Document 6524205

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Document 6524205

Deep Life Community -‐ The Deep Carbon Observatory – 2014-‐2015 ALFRED P. SLOAN FOUNDATION www.sloan.org | proposal guidelines PROPOSAL COVER SHEET Project Information Principal Investigator Mitchell L. Sogin, Ph.D. 7 MBL Street, Woods Hole MA 02543 mitchellsogin@gmail.com 5085661468 Grantee Organization: Woods Hole Amount Requested: st
Requested Start Date: January 1 , 2014 st
Requested End Date: December 31 , 2015 Deep Life Community-‐ The Deep Carbon Observatory—2014-‐2015 Project Goal The Deep Life Community (DLC) seeks to map the abundance and diversity of subsurface marine and continental microorganisms in time and space as a function of their phylogenomic and biogeochemical properties, and to explore their roles and interactions with the deep carbon cycle. Objectives This proposal will strengthen our nascent research and coordination organization dedicated to achieving DLC’s decadal goals. It will extend molecular studies to a greater number of samples from high-‐value marine and continental sites in order to describe diversity, distribution and functional adaptations of deep life. It will explore life’s interplay with geological processes in the deep subsurface including studies of microbial activities and distributions in hydrogen-‐rich habitats, which favor abiogenic synthesis of methane and higher hydrocarbons. We will: a) Explore the limits of deep life using improved life detection capabilities, b) Develop and apply tracer approaches to track the flow of carbon into biomolecules and cells, and c) Measure the interrelationship between composition of carbonaceous materials and deep life. To achieve these objectives, the DLC must seek additional resources and engage the best deep-‐life researchers from around the globe. Proposed Activities The Census of Deep Life (CoDL) will support marker gene analyses for 1600 new samples or metagenomic analyses of as up to 100 samples. The DLC will cohost a workshop with the Deep Energy Community (DEC) on abiotic H2 generation and will collaborate with DEC on methane isotopologues in biologically produced methane spanning temperatures from 20°C to 120°C. The DLC will use stable-‐ and radioisotope probing to trace the utilization and assimilation of carbon compounds in subsurface environments. The DLC will support laboratory activities and expenses associated with the preparation of compelling research proposals, workshops with the International Ocean Discovery Program (IODP) and the International Continental Scientific Drilling Program (ICDP) for developing biological drilling initiatives, and co-‐funded meetings with the NASA Astrobiology Institute (NAI) or the Center for Dark Energy Biosphere Investigations (C-‐DEBI) to develop new collaborations. This proposal will support DCL-‐wide meetings in 2014 and 2015, and will support DCL-‐wide participation at the 2015 Deep Carbon Observatory (DCO) “all hands” meeting. Expected Products Expected products of these proposed activities include publications about deep subsurface microbes and microbial mediated processes on the cycling of carbon; online molecular data describing deep life diversity and processes; new research proposals to leverage Sloan funding; and DLC-‐dedicated field missions with participation from other DCO communities. Expected Outcomes This proposed activities will generate new insights about diversity, evolution, and processes that govern deep life and its role in the cycling of deep carbon. Finally, it will expand the constituency of the DLC and will enlighten the public about microbes deep underground. PROPOSAL: DEEP LIFE COMMUNITY - THE DEEP CARBON OBSERVATORY
Project Advocates
Co-Principle Investigators:
Mitchell L. Sogin (mitchellsogin@gmail.com)
Kai-Uwe Hinrichs (khinrichs@uni-bremen.de)
Investigators:
Douglas H. Bartlett (dbartlett@ucsd.edu)
Antje Boetius (aboetius@mpi-bremen.de)
Frederick S. Colwell (rcolwell@coas.oregonstate.edu)
Isabelle Daniel (isabelle.Daniel@univ-lyon1.fr)
Steven D’Hondt (dhondt@gso.uri.edu)
Thomas L. Kieft (tkieft@nmt.edu)
Matthew O. Schrenk (schrenkm@ecu.edu)
Advocates:
Fumio Inagaki (inagaki@jamstec.go.jp)
Roland Winter (roland.winter@tu-dortmund.de)
Deep Life Community - The Deep Carbon Observatory – 2014-2015
TABLE OF CONTENT
1 - INTRODUCTION - STATE OF DEEP LIFE RESEARCH AND KEY QUESTIONS ……………….……..4
2 - DEEP LIFE COMMUNITY ORGANIZATION – PARTICIPANT QUALIFICATIONS…………………….6
3 - DLC RESEARCH ACCOMPLISHMENTS – 2012-2013…………………... ……………………….7
3.1 - Progress by the Census of Deep Life.(CoDL) …………..…………………………..7
3.2 - Progress by Deep Life I: Microbial Carbon Transformations in Rock-Hosted Deep
Subsurface Habitats Project (RHC) ...………………………………………………8
4 - THE PROPOSED PROJECT: DEEP LIFE RESEARCH AND COORDINATION NETWORK……………...9
4.1 - CENSUS OF DEEP LIFE – PHASE II-III………………………………………………..10
4.2 - DEEP LIFE II: ROCK-HOSTED COMMUNITIES………………………………………..12
4.2.1 - Metagenomics and Deep Carbon Cycling ……………...………………….12
4.2.2 - Abiotic H2, abiotic organic C, and origins of life. ……...………………….13
4.2.3 - Integration of data sets between studies. ……...…………………………...14
4.3 - LINKING DEEP LIFE TO DEEP ENERGY COMMUNITY INVESTIGATIONS. …………......14
4.4 - NEW FRONTIERS IN DEEP LIFE
………………………………...15
4.5 - PARTNERSHIPS THAT BUILD THE DEEP LIFE COMMUNITY………………………...…17
4.6- SUMMER SCHOOL DEEP MARINE BIOSPHERE ……….………………………..…....….21
4.7 - MBL INFORMATICS COURSE ……………...………………………………..……….21
4.8 - DATA SCIENCE …………………..………………………………………………....22
4.9 – ENGAGEMENT……………………………………………………………………....22
5 - OUTPUT OF RESEARCH PROJECT.………………………………………………………….......22
6 - BUDGET JUSTIFICATION AND LEVERAGING……………………………………..……….…….23
7 - PRIOR SLOAN SUPPORT…………………...………………………..…………….…….......23(7)
8 - BUDGET………………...………………...………………...………………...…………….…24
9 - CURRICULUM VITAE…………………...……………...………………...……….………........25
A - APPENDICES………………...………………...………………...………………...………..…38
A.1 - REFERENCES CITED………………...………………...………………...…………...38
A.2 - DECADAL GOALS………………...………………...………………...……………..39
A.3 - FUNDING THAT SUPPORTS ONE OR MORE DEEP LIFE’S DECADAL GOALS…………. 40
A.3.1 - Funded Projects………………...………………...…..……………...……40
A.3.2 - Pending Leveraged Proposals………………...………..………................42
A.4 - DEEP LIFE COMMUNITY PUBLICATIONS……………………………………...…….43
A.5 - POST DOCTORAL SUPPORT………………...………………...………………......…47
A.6 - MANAGEMENT PLAN ………………...………………...………………................. 48
A.6.1 - MEMBERSHIP OF DEEP LIFE SCIENTIFIC STEERING COMMITTEE……...…...48
A.6.2 – SCIENTIFIC STEERING COMMITTEE ACTIVITIES………………...……....... 48
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PROPOSAL: DEEP LIFE COMMUNITY - THE DEEP CARBON OBSERVATORY
1 - INTRODUCTION - STATE
OF
DEEP LIFE RESEARCH
AND
KEY QUESTIONS. Studies of
terrestrial and marine sediments reveal subsurface microbial ecosystems that harbor ≥1029
organisms with total carbon content possibly equaling all surface life [1, 2].
These deep and
dark biological reservoirs may extend to six km or more beneath the seafloor and continental
surface. Instead of tapping into solar power, members of deep subsurface microbial communities
harvest energy from geofuels or buried, refractory detrital matter, exploiting small disequilibria
between chemical redox states in order to drive the synthesis of macromolecules and biological
reproduction. These processes lead to large-scale transformations of inorganic and organic
compounds with an attendant impact on the deep carbon cycle. Within the deep biosphere, some
organisms survive and grow near the interface of the abiotic and biotic realms, where high
pressures, elevated temperatures and energy limitations require the ability to tolerate and adapt to
extreme conditions. How deep subsurface microbes differ from surface and near surface
organisms remains unknown. Adaptations of deep life to high pressures and temperatures,
limited energy resources, diffusion limited transport of nutrients and other environmental factors
may require different rule sets that govern primary production, competition, succession,
dispersal, and their mode of evolution. First order questions about organisms that inhabit this
largely unexplored environment include: Who is there? How is deep life distributed and what is
its biomass? How do they survive? How quickly do they reproduce and what provides a source
of energy? What factors govern their dispersal patterns and how do they rapidly adapt to a
changing environment? What is their impact on the deep carbon cycle?
The Deep Life Community (DLC), which explores the evolutionary and functional diversity of
Earth’s deep biosphere and its interactions with the carbon cycle, embraces three primary
Decadal Goals: 1) Determine the processes that define the diversity and distribution of deep life
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as it relates to the carbon cycle; 2) Determine the environmental limits of deep life; and 3)
Determine the interactions between deep life and carbon cycling. Each of these goals addresses
aspects of Quantities, Movements, Origins, and Forms (QMOF): Quantities (concentrations of
cells that constitute deep life and its carbon content), Movements (Dispersal and Distribution of
microbial life and its carbon substrates), Origins (Abiotic vs Biotic sources of substrates fueling
deep life) and Forms (Different genotypes and phenotypes, as well as compositional and redox
states of carbon) of deep life. Our research strategy will leverage DLC’s investment in
conducting a global census over time and space for all three domains of life and viruses in both
the marine and continental subsurface. Through omics we seek to explore mechanisms that shape
microbial evolution and dispersal in the deep biosphere and to identify the ecological rules that
shape community structures. Studies of the environmental limits of life employ a combination of
laboratory and field experiments to determine physical and chemical extremes that are
compatible with life. These measurements will inform modeling studies and potentially will
provide clues about differences between the biotic/abiotic interface that may have played a role
in the origins of life. Finally, Deep Life will explore patterns and mechanisms of bioticallymediated carbon transformations in the subsurface and the interaction of these processes with the
surface world. As described below, the DLC has progressed towards exploring the diversity and
distribution of life in marine and continental deep subsurface environments. Laboratory
experiments have investigated pressure limits on microbial survival, and omic studies have
provided insights about the role of microbes in the deep carbon cycle. Despite these
achievements, the DLC faces daunting challenges that require funding beyond what the Sloan
Foundation can provide. This proposal will continue building the DLC, provide resources for
research coordination activities, and support activities that can lead to newly funded initiatives.
