life” and “Limits of Life”. Using sediment samples acquired from Guaymas Basin, my C-DEBI research links these two themes by examining how the biogeographical distribution of sedimentary microorganisms is shaped by severe, life-limiting conditions. Although these samples are not from deep sediments, they exemplify deep biogeochemical processes that have been compressed to shallower depths by elevated hydrothermal activity. My research demonstrates how thermal and geochemical regimes interact to control the spatial extent of life by focusing on microbial zonation in an energetically diverse hydrothermal environment. My intention with this research was to accurately describe microbial biogeography and the physicochemical factors controlling it in these unique, compressed sediments, which can be a useful asset in preparation for future IODP sampling procedures and analyses as well as investigations in deep subsurface microbiology around the world.

Related Items

Publications
Publications > Thesis
Published: January 1, 2014
PhD thesis
Microbial Ecology of a man-made oil-spill in the Gulf of Mexico and a natural hydrothermal oil-seep in the Gulf of California
Authors: Luke J. McKay
C-DEBI Contribution Number: 253
Publications > Journal Article
Published: January 22, 2016
Environmental Microbiology Reports
Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California
Authors: Luke J. McKay, Vincent W. Klokman, Howard P. Mendlovitz, Douglas E. LaRowe, Daniel R. Hoer, Daniel B. Albert, Jan P. Amend, Andreas P. Teske
C-DEBI Contribution Number: 293
Publications > Journal Article
Published: February 18, 2016
Frontiers in Microbiology
The Guaymas Basin Hiking Guide to Hydrothermal Mounds, Chimneys, and Microbial Mats: Complex Seafloor Expressions of Subsurface Hydrothermal Circulation
Authors: Andreas P. Teske, Dirk de Beer, Luke J. McKay, Margaret K. Tivey, Jennifer F. Biddle, Daniel R. Hoer, Karen G. Lloyd, Mark A. Lever, Hans Røy, Daniel B. Albert, Howard P. Mendlovitz, Barbara J. MacGregor
C-DEBI Contribution Number: 319
Publications > Journal Article
Published: January 29, 2016
Frontiers in Microbiology
Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin
Authors: Frederick Dowell, Zena Cardman, Srishti Dasarathy, Matthias Y. Kellermann, Julius S. Lipp, S. Emil Ruff, Jennifer F. Biddle, Luke J. McKay, Barbara J. MacGregor, Karen G. Lloyd, Daniel B. Albert, Howard P. Mendlovitz, Kai-Uwe Hinrichs, Andreas P. Teske
C-DEBI Contribution Number: 349
Project Data
Project Data
Last Modified: January 29, 2016
Constraints on microbial biogeography in hydrothermally active sediments of Guaymas Basin: Energetic limits, physical stressors, and upward compression of metabolic zones
Project Maintainers: Luke J. McKay, Andreas P. Teske
Awards > Graduate Fellowships
Working around drilling contamination in deep cores: Costa Rica Margin
Awardee: Amanda J. Martino (Pennsylvania State University)
Current Placement: Assistant Professor, Saint Francis University, 2014-
Advisor: Christopher H. House (Pennsylvania State University)
Amount: $66,000.00
Award Dates: June 1, 2012 — May 31, 2014

Most microbiology work in marine subsurface sediments has been focused in the upper 100-200 meters of sediment, partially because the switchover from Advanced Piston Coring (APC) to Extended Core Barrel (XCB) coring generally occurs around this depth, which leads to large increases in drilling-induced contamination. Molecular studies in deeper samples may be greatly hindered by the potential interferences from these contaminating microbes. This project provides an extensive next-generation sequencing based study coupling the analysis of microbial community composition to great depth in the Costa Rica Margin subseafloor to the analysis of the drilling fluid used in the process of obtaining those samples. In nearly all samples examined, the influence of drilling-fluid in molecular analysis of the sediment samples was very low, even in several samples taken with XCB coring. One sample from 496 mbsf was shown to contain a high proportion of sequences potentially originated from drilling fluid, however, which suggests that it is still important to routinely include comparison to drilling fluid as a control in molecular analyses. This study also provides a first and extensive look at the microbial community composition of the Costa Rica Margin subseafloor from 2 sites on the upper plate of the erosive subduction zone between the Cocos and Caribbean plates. These 2 sites, while in close proximity and sharing many physical and chemical properties, showed distinction in terms of the relative abundances of microbial groups, particularly in the proportion of archaea to bacteria. Additionally, correlations assessed between microbial taxa and geochemistry variables suggest directions for future research into the metabolic capabilities of some uncharacterized subseafloor microbial lineages.

Related Items

Publications
Publications > Thesis
Published: January 1, 2014
PhD Thesis
Assessment and advancement of approaches for the study of subseafloor microbial communitites
Authors: Amanda J. Martino
C-DEBI Contribution Number: 252
Project Data
Project Data
Last Modified: August 30, 2017
Working around drilling contamination in deep cores: Costa Rica Margin
Project Maintainers: Amanda J. Martino
Awards > Graduate Fellowships
Nature of labile and refractory phosphorus pools fueling life in deep sub-seafloor sediments
Awardee: Delphine Defforey (University of California, Santa Cruz)
Current Placement: Associate Editor, Nature Communications, 2016-
Advisor: Adina Paytan (University of California, Santa Cruz)
Amount: $64,000.00
Award Dates: July 1, 2012 — June 30, 2014

Abstract

Phosphorus (P) is an essential nutrient that can limit biological activity in some environments. Yet, many components of its cycle remain unclear, including P uptake and cycling in deep-sea sediments. These are critical, since a significant portion of Earth's prokaryotes thrives in deep marine sediments, which are thought to mainly contain low bioavailable P in mineral phases. This suggests that microorganisms possess mechanisms to utilize recalcitrant P pools. The work performed focuses on identifying possible P sources to the deep biosphere, as well as microbial uptake mechanisms using stable oxygen isotope ratios in phosphate and 31P nuclear magnetic resonance spectroscopy on sediment samples collected during IODP 336 Expedition (North Pond).