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2 - DEEP LIFE COMMUNITY ORGANIZATION – PARTICIPANT QUALIFICATIONS. The 2010 DCO
Deep Life Workshop on Catalina Island California convened by Mitchell Sogin, Katrina
Edwards and Steve D’Hondt set DLC’s initial agenda. Microbiologists, biogeochemists, and
geochemists outlined research goals in the white paper Deep Subsurface Microbiology and the
Deep Carbon Observatory [3]. Major recommendations of the report included surveying the
deep biosphere through a Census of Deep Life (CoDL), investigating deep life’s evolutionary
history, exploring the global distribution of microbes in the deep biosphere, inventorying their
metabolic character, identifying how they have adapted to high pressures and high temperatures,
and determining the influence on microbes on the deep carbon cycle in both continental and
marine subsurface habitats. Fredrick Colwell and Mitchell Sogin developed a CoDL proposal
that the Alfred P. Sloan Foundation funded in late 2010 and the DCO recruited Isabelle Daniel
and Mitchell Sogin to serve as Co-Chairs of the DLC. In June 2011, the steering committee for
Deep Life met in Bremen to review DLC research proposals solicited by the DCO secretariat.
The DLC identified the most important common themes in the proposals and charged Matt
Schrenk and Isabelle Daniel with organizing the Deep Life I: Microbial Carbon Transformations
in Rock-Hosted Deep Subsurface Habitats Project (RHC). This multi-investigator project (with
11 laboratories spanning 7 countries) seeks to describe and quantify the metabolic activities of
microorganisms in the rock-hosted subsurface biosphere. The project includes observational
studies of key understudied deep subsurface environments coupled with experimental
investigations aimed at elucidating the physiological underpinnings of microbial adaptations to
these environments. This research focused on the hypothesis that rock-hosted deep biosphere
communities use abiotically-sourced carbon compounds and that unique high-pressure,
hydrogen-enriched environments shape the deep biosphere communities. In early 2013, Kai-Uwe
Hinrichs joined Mitchell Sogin as Co-Chair of the DLC. Isabelle Daniel remains on the DLC
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steering committee but has also assumed the chair of the Deep Energy Community. The section
CURRICULUM VITAE provides c.v’s of the advocates for this proposal including DLC Steering
Committee members who have led major efforts in Deep Life research projects.
3 - DLC RESEARCH ACCOMPLISHMENTS – 2012-2013. The CoDL and RHC have synergies that
have contributed to remarkable progress over 18 months. Seventeen research groups received
important data from the initial phase of CoDL’s marker gene (rRNA) survey. A second phase
enabled by reduced sequencing costs added sites to the census and offered opportunities for
shotgun metagenome surveys. Eleven laboratories participated in the RHC project. APPENDIX
A.4 provides a list of publications, manuscripts in review, and manuscripts in preparation.
APPENDIX A.3 cites leveraging activities that have supported DLC science.
3.1 - PROGRESS BY THE CENSUS OF DEEP LIFE (CODL) (F. Colwell, M. Sogin)
• Desulforudis audaxviator represents a “keystone species” in subsurface samples from South
African gold mines, seafloor crustal materials, and Great Basin wells and springs.
• A subglacial Icelandic microbiome lacks Archaea and consists of only five microaerophilic
and anaerobic chemolithoautotrophs [4]. This unique subsurface microbial community does
not receive input of energy from the surface (i.e., sunlight or photosynthetically-derived
organic matter) and could serve as an analogue for life in the subsurface of other planets.
• Firmicutes dominate deep methane hydrate zones in the sediments of the Indian Ocean
including zones above, within and below strata that contained hydrates [5]. The absence of
Archaea in these samples - and by inference, methanogens – agrees with prior reports that
concentrations of methane producing microbes must be very low in hydrate-bearing sediments
• Pilot scale geological sequestration of CO2 [6] will utilize deep basalt aquifers that host
diverse bacterial and archaeal communities. Microbes at the depth of planned CO2 injection
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are related to taxa that use hydrogen and single-carbon compounds. The metabolic activity of
these communities could impact long-term stability of carbon sequestered underground.
• High-resolution mineral colonization experiments in the sub-seafloor igneous crust reveal that
mineralogy and mineral chemistry dictate the types and diversity of attached microbes (Smith
et al. in review). Geological formations rich in olivine (e.g., slow-spreading ridges) serve as
hotspots for biological activity in oceanic crust, where biogeochemical processes on crustal
minerals rather than transported products of photosynthesis fuel microbial growth.
3.2 - PROGRESS BY DEEP LIFE I: MICROBIAL CARBON TRANSFORMATIONS IN ROCK-HOSTED
DEEP SUBSURFACE HABITATS PROJECT (RHC)– (Matt Schrenk, Isabelle Daniel, T Kieft)
• Molecular diversity studies, supported by measurements of H2, CH4 - rich and pH, of timeseries samples from active serpentinization environments of uplifted ultramafic oceanic crust
at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California
identified Betaproteobacteria and Clostridales as key taxa. Collaborations with the CoDL and
DOE community sequencing program have identified pathways such as assimilation of small
organic acids and carbon monoxide that putatively control the exchange of carbon and energy
between the deep Earth and the surface environment.
• Coupled molecular and
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C tracer studies of microbial communities in diffuse hydrothermal
fluids collected from the world’s deepest known hydrothermal vents at the Mid Cayman Rise
(MCR) in the Caribbean Sea documented microbial and functional diversity for abundant taxa
related to Methanococcales, Archaeoglobales, and Epsilonproteobacteria. Diffuse fluid
samples from vents located on basaltic and ultramafic substrates between 2000 and 5000 m
water depth hosted taxa typical of more well-known high temperature systems at the deeper
site (Piccard) and taxa that may be involved in methane production at the shallower ultramafic
rock site (Von Damm). These data will provide insight into links between the microbial
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communities and their geochemical environment. Gene sequencing and stable isotope tracer
experiments indicated that methanogenesis from formate occurs at the ultramafic hosted sites,
and is absent from the deeper, higher temperature basalt hosted sites such as Piccard.
• Fluorescently activated cell-sorting and taxonomic-screening of 10 samples from deep
fractures in Precambrian Shield environments of South Africa, Finland, and Canada identified
close relatives of Candidatus Desulforudis audaxviator, which dominated communities in
earlier studies of South African gold mines. To understand the ecology, population genetics,
and biogeography of these microbes in the deep subsurface, the JGI Community Sequencing
Program, will generate draft genome sequences for 200 single-cell genomic preparations.
• The RHC project has isolated and characterized 5-10 new strains of novel, thermophilic,
piezophilic organisms from the MCR and the Precambrian Shield environments. One of the
strains isolated from the MCR grows well at 120 MPa (corresponding to 12 km water depth!).
Physiologic and genomic characterization of these isolates will provide insight into the
adaptations of microorganisms to deep subsurface, high-pressure environments.
• Biophysical and biochemical studies of Shewanella oneidensis adapted in the lab to 2.5 GPa
(comparable to depths of ~75 km), identified two pressure domains. Beyond 500 MPa, the
physiology of the P-adapted S. oneidensis appears to be very different. Quasi Elastic Neutron
Scattering experiments to 200 MPa revealed that the mobility of water across cell membranes
decreases slightly with pressure but is many orders of magnitude less than the decrease in
metabolic activity measured over the same pressure range using X-ray spectroscopy.
4 - THE PROPOSED PROJECT: DEEP LIFE RESEARCH
AND
COORDINATION NETWORK. The
Deep Life Community steering committee has developed a research agenda / networking plan
that leverages advances from the CoDL and the RHC project, and outlines opportunities to
engage initiatives beyond the current umbrella of the Deep Carbon Observatory. This plan
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incorporates new elements that address key objectives in each of the three primary Decadal
Goals (APPENDIX A.2). Beyond scheduled meetings and modest continued funding for the
Census of Deep Life, the DLC must seek sources of funding from other foundations and
agencies. Over the next two years, the DLC will strategically deploy limited resources to support
community building (networking), workshops, logistical expenses of writing new proposals e.g.
travel to other laboratories, small-scale laboratory and field experiments (including the collection
of samples of opportunity and collaborative initiatives with other DCO communities), and the
purchase of affordable equipment or accessories that would further the research agenda of the
DLC. The collective goal is to advance deep life science through discovery based research and
enablement through new successful research proposals. The appendix A.6.2 describes the
mechanisms and guidelines for submitting ideas to the DLC steering committee and the criteria
that we will use to render decisions about resource deployment. Unlike more traditional pilot
project opportunities, decisions about support will largely hinge upon the potential impact on
success of new funding proposals to other agencies or foundations.
4.1 - CENSUS OF DEEP LIFE – PHASE II-III – (A. Boetius, R. Colwell, S. D’Hondt, M. Sogin).
The Census of Deep Life (CoDL), seeks to identify the diversity and distribution of microbial
life in continental and marine deep subsurface environments. This project directly addresses deep
life’s Decadal Goal I to develop a global 3-D census of diversity in continental and marine deep
subsurface environments and to explore mechanisms that govern microbial evolution and
dispersal in the deep biosphere. It contributes to Decadal Goal II by informing us about the
limits of life and metabolic properties necessary to adapt to deep subsurface environments.
CoDL activities integrate closely with the RHC project by providing a taxonomic framework for
describing and comparing deep subsurface communities. With the introduction of shotgun
metagenomics, the CoDL will address key functional questions about deep life.
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During Phase I of the CoDL, 17 laboratories submitted samples for analysis. Phase II of the
project accepted a second round of samples from 12 research groups (in progress) and Phase III
(supported through this proposal) will support a larger number of samples but at significantly
reduced costs. Samples for analysis will continue to include drill cores of rock and sediment,
water pumped from newly drilled wells, seeps in mines, crustal fluids, in situ colonized media
from CORKS as well as samples of opportunity from other DCO communities.
CoDL’s general experimental strategy relies upon massively parallel DNA sequencing for 1)
“marker gene” studies that inform us about the relative abundance and kinds of microbes in a
sample, and 2) shotgun metagenomics investigations that capture information about the
metabolic potential of microbial communities. Both extract information from microbial DNA
from deep subsurface samples. Our original strategy employed pyrosequencing technology but
the CoDL transitioned to the Illumina MiSeq platform, which can reduce sequencing
costs/sample by ~100 fold. The Phase 3 CoDL project will accept many more samples with an
investment of less than $100,000. The CoDL portal on the web site VAMPS
(http://vamps.mbl.edu) will provide access to the data and a wide range of analytical capabilities
including the ability to process data through the QIIME paradigm [7]. Cross project synthesis
activities through formation of a collaborating working group will provide descriptions of
distribution and dispersal patterns for microbes in the deep subsurface.
For metagenomic analyses, the CoDL will take advantage of an Illumina HiSeq platform, which
provides ~6 fold coverage for any 2-4 Mbp genome that accounts for >0.2% of the microbial
genomes in a sample. This information has the potential to provide detailed genotypic
descriptions of the metabolic and functional capabilities of typical communities from deep
subsurface environments. By coupling estimates of community diversity from marker gene
analyses with shotgun metagenomics, we will be able to titrate the amount of shot-gun
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metagenomic sequencing required to infer the functional properties of microbial populations in
deep subsurface communities. With appropriate sample preparation to isolate viral particles, this
technology will support shotgun metagenomic analysis of viral populations.
4.2 - DEEP LIFE II: ROCK-HOSTED COMMUNITIES. Projects listed below are being generously
supported during the current funding cycle. In the 2014-2015 funding period, we anticipate that
the activities by the RHC will be increasingly supported by leveraged funds. The DLC will
deploy additional resources as requested to complete tasks necessary for data synthesis and for
securing funding from outside sources.
4.2.1 - METAGENOMICS
AND
DEEP CARBON CYCLING (M. Schrenk, T. Kieft). In just a few
short years, the CoDL and RHC studies have dramatically improved our understanding of
microbial diversity in deep subsurface environments, spanning both marine and terrestrial realms
and advanced our understanding of the interplay between abiotic, geological processes operating
at depth and deep life, capitalizing upon coincident advances made in the technology of gene
sequencing. These studies have fed into complementary “–omics” approaches, including
metagenomics, transcriptomics, and single cell genomes which have enabled a broad view of
microbial metabolic potential, activity, and population genetics in subsurface environments.
Focused efforts have made headway in the collection and preparation of samples from low
biomass environments and assembly from short sequence reads. Coupled with leveraged
resources, such as the DOE Joint Genome Institute Community Sequencing Program, these
efforts have begun to pay dividends in terms of the accumulation of massive amounts of genomic
data. Automated sequence annotation, using programs such as the MG-RAST server have
permitted the initial high-throughput analysis of these datasets. However, the accurate annotation
of these genes requires verification with reference organisms harboring sequences coding for
bonafide functions. Further, a sequences-specific phylogenomic approach allows for analysis of
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the evolutionary relatedness of these microbial communities. Alignments have been constructed
for several genes expected to be critical for carbon cycling in the deep subsurface (e.g.
methanogenesis, carbon fixation, formate assimilation) and will be expanded to include other
genes related to carbon processing. These alignments will facilitate the rapid analysis of new
metagenomics datasets, expected to be a part of the next phase of the CoDL, and for
phylogenetic analyses relating deep life across habitats. Genomic information gathered by the
RHC will address central goals in the DLC’s agenda but will require additional efforts in
annotation and phylogenetic reconstruction. We anticipate several requests for modest support to
resolve these questions.
4.2.2 - ABIOTIC H2,
ABIOTIC ORGANIC
C,
AND ORIGINS OF LIFE.
(M. Schrenk, T. Kieft, I.
Daniel, D. Bartlett). In certain subsurface settings, deep life is independent of photosynthetically
generated energy and instead relies on abiotic H2 derived from either rock-water reactions [8] or
radiolysis of water [9], or on simple organic C compounds generated abiotically via FischerTropsch-type reactions [10]. Subsurface habitats harboring these chemosynthetic ecosystems
fueled by abiogenic H2 have even been suggested as sites for the origins and early evolution of
life [11]. The RHC project has facilitated a range of research projects that investigate the
physiology and ecology of hydrogen-utilizing subsurface microorganisms, including those
influenced by serpentinization (CROMO and Cayman Ridge) and radiolysis (Witwatersrand
Basin, South Africa), and the DEC focuses on the abiogenic production of organic compounds.
We will strengthen this framework through investigations that link the process of carbon
assimilation in abiotic H2-generating environments with analysis of microbial genomes. The
work will build upon the RHC’s and DLC’s expertise in stable isotope probing, isotope analysis
of various carbon pools from bulk to cellular and molecular levels, and single-cell genomics and
will link studies of carbon reservoirs and fluxes conducted by DE, e.g., at the CROMO site in
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California, USA, and the Bay of Prony site in New Caledonia. We seek to identify microbes that
utilize abiogenically produced H2 and carbon substrates, and to obtain genetic and biochemical
information to reveal evolutionary relationships and metabolic pathways. Beyond explaining
how microorganisms in the deep subsurface assimilate carbon, these analyses will provide a
framework for inferring relationships between the biochemistry of extant systems and origins of
life scenarios in the deep subsurface. 4.2.3 - INTEGRATION OF DATA SETS BETWEEN STUDIES (M. Schrenk, M. Sogin, I. Daniel). The
RHC sub-projects will continue to integrate with each other and the CoML. The Census of Deep
Life will anchor taxonomic descriptions and comparison of deep subsurface ecosystems.
Measurements using similar protocols for stable isotope tracer measurements across each of the
field sites, will allow comparison of the rates and types of operative metabolism. The sharing of
samples and microbial cultures among research teams will facilitate comparative analyses into a
larger synthesis that describes carbon cycling by the rock-hosted microbial biosphere. We seek
to compare microbiomes across all different subsurface realms, including continental vs marine,
rock hosted vs sedimentary, organic rich vs organic poor, hot vs cold.
4.3 - LINKING DEEP LIFE TO DEEP ENERGY COMMUNITY INVESTIGATIONS. During the past few
years, an important synergy has developed between projects pursued in the Rock-Hosted
Communities (RHC) project and the Deep Energy Community (DEC) of the DCO. The RHC
project has made headway in understanding microbial activities and distributions in hydrogenrich subsurface habitats, which favor the abiogenic synthesis of methane and higher
hydrocarbons. In parallel, the DEC has initiated a range of investigations, including fieldwork in
both marine and terrestrial settings and laboratory experiments, to identify sources and signatures
of methane and other hydrocarbons. The process of serpentinization, the aqueous alteration of
ultramafic rocks characteristics of Earth’s upper mantle has become a centerpiece in both types
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of investigations. Likewise, the joint interest in carbon transformations and microbial
communities in subsurface zones associated with the biotic-abiotic interface unifies both DCO
communities and will provide a breeding ground for future collaboration.
Several areas of focus have emerged. Studies in both Deep Life and Deep Energy have strived to
inventory microbial processes and their impact upon carbon biogeochemistry in subseafloor
rocks from locations such as the Mid-Cayman Rise and the Mid Atlantic Ridge. Studies initiated
through the CoDL and the DEC are examining microbes in shallow sea hydrothermal chimneys
in New Caledonia venting volatile-rich, high pH fluids. Scientists in both communities took part
in the Oman Drilling Workshop, co-sponsored by ICDP and DCO, in Palisades, NY in
September 2012. Laboratory experiments in both communities are serving to constrain the
geochemical processes and signatures associated with abiogenic hydrocarbon production, and
how they are intertwined with the deep biosphere. These same processes may ultimately be
operative at the depth limits to the biosphere in the uppermost mantle and lower crust, and in
forearc basins associated with subduction zones. Serpentinization-associated processes may play
important roles in influencing the exchange of carbon and energy between the deep Earth and the
biosphere. Furthermore, these mineral catalytic systems are believed to have played a role in the
origins and early evolution of life. Serpentinizing environments inhabited by microorganisms
may contain biochemical relicts of ancient prebiotic processes.
We propose to build upon these efforts with a series of strategic investments, e.g., in the form of
collaborations between DLC and DEC, including:
• Co-hosting a workshop with the DEC on the topic of abiotic H2 generation and the associated
potential to support life. This workshop will highlight both geochemical and biochemical
aspects of the process and its impact on the carbon cycle through time and be hosted at a site
near a serpentinizing ophiolite (e.g. Portugal, Northern Italy). (I. Daniel, M. Schrenk)
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• Collaboration on methane isotopologues (K.-U. Hinrichs; with B. Sherwood Lollar, DE) –
DLC will collaborate with DEC on the examination of clumped isotopes in biologically
produced methane covering a temperature range from 20°C to 120°C. A good fraction of this
temperature range overlaps with temperatures at which methane may be formed abiotically in
subsurface systems. Examination of the associated signals will be crucial for the development
of methane’s clumped isotopes as an indicator of its formation pathway.
• Cataloguing microbial abundance and diversity (M. Schrenk, R. Colwell, T. Kieft, D. Bartlett,
I. Daniel) in sites that are currently being investigated by the DEC, but which lack a
microbiological component (e.g. gas fluxes studies of serpentinizing ophiolites, carbonated
seafloor rocks, active drilling projects, etc.). Cultivation efforts will allow physiological
studies at high pressures in the laboratory.
4.4 - NEW FRONTIERS IN DEEP LIFE (K.-U. Hinrichs). The DLC has identified a number of key
tasks of direct relevance to our ability to reach our decadal goals. For example, we must improve
life detection capabilities, develop new tracer approaches to track the flow of carbon into
biomolecules and cells, and advance our ability to measure the interrelationship between
composition of carbonaceous materials and deep life. The DLC Steering community will
encourage submission of ideas for modest short-term support that will address these and other
relevant / meritorious efforts with high potential to attract new funding from other agencies and
foundations. (see section A. 6.2.).
• Investments in stable- and radioisotope probing experiments, for example in the context of the
RHC project, to trace the utilization and assimilation of carbon compounds commonly found
in subsurface environments (e.g. CO2, formate, acetate, methane) linked with single-cellgenomic approaches to query their genetic potential and diversity.
16
• Generation of biochemical profiles from novel microbial isolates obtained from subsurface
ecosystems, including lipid biomarkers, sporulation-related molecules, and Raman
spectroscopic signatures that can inform and expand upon geochemical studies [12].
• Improving life detection capabilities in order to differentiate between live and dead cells, to
develop and implement molecular markers diagnostic of active cells, and to reduce detection
limits of cellular and molecular life markers. Future initiatives targeting the biotic-abiotic
interface (see below) will inherently depend on these improvements.
• Advancing our quantitative and qualitative understanding of the relationship between deep life
and cycling of carbon. For example, the impact of deep life on the fluxes and redox state of
carbon entering subduction zones [13] as well as the influence of deep subseafloor life on
oceanic carbon budgets are poorly constrained. Likewise, the biochemical mechanisms
associated with the microbial utilization of kerogen, Earth’s largest organic carbon pool, are
essentially unknown. We hypothesize that structural properties of kerogen strongly influence
the release kinetics of metabolizable smaller carbon compounds and are thus intimately linked
to the activity of deep heterotrophic life. The DLC will support field and experimental studies
targeting the detection, biochemical mechanisms and kinetics of microbially-induced
structural modification of organic matter in the subsurface using modern mass spectrometry,
spectroscopy, NMR, rate assays, metabolomics and genomics approaches.
As described above under 4 - THE PROPOSED PROJECT: DEEP LIFE RESEARCH AND COORDINATION
NETWORK, initiating and developing these frontiers may require seed funding to capture
preliminary data for new applications to foundations and agencies. Appendix A.6.2 STEERING
COMMITTEE ACTIVITIES. Expanding Deep Life Support; for selection mechanism and criteria.