Related Items

Publications
Publications > Proceedings
Published: September 2, 2015
Proceedings of the IODP
Data report: characteristics of sedimentary phosphorus at North Pond, IODP Expedition 336
Authors: Delphine Defforey, Adina Paytan
C-DEBI Contribution Number: 256
Publications > Journal Article
Published: February 1, 2017
Limnology and Oceanography: Methods
A new solution 31P NMR sample preparation scheme for marine sediments
Authors: Delphine Defforey, Barbara J. Cade-Menun, Adina Paytan
C-DEBI Contribution Number: 353
Project Data
Project Data
Last Modified: November 7, 2016
A new marine sediment sample preparation scheme for solution 31P NMR analysis
Project Maintainers: Adina Paytan, Delphine Defforey, Barbara J. Cade-Menun
Project Data
Last Modified: November 7, 2016
Phosphorus cycling in ridge-flank sediments
Project Maintainers: Adina Paytan, Delphine Defforey
Project Data
Last Modified: November 7, 2016
Potential phosphorus uptake mechanisms of the deep sedimentary biosphere
Project Maintainers: Adina Paytan, Benjamin J. Tully, Jason B. Sylvan, Delphine Defforey, Barbara J. Cade-Menun, Brandi Kiel Reese, Laura A. Zinke
Awards > Graduate Fellowships
Genomic analyses and microbial cultivations in unexplored sub-seafloor ridge flank and continental margin environments
Awardee: Joseph A. Russell (University of Delaware)
Current Placement: Senior Scientist, MRIGlobal
Advisor: Jennifer F. Biddle (University of Delaware)
Amount: $64,000.00
Award Dates: July 1, 2012 — June 30, 2014

Over the course of two years of C-DEBI support, I have investigated subseafloor microbial ecology in three separate environments; the basaltic crust aquifer underneath the sediments of North Pond, the sediments of North Pond, and the sediments of the Iberian Margin at IODP site U1385. At North Pond, my research was primarily cultivation-based, with enrichments for multiple metabolisms across basalt and sediment samples. Shallow and deep heterotrophic isolates from the sediment column at site U1382B offer an opportunity to ask unique research questions regarding the breakdown of fresher, more labile organic carbon vs. older, more refractory organic carbon. At the Iberian margin, my research was primarily molecular-based, with several enrichment and cultivation efforts initiated after compelling evidence for particular metabolisms associated with individual groups of microbes. Diversity studies using high-throughput sequencing of 16S/18S rRNA amplicons examined the distribution and abundance of bacteria, archaea, and microbial eukaryotes. To further investigate ecological trends and the biology of particular community members, metagenomes were generated from the same DNA pools as the amplicon data.

Related Items

Publications
Publications > Journal Article
Published: May 10, 2016
Frontiers in Microbiology
Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria
Authors: Joseph A. Russell, Rosa León-Zayas, Kelly Wrighton, Jennifer F. Biddle
C-DEBI Contribution Number: 326
Project Data
Project Data
Last Modified: November 19, 2015
Genomic analyses and microbial cultivations in unexplored sub-seafloor ridge flank and continental margin environments
Project Maintainers: Joseph A. Russell, Jennifer F. Biddle
Awards > Graduate Fellowships
Key variables for modeling rates of microbially mediated sulfate reduction
Awardee: Kiana L. Frank (Harvard University)
Current Placement: Assistant Research Faculty, University of Hawaii, 2014-
Advisor: Peter R. Girguis (Harvard University)
Amount: $48,000.20
Award Dates: July 1, 2012 — June 30, 2014

During my tenure as a C-DEBI graduate fellow, my work fell into Research Theme I: Activity in the Deep Subseafloor Biosphere: function & rates of global biogeochemical processes. Few studies have directly measured sulfate reduction at hydrothermal vents, and relatively little is known about how environmental or ecological factors influence rates of sulfate reduction (SR) in vent environments. This work features laboratory studies using radioisotopic 35S-tracer techniques to elucidate rates of microbially mediated sulfate reduction from hydrothermal vents in the Middle Valley and Main Endeavor vent field along the Juan de Fuca Ridge, as well as assessments of bacterial and archaeal diversity, estimates of total biomass and the abundance of functional genes related to sulfate reduction, and in situ geochemistry. The rates of sulfate reduction measured suggest that-within anaerobic niches of hydrothermal deposits-heterotrophic sulfate reduction may be quite common and can contribute substantially to secondary productivity, underscoring the potential role of this process in both sulfur and carbon cycling at vents and the deep subsurface. Direct metabolic rate measurements of sulfate reduction help to facilitate defining key environmental and energetic parameters for microbial community colonization in hydrothermal vents. Better understanding of the metabolic and taxonomic relationship of these endolithic communities in the geochemical context of hydrothermal vents will help to constrain the microbial impact on global biogeochemical cycling.

Related Items

Publications
Publications > Journal Article
Published: March 28, 2013
The ISME Journal
Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents
Authors: Kiana L. Frank, Daniel R. Rogers, Heather C. Olins, Charles Vidoudez, Peter R. Girguis
C-DEBI Contribution Number: 168
Project Data
Project Data
Last Modified: November 19, 2015
Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents
Project Maintainers: Peter R. Girguis, Kiana L. Frank

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