4.5 – STRATEGIC PARTNERSHIPS
THAT BUILD THE
DEEP LIFE COMMUNITY. The Integrated
Ocean Drilling Program (IODP) and the International Continental Scientific Drilling Program
17
(ICDP) support expensive scientific field projects that drill into the subsurface. IODP and ICDP
have sponsored drilling for biologically useful samples that led to important findings that
appeared in high profile research papers. The path to funding drilling from these organizations is
arduous and highly competitive. We envision multiple avenues for DCO to work with IODP and
ICDP to foster further deep carbon-relevant studies that involve deep life. These range from
small studies with short lead times to long-term development of a transformational combined
marine/continental drilling projects that address DL Decadal Goals. Deep Life proposes to
leverage IODP and ICDP funding in support of biological studies in three ways:
• DLC support (up to $10K inclusive of travel, supplies e.g. drilling fluid tracers and lab
expenses) for PIs and/or their students to join near term deep drilling projects (<1 year in the
future) that have a high potential to generate biologically useful samples, but that currently
have no participating biologists on board. This modest level of support will supplement
existing dedicated funding opportunities on the national level for post-expedition research
available in several countries (e.g., small science-directed grants from U.S. Science Support
Program with the Consortium of Ocean Leadership) and could also allow support of DLC
investigators to participate in non-IODP/non-ICDP deep drilling programs that access the
subsurface (e.g., US Department of Energy related projects).
• Workshops to develop new proposals. Deep Life will fund workshops either directly at ~$30k
or with ~$15k to match IODP or ICDP funds, e.g. for so-called Magellan Workshops to
develop deep biosphere-inspired drilling projects that often result in full drilling proposals to
IODP or ICDP, or to initiate / strengthen the microbiological component of existing proposals
previously designed from a geological perspective. These will be multidisciplinary but will
have deep life and deep carbon as central themes. Smaller workshops will support
participation of ~five DLC members to develop projects of opportunity in the framework of
18
IODP via so-called ancillary project letters (APL) that seek to take advantage of scheduled
deep drilling expeditions with no obvious link to DL but which could be extended by a DLdedicated hole. We will also support joint workshops with the NASA Astrobiology Institute
(NAI) and the Center for Dark Energy Biosphere Investigations (C-DEBI) to develop
collaborative projects that span marine and continental subsurface systems.
• We will also explore the concept of merging IODP and ICDP support for drilling an onshoreoffshore transect to address scientific questions that straddle continental marine boundaries.
IODP and ICDP achieved this while coring the New Jersey Margin, [14] and scientific
questions involving processing of carbon in the deep biosphere across marine/continental
gradients could warrant such an ambitious drilling effort. As just one example, high-latitude
sites where permafrost and methane hydrates sensitive to temperature change link the deep
biosphere to the planet’s surface along a continental/marine transect [15]. The DLC will start
this long-term (ca. 6-year) team-building, fund-raising effort by co-organizing a workshop and
soliciting funding and participation from other DCO Communities, as well as IODP, ICDP,
NAI, and C-DEBI to develop collaborative projects that span marine and continental
subsurface systems. Products from the workshops include accelerated involvement of DLC
researchers in ongoing expedition planning, alignment of expedition research questions with
the DL Decadal goals, identification of essential scientific disciplines and key teams for
addressing those questions, and a workable plan for funding a PI or small group of PIs (e.g.,
from NSF, the Moore Foundation, the Keck Foundation) to develop full proposals to IODP
and ICDP and to advocate with these organizations and funding agencies for support. DLC
will assign liaisons with IODP and ICDP who will maintain an active list of current projects
from these two programs that could serve the DLC and vice versa.
19
• With participation of representatives from the DE and RF communities, the DLC will prepare
and lead a deep ocean drilling proposal (submission of a pre-proposal is schedule for Oct 1,
2013) to utilize DV Chikyu for probing the presumed biotic/abiotic temperature interface in
deeply buried, geothermally heated subseafloor sediments in the Shikoku Basin off Japan. At
two sites that have been previously drilled during ODP Leg 190 (Sites 1173 and 1174), the
critical temperature zone between 80 and 140°C could be probed over a several hundred
meters at a total subseafloor depth of less than 1 km. Previous initial studies of deep life at
these sites by John Parkes and colleagues [16, 17] have demonstrated overlapping zones of
deep life and abiotic, thermal processes that supply substrates and thereby potentially
stimulate microbial communities. Based on existing cellular count data [18] however, the
subsurface strata in which sterilization is likely to occur has not been possible due to high
detection limits on the order of around 105 cells/mL. This location provides an excellent
opportunity to determine the temperature limit in a sedimentary subseafloor microbial
ecosystem and characterize the zones where life goes extinct. A dedicated expedition with a
science team dedicated to DL and DE objectives would benefit from the advances in deep life
investigative strategies made during the last decade. Fundamental research goals could be
accomplished at this location; these include “constraining the T-limit of life in the sedimenthosted subseafloor; studying the relationship of abiotic chemical reactions at high T and
biology; the physical and chemical characterization of horizons where life becomes extinct.
Constraining the deepest limits of life is one of the most fundamental questions for the DLC
community (Decadal Goal 2). The discoveries resulting from this would be of great interest to
geoscientists, life scientists and astrobiologists and the public.
• Partnerships with private industry. Both the mining and oil and gas industries offer
opportunities for exploring deep microbial life by providing access to sample cores, drilling
20
fluids, or resources for analysis. For example, S. D’Hondt and M. Sogin are working with
ExxonMobil Upstream Research to develop an exploratory project to study microbial
community structure in a wide range of subsurface and surface environments. The project will
utilize sequencing technologies described for the CoDL to analyze samples from globally
distributed reference sites collected by different IODP expeditions and oceanographic
expeditions. ExxonMobil Upstream Research will provide $250,000 for a pilot project and if
successful will significantly expand the project over the next decade.
4.6. - SUMMER SCHOOL DEEP MARINE BIOSPHERE. DL co-chair Kai-Uwe Hinrichs will organize
the 2014 ECORD (European Consortium of Ocean Research Drilling” summer school
“Subseafloor Biosphere: recent advances and future challenges” at MARUM, University of
Bremen. This 8th annual ECORD summer school will provide a unique program of training for
30 international graduate students and postdocs working in the broader DLC. The program
consists of one week of lectures by international experts, many of them directly associated with
DLC, and a second week of “virtual ship” experience with hands-on laboratory work that
includes methods such a microbial cell counts and sediment core descriptions, supervised by
scientist and staff from the Bremen IODP core repository (leveraging: $32,000 in funds by
ECORD and MARUM to support travel of international lecturers and the virtual ship experience.
4.7 - MBL INFORMATICS COURSE.
M.L. Sogin will direct the course “Strategies and
Techniques for Analyzing Microbial Population Structures”. This 10-day immersion course will
focus on design and analysis of marker gene and shotgun metagenomic projects for advanced
graduate students, postdoctoral fellows and established investigators who seek to leverage the
power of massively-parallel DNA sequencing technologies for investigations of microbial
communities from a range of environments that span the deep subsurface to the human
microbiome.
21
4.8 - DATA SCIENCE. Mitch Sogin serves as the liaison to the Data Science Advisory Committee
led by Peter Fox. The DLC stands ready to contribute meta data and information about samples
and projects to the Data Science Group. The CoDL and associated genomic investigations
require data capabilities that extend beyond the scope of the Data Science Group. Instead, the
WEB site VAMPS (http://vamps.mbl.edu) provides an analytical platform for analysis and
visualization of marker gene surveys. It offers a portal that links all metadata including detailed
project descriptions to the large molecular datasets. It also provides functional ties to the QIIME
analysis pipeline and soon will link into the Earth Microbiome Project through VAMPS and
QIIME. Shotgun metagenomic data will be submitted by users for analysis on the MGRAST
platform [19]. The DLC will follow a data release policy that requires release of data within 9
months of generation of immediate release of data that appears in published manuscripts.
4.9 – ENGAGEMENT. Steve D’Hondt serves as the Liaison to the Engagement team led by Sara
Hickox, both at URI-GSO. He will convey information about scientific developments/successes,
new collaborations, workshops, and DLC meetings to the Engagement team. Steve D’Hondt has
led IODP expeditions and is co-PI on the C-DEBI Science and Technology Center.
5 - OUTPUT OF RESEARCH PROJECT
• Expanded opportunities for students and postdocs to study deep life
• Two intensive training courses (informatics and deep marine biosphere)
• Expanding the international DL community to include the best deep life scientists
• Development of novel methods for identifying biosignatures in the deep subsurface
• Quantification of live vs. dead, active vs. inactive, and vegetative cells vs. spores
• Document and characterize abiotically derived carbon assimilation in serpentinization
environments in collaboration with the Deep Energy Directorate including methane
isotopologue studies to discriminate biotic from abiotic methane in the deep subsurface
• Document how deep subsurface life adapts and evolves through evolutionary genomics
22
• Inventory of organic C forms in select deep marine and continental sites
• Identification of microbes metabolizing those organic C compounds
• Extend the CoDL to include other sites and those under investigation by DCO communities.
• Addition of a microbiological component to non-biologically oriented subsurface projects
• New biology-driven IODP and ICDP deep scientific drilling projects
• Will perform a cross project synthesis of life’s distribution in the deep subsurface
• Publication of key scientific findings in open access journals
6 - BUDGET JUSTIFICATION
AND
LEVERAGING. In contrast to the DLC’s research activities
enabled by generous funding from the Alfred P. Sloan Foundation, this proposal describes a
strategy for securing resources necessary to realize Deep Life’s primary Decadal Goals within
the next eight to ten years. It builds upon research success over the past two years and the
growing interest in Deep Life. We describe a science plan that will require significantly greater
resources – some of which are already in hand. The Deep Life has community has identified
~$26,000,000 to fund science that addresses some of our primary decadal goals (See Appendix
A.3). The budget in this proposal will sustain CoDL activities, build the Deep Life community
through a modest size annual meeting, fund Steering committee activities, support workshops
and data synthesis groups, and participation in the 2015 DCO meeting. We have also reserved
significant resources for to support travel, workshops, and small-scale science projects for Post
Doctoral Students, Graduate Students and Investigators who seek to advance the decadal goals of
the DLC.
The BUDGET provides full details and Appendix A.6.2 STEERING COMMITTEE
ACTIVITIES describes the rationale for allocating resources, the application mechanism, review
criteria and the review process for the funding of DLC activities.
7 - PRIOR SLOAN SUPPORT: See - 3 – DLC RESEARCH ACCOMPLISHMENTS – 2012-2013. page 7
23
8 - BUDGET
9 - CURRICULUM VITAE
Kai-Uwe Hinrichs Ph.D. – Co-PI.
Dean and Professor, Department of Geosciences; Head, Organic Geochemistry Group (Hinrichs
Lab), MARUM Center for Marine Environmental Sciences, University of Bremen, Germany
Education and Training
1994
Diploma (equiv. to M.Sc.), Chemistry, Institute for Chemistry and Biology of
the Marine Environment (ICBM), U Oldenburg, Germany.
1997
Ph.D., ICBM, U Oldenburg, Germany, thesis in Organic Geochemistry.
Appointments
1994-1997
Research Assistant, ICBM, University of Oldenburg
1997-2000
Postdoctoral Investigator/Fellow, Dept. of Geology & Geophysics, WHOI
2000-2002
Assistant Scientist, tenure-track, Dept. of Geology & Geophysics, WHOI
2002-2004
Professor (C3, tenured), Dept. of Geosciences, U Bremen
2004-2010
Adjunct Scientist, Dept. of Geology & Geophysics, WHOI
2004-present Full Professor (W3 with tenure), Dept. of Geosciences, U Bremen
Honors
2000
2009
2011
Fellow, Hanse Institute of Advanced Studies, Delmenhorst, Germany
Advanced Grant by the European Research Council, 2.9 M€
Gottfried Wilhelm Leibniz Price (Germany’s most prestigious res. prize), 2.5M€
Representative Publications
(senior/first author contributions only, out of currently 99 peer-reviewed)
Hinrichs, KU, Hayes, JM, Sylva, SP, Brewer, PG, and DeLong, EF Methane-consuming
archaebacteria in marine sediments. Nature, 398, 802-805. (1999)
Hinrichs KU, Hmelo LR, and Sylva, SP Molecular fossil record of elevated methane levels in
late Pleistocene coastal waters, Science, 299, 1214-1217. (2003)
Sturt, HF, Summons, RE, Smith, KJ, Elvert, M, and Hinrichs, KU Intact polar membrane lipids
in prokaryotes and sediments deciphered by ESI-HPLC-MSn – new biomarkers for
biogeochemistry and microbial ecology. Rap Comm Mass Spectr, 18, 617-628. (2004)
Hinrichs, KU, Hayes, JM, Bach, W, Spivack, A, Hmelo, LR, Holm, N, Johnson, CG, Sylva, SP
Biological formation of ethane and propane in the deep marine subsurface. PNAS, 103, 1468414689. (2006)
Biddle, JF, Lipp, JS, Lever, M, Lloyd, K, Sørensen, K, Anderson, R, Fredricks, HF, Elvert, M,
Kelly, TJ, Schrag, DP, Sogin, ML, Brenchley, JE, Teske, A, House, CH, Hinrichs, KU
Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. PNAS, 103, 38463851. (2006)
Lipp, JS, Morono, Y, Inagaki, F, Hinrichs, KU Significant contribution of Archaea to extant
biomass in marine subsurface sediments. Nature, 454, 991-994. (2008).
24
Heuer, VB, Pohlman, JW, Torres, ME, Elvert, M, Hinrichs, KU The stable carbon isotope
biogeochemistry of acetate and other dissolved carbon species in deep sub-seafloor sediments at
the northern Cascadia Margin. Geochim Cosmochim Acta, 73, 3323-3336. (2009)
Schubotz, F, Wakeham, SG, Lipp, JS, Fredricks, HF, Hinrichs, KU Detection of microbial
biomass by intact membrane lipid analysis in the water column and surface sediments of the
Black Sea, Env Microbiol, 11, 2720-2734. (2009)
Sepúlveda, JC, Wendler, J, Summons, RE, Hinrichs, KU Rapid resurgence of marine
productivity at the Cretaceous-Paleogene mass extinction event, Science, 326, 129-132. (2009)
Schubotz, F, Lipp, JS, Elvert, M, Hinrichs, KU, Stable carbon isotopic compositions of intact
polar lipids reveal complex carbon flow patterns among hydrocarbon degrading microbial
communities at the Chapopote asphalt volcano, Geochim Cosmochim Acta, 75, 4399-4415.
(2011)
Schmidt, F, Koch, B, Elvert, M, Schmidt, G, Witt, M, Hinrichs, KU Diagenetic transformation
of dissolved organic nitrogen compounds under contrasting sedimentary redox conditions in the
Black Sea, Env Sci Tech, 45, 5223-5229. (2011)
Rossel, PE, Elvert, M, Ramette, A, Boetius, A, Hinrichs, KU Factors controlling the distribution
of anaerobic methanotrophic communities in marine environments: evidence from intact polar
membrane lipids, Geochim Cosmochim Acta, 75, 164-184. (2011)
Kellermann, MY, Wegener, G, Elvert, M, Yoshinaga, MY, Lin, YS, Holler, T, Mollar, XP,
Knittel, K, Hinrichs, KU Autotrophy as predominant mode of carbon fixation in thermophilic
anaerobic methane-oxidizing microbial communities, PNAS, 109, 19321-19326. (2012)
Liu, XL, Lipp, JS, Simpson, JS, Lin, YS, Summons, RE, Hinrichs, KU Mono- and dihydroxyl
glycerol gibiphytanyl glycerol tetraethers in marine sediments: identification of both core and
intact polar lipid forms, Geochim Cosmochim Acta, 89, 102-115. (2012)
Lin, YS, Lipp, JS, Elvert, M, Holler, T, Hinrichs, KU Assessing production of the ubiquitous
archaeal diglycosyl tetraether lipids in marine subsurface sediment using intramolecular stable
isotope probing, Environ Microbiol, 15, 1634-1646. (2013)
Lever, MA, Rouxel, O, Alt, JC, Shimizu, N, Ono, S, Coggon, RM, Shanks, WC, Lapham, L,
Elvert, M, Prieto-Mollar, X, Hinrichs, KU, Inagaki, F, Teske, A Evidence for microbial carbon
and sulfur cycling in deeply buried ridge flank basalt, Science, 339, 1305-1308. (2013)
Xie, S, Lipp, JS, Wegener, G, Ferdelman, TG, Hinrichs, KU, Turnover of microbial lipids in the
deep biosphere and growth of benthic archaeal populations, PNAS, 110, 6010-6014. (2013)
Mitchell L. Sogin, Ph.D Co-PI.
Director, Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA
1967
University of Illinois, Urbana B.S. Chemistry and Microbiology
1969
University of Illinois, Urbana M.S. Industrial Microbiology
1972
University of Illinois, Urbana Ph.D., Microbiology & Molecular Biology
25
Appointments
1972-1976
National Jewish Center, Denver, CO. Postdoctoral NIH Fellowship
1976-1989
Senior Staff Scientist, National Jewish Center, Denver, CO.
1980-1986
Assist. Professor, University of Colorado Health Sciences Center
1987-1989
Assoc. Professor, University of Colorado Health Sciences Center
1986-1999
Associate Fellow, Canadian Institute for Advanced Research
1997-1998
Visiting Miller Research Professor, UC Berkeley
1989-present Senior Scientist, Marine Biological Laboratory, Woods Hole, MA
1996-present Director of Josephine Bay Paul Center for Comparative Molecular Biology and
Evolution at the MBL.
2004-present Professor (MBL), Department of Molecular Biology, Cell Biology and
Biochemistry, Brown University, Providence, RI
Honors
1992
1993
1995
9/96-present
1998-present
1998-present
2007
Division Lecturer - American Society for Microbiology
Stoll Stunkard Award - American Society of Parasitologists
Elected Chairman - Division R, American Society of Microbiologists
Fellow of the American Academy of Microbiology
Fellow of the American Academy of Arts and Sciences
Fellow of the American Association for the Advancement of Science
American Society for Microbiology – Roger Porter Award.
Representative Publications (230 TOTAL)
Biddle, J.F., J.S. Lipp, M.A. Lever, K.G. Lloyd, K.B. Sørensen, R. Anderson, H.F. Fredricks, M.
Elvert, T.J. Kelly, D.P. Schrag, M.L. Sogin, J.E. Brenchley, A. Teske, C.H. House and K.-U.
Hinrichs. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc.
Natl. Acad. Sci. USA 103(10): 3846-3851 (2006).
Sogin, M.L., H.G. Morrison, J.A. Huber, D. Mark Welch, S.M. Huse, P.R. Neal, J.M. Arrieta,
and G.J. Herndl. Microbial diversity in the deep sea and the under-explore "rare biosphere".
Proc. Natl. Acad. Sci. USA 103(32): 12115-12120 (2006)
Morrison, H.G., A.G. McArthur, F.D. Gillin, S.B. Aley, R.D. Adam, G.J. Olsen, A.A. Best, Z.
Cande, F. Chen, M.J. Cipriano, B.J. Davids, S.C. Dawson, H.G. Elmendorf, A.B. Hehl, M.E.
Holder, S.M. Huse, U.U. Kim, E. Lasek-Nesselquist, G. Manning, A. Nigam, J.E. Nixon, D.
Palm, N.E. Passamaneck, A. Prabhu, C.I. Reich, D.S. Reiner, J. Samuelson, S. G.Svard,
M.L.Sogin. Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia.
SCIENCE 317:1921-1926. (2007)
Huber, J.A., D.M. Welch, H.G. Morrison, S.M. Huse, P.R. Neal, D.A. Butterfield and M.L.
Sogin. Microbial Population Structures in the Deep Marine Biosphere. SCIENCE 318:97-100
(2007)
Santelli, C.A., B.N. Orcutt, E. Banning, W. Bach, C.L. Moyer, M.L. Sogin, K. J. Edwards.
Abundance and diversity of microbial life in the ocean crust, Nature 453: 653-656 (2008).
Huber, J.A., H.G. Morrison, S.M. Huse, P.R. Neal, M.L. Sogin, and D.B. Mark Welch. Effect of
PCR amplicon size on assessments of clone library microbial diversity and community structure.
Environmental Microbiology 11(5): 1292-1302 (2009).
Bodaker, I, I. Sharon, M.T. Suzuki, R. Feingersch, M. Shmoish, E. Andreishcheva, M.L. Sogin,
26
M. Rosenberg, M.E. Maguire, S. Belkin, A. Oren, O. Be´ja. Comparative community genomics
in the Dead Sea: an increasingly extreme environment. ISME J. 4: 399-407 (2009)
Brazelton, W.J., M.L. Sogin, and J.A. Baross, Multiple scales of diversification within a single
population of archaea in a hydrothermal vent biofilm. Environmental Microbiology, 2(2): 236242 (2010).
Hasegawa, Y., J.L. Mark Welch, A.Valm, C. Rieken, M.L. Sogin, and G. Borisy. Imaging
marine bacteria with unique 16S rRNA V6 sequences by fluorescence in situ hybridization and
spectral analysis. 27(3): 251-260 (2010)
Brazelton, W.J., K.A. Ludwig, M.L. Sogin, E.N. Andreishcheva, D.S. Kelley, C. Shen, R.L.
Edwards, J.A. Baross. Archaea and bacteria with surprising microdiversity show shifts in
dominance over 1000-year time scales in hydrothermal chimneys. Proc. Natl. Acad. Sci. USA,
107: 1612-1617 (2010).
Huse, S.M., D. Mark Welch, H. G. Morrison, M.L. Sogin, Ironing Out the Wrinkles in the Rare
Biosphere. Environmental Microbiology 12(7): 1889-1898 (2010).
Huber, J., Cantin, H., Huse, S., Mark Welch, D., Sogin, M.L., Butterfield, D. Isolated
communities of Epsilon-proteobacteria in hydrothermal vent fluids of the Mariana Arc
seamounts. FEMS Microbiology Ecology, 73:538-549 (2010).
Zinger L, L.A. Amaral-Zettler, J.A. Fuhrman, M.C. Horner-Devine, S.M. Huse, D.B. Mark
Welch, J.B.H. Martiny, M.L. Sogin, A. Boetius, A. Ramette. Global Patterns of Bacterial BetaDiversity in Seafloor and Seawater Ecosystems PLoS ONE 6(9): e24570.
doi:10.1371/journal.pone.0024570 (2011).
Gobet, A., S.I. Bo ̈er, S.M. Huse, J.E.E. van Beusekom, C. Quince, M.L. Sogin, A. Boetius A.,
Ramette, A. Diversity and dynamics of rare and of resident bacterial populations in coastal
sands. ISME Journal, 6:542-553 (2012).
Siam, R., G.A. Mustafa, H. Sharaf, A. Moustafa, A. Ramadan, A. Antunes, V.B. Bajic, U. Stingl,
N.G.R. Marsis, M.J.L. Coolen, M.L. Sogin, A.J. Ferreira, H. El-Dorry. Unique Prokaryotic
Consortia in Geochemically Distinct Sediments from Red Sea Atlantis II and Discovery Deep
Brine Pools. PLOS One. 7(8), e42872 (2012).
Amend, A.S., T.A. Oliver, L.A. Amaral-Zettler, A. Boetius, J.A. Fuhrman, M. Claire HornerDevine, S.M. Huse, D.B. Mark Welch, A.C. Martiny, A. Ramette, L. Zinger, M.L. Sogin, J.B.H.
Martiny.. Macroecological patterns of marine bacteria on a global scale. Journal of
Biogeography. DOI: 10.1111/jbi.12034 (2012).
Sul, W.J., T.A. Oliver, H.W. Ducklow, L.A. Amaral-Zettler, M.L. Sogin. Marine bacteria exhibit
a bipolar distribution. PNAS. 110(6) 2342-2347 (2013).
Eren, A. M. H.G. Morrison, S.M. Huse and M.L. Sogin, DRISEE Overestimates Errors in
Metagenomic Sequencing Data, Briefings in Bioinformatics. In press (2013).
Eren, A.M., J.H. Vineis, H.G. Morrison and M.L. Sogin. A Filtering Method to Generate High
Quality Short Reads Using Illumina Paired-End Technology. PLOS ONE. In press (2013)
Douglas H. Bartlett Ph.D. Co-I.
27
Professor, Scripps Institution of Oceanography, La Jolla, CA
1979 Valparaiso University, Biology B.S.
1985 University of Illinois, Molecular Biology Ph.D.
Appointments
1985-1987
The Agouron Institute, Postdoctoral Scholar
1987-1989
The Agouron Institute, Research Scientist
1989-1995
Scripps Institution of Oceanography, Assistant Professor
1995-2001
Scripps Institution of Oceanography, Associate Professor
2001-Present Scripps Institution of Oceanography, Professor
Vezzi, A., Campanaro, S., D’Angelo, M., Simonato, F., Vitulo, N., Lauro, F. M., Cestaro, A.,
Malacrida, G., Simionati, B., Cannata, N., Romualdi, C., Bartlett D. H., and Valle, G. Life at
depth: Photobacterium profundum genome sequence and expression analysis. Science 307:14591463. 2005.
Lauro, F. M., Tran, K. , Vezzi, A., Vitulo, N., Valle, G. , Bartlett, D. H. Large-scale transposon
mutagenesis of Photobacterium profundum SS9 reveals new genetic loci important for growth at
low temperature and high pressure. J. Bacteriol. 190:1699-1709. 2008.
Nagata, T., Tamburini, C., Arístegui, J., Baltar, F., Bochdansky, A., Fonda-Umani, S., Fukuda,
H., Gogou, A., Hansell, D. A., Hansman, R. J., Herndl, G. J., Panagiotopoulos, C., Reinthaler,
T., Sohrin, R., Verdugo, P., Yamada, N., Yamashita, Y., Yokokawa, T., Bartlett, D. H. Emerging
concepts on microbial processes in the bathypelagic ocean–ecology, biogeochemistry, and
genomics. Deep-Sea Research II 57: 1519-1536. 2010.
Yoshioka, H., Maruyama, A., Nakamura, T., Higashi, Y., Fuse, H., Sakata, S., Bartlett, D. H.
Activities and distribution of methanogenic and methane-oxidizing microbes in marine
sediments from the Cascadia Margin. Geobiology 8:223-233. 2010.
Eloe, E. A., Malfatti, F., Gutierrez, J., Hardy, K., Schmidt, W. E., Pogliano, K., Pogliano, J.,
Azam, F. and D. H. Bartlett.. Isolation and characterization of the first psychropiezophilic
Alphaproteobacterium. Appl. Environ. Microbiol. 77:8145- 8153. 2011
Oger, P., Sokolova, T. G., Kozhevnikova, D. A., Chernyh, N. A., Bartlett, D. H., BonchOsmolovskaya, E. A., Lebedinsky, A. V. Complete genome sequence of the hyperthermophilic
archaeon Thermococcus sp. AM4 capable of organotrophic growth and growth at the expense of
hydrogenogenic or sulfidogenic oxidation of carbon monoxide. J. Bacteriol. 193:7019-7020.
2011.
Eloe, E. A., Fadrish, D. W., Novotny, M., Zeigler Allen, L., Kim, M., Lombardo, M.- J., YeeGreenbaum, J., Yooseph, S., Allen, E. A., Lasken, R., Williamson, S. J., Bartlett, D. H. Going
deeper: metagenome of a hadopelagic microbial community. PLoS ONE. 6: e20388. 2011.
Eloe, E., Shulse, C. N., Fadrosh,D. W., Williamson, S. J., Allen, E. E. and Bartlett, D. H.
Compositional differences in particle-associated and free-living microbial assemblages from an
extreme deep-ocean environment. Environ. Microbiol. Reports. 3: 449–458. 2011.
Campanaro, S, DePascale, F., Telatin, A., Schiavon, R., Bartlett, D. H. and Valle, G. The
transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR
28
mutant and its parental strain. BMC Genomics 13: article 5672012.
Filip Meersman, Isabelle Daniel, Douglas H. Bartlett, Roland Winter, Rachael Hazael and Paul
F. McMillan. High-pressure biochemistry and biophysics. In Deep Carbon (R. M. Hazen, ed.).
Mineralogical Society of America and The Geochemical Society (Chantilly VA), pp. 607-648.
2013.
Antje Boetius Ph.D. Co-I.
Head of the Helmholtz - Max Planck Research Group on Deep Sea Ecology and Technology,
Bremerhaven/Bremen, Germany
1992 Diploma in Biology, Hamburg University, Germany
1996 Ph.D., Bremen University, Germany
2001 Professor for Microbiology, Jacobs Univ. Bremen, Germany
Appointments
2008-present Leader HGF MPG Research Group, Alfred Wegener Institute Helmholtz Centre
for Polar and Marine Research
2008-present Full Professor of Geomicrobiology at Bremen University
2003-present Group leader, Microbial Habitat Group, Max Planck Institute for Marine
Microbiology
2008
Full Professor of Microbiology at Jacobs University Bremen
2003-2007
Associate Professor of Microbiology at Jacobs University Bremen
2001-2003
Assistant Professor of Microbiology at Intenational University Bremen,
1999-2000
Postdoc at Max Planck Institute for Marine Microbiology
1996-1999
Postdoc at Institute for Baltic Sea Research, Warnemünde
1993-1996
Research Assistant (PhD) at AWI, Bremerhaven
1989-1990
Laboratory Assistant at Scripps Institution of Oceanography, La Jolla, USA
Honors
2012
2011
2010
2009
2009
2006
2004
Heinrich-Hertz Professor of the KIT
Member of the Academy of Sciences and Literature Mainz
External Scientific Member of the Max Planck Society
Member of the National Academy of Sciences (Leopoldina)
Gottfried-Wilhelm-Leibniz Price of the DFG
Medaille de la Societe d’Oceanographie de France
Guest Professor of the University Paris 6 (UPMC)
Representative Publications (163 total)
Treude T, Knittel K, Blumenberg M, Seifert R, Boetius A., Subsurface microbial methanotrophic
mats in the Black Sea. AEM 71: 6375-6378. (2005)
Inagaki F, Kuypers MM, Tsunogai U, Ishibashi J, Nakamura K, Treude T, Ohkubo S,
Nakaseama M, Gena K, Chiba H, Hirayama H, Nunoura T, Takai K, Jørgensen BB, Horikoshi
K, Boetius A Microbial community in a sediment-hosted CO2 lake of the southern Okinawa
Trough hydrothermal system. PNAS 103 (38), 13899-13900 (2006)
29
Niemann H, Lösekann T, de Beer D, Elvert M, Nadalig T, Knittel K, Amann R, Sauter EJ,
Schlüter M, Klages M, Foucher JP, Boetius A., Novel microbial communities of the Haakon
Mosby mud volcano and their role as methane sink. Nature, (443) 854-858. (2006)
Nauhaus K., Albrecht M., Elvert M., Boetius A., Widdel F., In Vitro cell growth of marine
archaeal-bacterial consortia by anaerobic oxidation of methane with sulphate. Environmental
Microbiology, 9(1), 187–196. (2007)
Jørgensen BB, Boetius A., Feast and famine – microbial life in the deep-sea bed. Nature
Microbiology Reviews, 5, 770-781. (2007)
Omoregie EO, Mastalerz V, de Lange G, Straub KL, Kappler A, Røy H, Stadnitskaia A, Foucher
JP, Boetius AB., Biogeochemistry and Community Composition of Iron- and SulfurPrecipitating Microbial Mats at the Chefren Mud Volcano (Nile Deep Sea Fan, Eastern
Mediterranean). Appl Environ Microbiol 74 (10): 3198–3215. (2008).
Wegener, G; Boetius, A., An experimental study on short-term changes in the anaerobic
oxidation of methane in response to varying methane and sulfate fluxes. BIOGEOSCIENCES 6
(5): 867-876 (2009).
Omoregie E. O., Niemann, H., Mastalerz, V., de Lange, G., Stadnitskaia, A., Mascle, J., Foucher
, J.P. Boetius, A., Microbial methane oxidation and sulfate reduction at cold seeps of the deep
Eastern Mediterranean Sea. Marine Geology. 261:114-127. (2009).
Felden J, Wenzhöfer F, Feseker T, Boetius A., Transport and consumption of oxygen and
methane in different habitats of the Håkon Mosby Mud Volcano. Limnology and Oceanography
55(6), 2010, 2366–2380. (2010).
Wei C-L, Rowe GT, Escobar-Briones E, Boetius A, Soltwedel T, et al. Global Patterns and
Predictions of Seafloor Biomass Using Random Forests. PLoS ONE 5(12): e15323.
doi:10.1371/journal.pone.0015323. (2010).
Holler T., Widdel F., Knittel K., Amann R., Kellermann M., Hinrichs K.U., Teske A., Boetius
A., Wegener G., Thermophilic anaerobic oxidation of methane by marine microbial consortia.
ISME doi:10.1038/ismej.2011.77. (2011).
Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, Mark Welch DB,
Martiny JBH, Sogin M, Boetius A, Ramette A., Global patterns of bacterial beta-diversity in
seafloor and seawater ecosystems. PLoS ONE 6(9): e24570. (2011).
Holler, T; Wegener, G; Niemann, H; Deusner, C; Ferdelman, TG; Boetius, A; Brunner, B;
Widdel, F., Carbon and sulfur back flux during anaerobic microbial oxidation of methane and
coupled sulfate reduction. PNAS 108:52 E1484-E1490
DOI: 10.1073/pnas.1106032108.
(2011).
Wegener G, Bausch M, Holler T, Thang NM, Prieto Mollar X, Kellermann MY, Hinrichs KU,
Boetius A., Assessing sub-seafloor microbial activity by combined stable isotope probing with
deuterated water and 13C-bicarbonate. Environmental Microbiology, DOI: 10.1111/j.14622920.2012.02739.x. (2012).
Felden, J., Lichtschlag, A., Wenzhöfer, A., de Beer, F., Feseker, D., Pop Ristova, T., P., de
Lange, G., Boetius, A. Limitations of microbial hydrocarbon degradation at the Amon Mud
Volcano (Nile Deep Sea Fan). Biogeosciences 10, 3269–3283. (2013).
30
Frederick S. Colwell, Ph.D. Co-I.
Professor, Oregon State University
1977
B.A., Biology, Whitman College, Walla Walla, WA
1982
M.S., Microbiology, Northern Arizona University, Flagstaff, AZ
1986
Ph.D., Microbiology, Virginia Tech, Blacksburg, VA
Appointments
1986-1988
Postdoctoral Fellow, Biotechnol. Dept., INL
1988-1990
Scientist, Biotechnol. Dept., INL
1990-1992
Senior Scientist, Biotechnol. Dept., INL
1992-1994
Scientific Specialist, Biotechnol. Dept., INL
1994-1998
Advisory Scientist, Biotechnol. Dept., INL
1998-2006
Consulting Scientist, Biotechnol. Dept., Idaho National Laboratory (INL)
2006-present Professor, College of Oceanic & Atmos. Sci., Oregon State Univ.
Reed, D.W., Y. Fujita, M. Delwiche, D.B. Blackwelder, P.P. Sheridan, T. Uchida, and F.
Colwell. Microbial communities from methane hydrate-bearing deep marine sediments in a
forearc basin. Appl. Environ. Microbiol. 68: 3759-3770. 2002.
Mikucki, J.A., Y. Liu, M. Delwiche, F.S. Colwell, and D.R. Boone. Isolation of a methanogen
from deep marine sediments that contain methane hydrates, and description of Methanoculleus
submarinus sp. nov. Appl. Environ. Microbiol. 69: 3311-3316. 2003.
Colwell, F., R. Matsumoto, and D.W. Reed. A review of the gas hydrates, geology, and biology
of the Nankai Trough. Chem. Geol. 205: 391-404. 2004.
Inagaki, F. T. Nunoura, S. Nakagawa, A Teske, M. Lever, A. Lauer, M. Suzuki, K. Takai, M.
Delwiche, F.S. Colwell, K.H. Nealson, K. Horikoshi, S. D’Hondt, and B.B. Jørgensen.
Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine
sediments on the Pacific Ocean Margin. Proc. Nat. Acad. Sci. USA. 103: 2815-2820. 2006.
Colwell, F.S., S. Boyd, M.E. Delwiche, D.W. Reed, T.J. Phelps, and D.T. Newby. Estimates of
biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia Margin.
Appl. Environ. Microbiol. 74: 3444-3452. 2008.
Caldwell, S.L., J.R. Laidler, E.A. Brewer, J.O. Eberly, S.C. Sandborgh, and F.S. Colwell.
Anaerobic oxidation of methane: Mechanisms, bioenergetics, and the ecology of associated
microorganisms. Environ. Sci. Technol. 42: 6791-6799. 2008.
Briggs, B.R., J. Pohlman, M. Torres, M. Riedel, E. Brodie, and F.S. Colwell. Macroscopic
biofilms of the anaerobic oxidation of methane consortia in subseafloor sediment fractures. Appl.
Environ. Microbiol. 77: 6780-6787. 2011.
Gu, G., G.R. Dickens, G. Bhatnagar, F. Colwell, G. Hirasaki, and W.G. Chapman. Abundant
early Palaeogene marine gas hydrates despite warm deep ocean temperatures. Nature –
Geoscience. DOI: 10.1038/NGEO1301. 2011.
Briggs, B.R., F. Inagaki, Y. Morono, T. Futagami, C. Huguet, A. Rosell-Mele, T. Lorenson, and
31
F.S. Colwell. Bacterial dominance in subseafloor sediments characterized by gas hydrates.
FEMS Microbiol. Ecol. 81: 88-98. 2012.
Edwards, K.J., K. Becker, and F. Colwell. The deep, dark energy biosphere: Intraterrestrial life
on Earth. Ann. Rev. Earth Planet. Sci. 40: 551-568. 2012.
Isabelle Daniel, Ph.D Co-PI.
Professor University Claude Bernard Lyon 1
1991 Teaching degree (Agrégation) in Earth and life Sciences
1992 Master in Earth Sciences (ENS Lyon, University of Rennes 1)
1995 Ph.D. Geology, University Lyon 1
2002 Habilitation, University Lyon 1
Appointments
1996-2004
Assistant professor, University Lyon 1, Dept of Earth Sciences
2004-2010
Professor of Mineralogy, University Lyon 1, Dpt of Earth Science
2010–2013 Chair of the Department of Earth Sciences, University Lyon 1
Honors
2008-2010
Junior fellow of the Institut Universitaire de France
Fellow of the Mineralogical Society of America
Representative Publications (57 TOTAL)
Auzende, A.L., I. Daniel, C. Lemaire, B. Reynard, F. Guyot High-pressure behavior of
serpentine minerals: a Raman spectroscopic study, Physics Chemistry of Minerals, 31, 269-277.
(2004)
Perrillat, J.P., I. Daniel, K.T. Koga, B. Reynard, H. Cardon, W.A. Crichton (2005) Kinetics of
antigorite dehydration: a real-time X-ray diffraction study, Earth and Planetary Science Letters
236:899-913. (2005)
Daniel, I., Oger, P.M. and Winter, R. Origins of life and biochemistry under high-pressure
conditions. Chemical Society Reviews, 35, 858-875. (2006)
Hilairet, N., B. Reynard, Y. Wang, I. Daniel, S. Merkel, N. Nishiyama, S. Petitgirard Highpressure creep of serpentine, interseismic deformation and initiation of subduction, Science, 318,
1910-1913. (2007)
Picard, A., I. Daniel, G. Montagnac, P.M. Oger In situ monitoring by quantitative Raman
spectroscopy of alcoholic fermentation by Saccharomyces cerevisiae under high pressure,
Extremophiles, 11, 445-452. (2007)
Chollet, M., Daniel, I., Koga, K.T., Petitgirard, S., and Morard, G. Kinetics and mechanism of
antigorite dehydration: implications for subduction zone seismicity. Journal of Geophysical
Research, 116, B04203. (2011)
Picard, A., I. Daniel et al., Monitoring microbial redox transformations of metal and metalloid
elements under high pressure using in situ X-ray absorption spectroscopy. Geobiology, 9, doi:
10.1111/j.1472-4669.2010.00270.x. (2011)
32
Feuillie, C., Merheb, M., Gillet, B., Montagnac, G., Hänni, C., and Daniel, I. Enzyme-free
detection and quantification of double-stranded nucleic acids. Analytical and Bioanalytical
Chemistry, 404(2), 415-422. (2012)
Picard, A., Testemale, D., Hazemann, J.-L., and Daniel, I. The influence of high hydrostatic
pressure on bacterial dissimilatory iron reduction. Geochimica Cosmochimica Acta, 88, 120–
129. (2012)
Feuillie, C., Daniel, I., Michot, L., and Pedreira Segade, U. Adsorption of ribonucleotides to FeMg-Al rich swelling clays. Geochimica Cosmochimica Acta, (2013) in press.
Steven D’Hondt, Ph.D. Co-I.
Professor, Graduate School of Oceanography (GSO), University of Rhode Island (URI),
Narragansett, RI
1984
Stanford University, Geology, B.S.
1990
Princeton University, Geological and Geophysical Sciences, Ph.D.
Appointments
1989-1995
Assistant Professor, URI, GSO
1995-2000
Associate Professor, URI, GSO
2011-2012
Interim Dean, URI, GSO
2000-present Professor, University of Rhode Island, Graduate School of Oceanography
Representative Publications (10 examples of ~80).
D'Hondt, S., P. Donaghay, J.C. Zachos, D. Luttenberg, and M. Lindinger, Organic carbon fluxes
and ecological recovery from the Cretaceous/Tertiary mass extinction, Science 282, 276-279.
1998.
Rutherford, S.D., S. D'Hondt, and W. Prell, Environmental controls on the geographic
distribution of zooplankton diversity, Nature 400, 749-753. 1999.
D'Hondt, S., Rutherford, S., Spivack, A.J. Metabolic activity of the subsurface biosphere in
deep-sea sediments, Science 295: 2067-2070. 2002.
D’Hondt, S, Jørgensen, B.B., Miller, D.J., and 32 others. Distributions of microbial activities in
deep subseafloor sediments, Science 306: 2216-2221. 2004.
Jørgensen, B.B., and S. D’Hondt, A starving majority deep beneath the seafloor, Science 314,
932-934. 2006.
D’Hondt, S., and 11 others. Subseafloor sedimentary life in the South Pacific gyre, PNAS
106(28): 11651-11656. 2009.
D’Hondt, S., F. Inagaki, C.A. Alvarez Zarikian, and the Expedition 329 Scientists, South Pacific
Gyre Subseafloor Life, Proceedings IODP, 329: Tokyo (Integrated Ocean Drilling Program
Management International, Inc.). doi:10.2204/ iodp.proc.329.2011. 2011.
Kallmeyer, J., R. Pockalny, R. Adhikari, D.C. Smith and S. D’Hondt, Global distribution of
subseafloor sedimentary biomass, Proceedings of the National Academy of Science (PNAS)
109(40), 16213-16216. 2012.
33
Røy, H., J. Kallmeyer, R.R. Adhikari, R. Pockalny, B.B Jørgensen and S. D’Hondt, Aerobic
microbial respiration in 86-million-year-old deep-sea red clay, Science 336 (6083), 922-925,
DOI: 10.1126/science.1219424. 2012.
Lomstein, B.A., A.T. Langerhuus, S. D’Hondt, B.B. Jørgensen and A.J. Spivack, Spore
abundance, microbial growth and necromass turnover in deep subseafloor sediment, Nature 484,
101–104, doi:10.1038/nature10905. 2012.
Thomas L. Kieft Ph.D. Co-I.
Department of Biology, New Mexico Institute of Mining and Technology (New Mexico Tech) /
Socorro, New Mexico
1973
Carleton College, B.A. Biology
1978
New Mexico Highlands University M.S. Biology
1983
University of New Mexico, Ph.D. Biology
Appointments
09/83 - 08/85
01/97 - 12/97
01/05 - 07/05
08/05 - present
08/85 - present
Post-doc, Plant and Soil Biology, Univ. of California, Berkeley, CA
Sabbatical leave, Northwest National Laboratory, Richland, WA
Sabbatical leave, Los Alamos Nat’l Lab, Los Alamos, NM
Adjunct Professor, Hydrology Program, New Mexico Tech
Faculty member (Professor, 1993 - present), Biol. Dept., NM Tech
Kieft, T.L., S.M. McCuddy, T.C. Onstott, M. Davidson, L.-H. Lin, B. Mislowac, L. Pratt, E.
Boice, B. Sherwood Lollar, J. Lippmann-Pipke, S.M. Pfiffner, T.J. Phelps, T. Gihring, D. Moser,
A. van Heerden. Geochemically generated, energy-rich substrates and indigenous
microorganisms in deep, ancient groundwater. Geomicrobiol. J. 22:325-335. 2005.
Gihring, T., D.P. Moser, L.-H. Lin, M. Davidson. T.C. Onstott, L. Morgan, M. Milleson, T. L.
Kieft, E. Trimarco, D.L. Balkwill, M.E. Dollhopf. The distribution of microbial taxa in the
subsurface water of the Kalahari Shield, South Africa. Geomicrobiol. J. 23:415-430. 2006.
Kieft, T. L., Phelps, T. J., J. K. Fredrickson. Drilling, coring, and sampling subsurface
environments. pp. 799-817, In: Manual of Environmental Microbiology, Third Edition. Hurst,
C.J. (Ed.), ASM Press, Washington, DC. 2007.
Onstott, T.C., L.-H. Lin, M. Davidson, B. Mislowac, M. Borcsik, J. Hall, G. Slater, J. Ward, B.
Sherwood Lollar, J. Lippmann-Pipke, E. Boice, L. Pratt, B. S. Pfiffner, D. Moser, T. Gihring, T.
L. Kieft, T. J. Phelps, E. van Heerden, D. Litthauer, M. DeFlaun, and R. Rothmel. The origin and
age of biogeochemical trends in deep fracture water of the Witwatersrand basin, South Africa.
Geomicrobiol. J. 23:369-414. 2006.
Sahl, J.W., R. Schmidt, E.D. Swanner, K.W. Mandernack, A.S. Templeton, T.L. Kieft, R.L.
Smith, W.E. Sanford, R.L. Callaghan, J.B. Mitton, and J.R. Spear. Subsurface microbial
diversity in deep-granitic fracture water in Colorado. Appl. Environ. Microbiol. 74:143-152.
2008.
Kminek, G., J.D. Rummel, C.S. Cockell , R. Atlas, N. Barlow, D. Beaty, W. Boynton, M. Carr,
S. Clifford, C.A. Conley, A.F. Davila, A. Debus, P. Doran, M. Hecht, J. Heldmann, J. Helbert,
34
V. Hipkin, G. Horneck, T.L. Kieft, G. Klingelhoefer, M. Meyer, H. Newsom, G.G. Ori, J.
Parnell, D. Prieur, F. Raulin, D. Schulze-Makuch, J.A. Spry, P.E. Stabekis, E. Stackebrandt, J.
Vago, M. Viso, M. Voytek, L. Wells, F. Westall. Report of the COSPAR mars special regions
colloquium. Adv. Space Res. 46:811-829. 2010.
Tang, H., P. Zhang, T.L. Kieft, S.J. Ryan, S.M. Baker, W.P. Wiesmann, S. Rogelj Antibacterial
action of a novel functionalized chitosan-arginine against gram-negative bacteria. Acta
Biomaterialia 6:2562-2571. 2010.
Silver, B.J., T.C. Onstott, G. Rose, L.-H., Lin, C. Ralston, B. Sherwood-Lollar, S. M. Pfiffner, T.
L. Kieft, S. McCuddy. 2010. In situ cultivation of subsurface microorganisms in a deep mafic
sill: implications for SLiMEs. Geomicrobiol. J. 27:329-348. 2010.
Kieft, T.L. Sampling the Deep Sub-surface using drilling and coring techniques. pp. 3427-3441,
In: Microbiology of Hydrocarbons and Lipids. K.N. Timmis (Ed.), Springer Verlag, Berlin.
2010.
Davidson, M.M., B.J. Silver, T.C. Onstott, D.P. Moser, T.M. Gihring, L.M. Pratt, E.A. Boice, B.
Sherwood Lollar, J. Lippmann-Pipke, S.M. Pfiffner, T.L. Kieft, W. Seymore, C. Ralston.
Planktonic microbial diversity reflects geochemistry of subsurface fluid-filled fractures, Evander
Basin, South Africa. Geomicrobiol. J. 18:275-300. 2011.
Matthew O. Schrenk Ph.D. Co-I.
Assistant Professor, East Carolina University, Department of Biology, Howell Science Complex,
S303
1998
B.Sc. in Geology & Geophysics and S. Asian Studies, University of WisconsinMadison
2001
M.Sc.in Oceanography, University of Washington
2005
Ph.D. in Oceanography, Certificate in Astrobiology, University of Washington
2005-2008
Postdoctoral appointment in Astrobiology, Carnegie Institution for Science
Appointments
1996-1998
Undergraduate Research Assistant, University of Wisconsin-Madison,
Department of Geology and Geophysics
2000, 2013 Consultant, American Museum of Natural History, New York, NY
1998-2005
Research/Teaching Assistant, University of Washington, School of Oceanography
2005-2007
Postdoctoral Fellow, NASA Astrobiology Institute
2007-2008
Postdoctoral Associate, Carnegie Institution of Washington, Geophysical
Laboratory and Department of Terrestrial Magnetism
2008-2013
Assistant Professor, Department of Biology,
Adjunct Professor, Department of Geological Sciences
East Carolina University, Greenville, NC
2013-present Assistant Professor, Department of Geological Sciences & Department of
Microbiology and Molecular Genetics, Michigan State University, East Lansing,
MI
Schrenk, M.O., K.J. Edwards, R.M. Goodman, R.J. Hamers, and J.F. Banfield. Distribution of
35
Thiobacillus ferrooxidans and Leptospirillum ferrrooxidans: implications for generation of acidic
mine drainage. Science. 279:1519-1522. 1998.
Schrenk, M.O., D.S. Kelley, J.R. Delaney, and J.A. Baross. Incidence and diversity of
microorganisms within the walls of an active black smoker hydrothermal chimney. Appl.
Environ. Microbiol. 69(6): 3580-3592. 2003.
Schrenk, M.O., S.A. Bolton, D.S. Kelley, and J.A. Baross. Low archaeal diversity linked to
subseafloor geochemical processes at the Lost City Field, Mid Atlantic Ridge. Environ.
Microbiol. 6(10):1086-1095. 2004.
Kelley, D.S., J. Karson, G. Früh-Green, D. Yoerger, T. Shank, D. Butterfield, J. Hayes, M.O.
Schrenk, E. Olson, G. Proskurowski, M. Jakuba, A. Bradley, B. Larson, K. Ludwig, D. Glickson,
K. Buckman, A.S., Bradley, W. Brazelton, K. Roe, M. Elend, A. Delacour, S. Bernasconi, m.
Lilley, J. Baross, R. Summons, S. Sylva. A Serpentinite-hosted ecosystem: The Lost City
Hydrothermal Field. Science. 307: 1428-1434. 2005.
Brazelton, W.J. , M.O. Schrenk, D.S. Kelley, J.A. Baross. Methane and sulfur metabolizing
microbial communities dominate in the Lost City Hydrothermal Field ecosystem. Appl. Environ.
Microbiol. 72(9):6257-6270. 2006.
Schrenk, M.O., J.A. Huber, K.J. Edwards. Microbial Provinces in the Subseafloor. Annual
Review of Marine Science. 2:279-304. 2010.
Jiao, Y., G.D. Cody, A.K. Harding, P. Wilmes, M. Schrenk, K.E. Wheeler, J.F. Banfield, M.P.
Thelen. Characterization of Extracellular Polymeric Substances from Acidophilic Microbial
Biofilms. Appl. Environ. Microbiol. 76: 2916-2922. 2010.
Brazelton, W.J., B. Nelson, M.O. Schrenk. Metagenomic evidence of H2 oxidation and H2
production by serpentinite-hosted subsurface microbial communities. Frontiers in Microbiology.
2:doi:10.3389/fmicb.2011.00268. 2012.
Schrenk, M.O., W.J. Brazelton, S.Q. Lang. Serpentinization, carbon, and deep life. Reviews in
Mineralogy and Geochemistry. 75:575-606. 2013.
Brazelton, W.J., P.L. Morrill, N. Szponar, M.O. Schrenk. Microbial communities associated
with subsurface geochemical processes in continental serpentinite springs. Appl. Environ.
Microbiol. 7: 2013. In press.
A - APPENDICES
A.1 - REFERENCES CITED
A.1 - REFERENCES CITED
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Lomstein, B.A., et al., Endospore abundance, microbial growth and necromass turnover
in deep sub-seafloor sediment. Nature, 2012 . 484(7392): p. 101-4.
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Natl Acad Sci U S A, 1998. 95(12): p. 6578-83.
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Sogin, M.L., K.T. Edwards, and S. D'Hondt, 2010. Deep Subsurface Microbiology and
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methane hydrates. FEMS Microbiol. Ecol. , 2012. 81: p. 88-98.
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Lavalleur, H.J. and F.S. Colwell, Microbial characterization of basalt formation waters
targeted for geological carbon sequestration. FEMS Microbiol Ecol, 2013.
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Kuczynski, J., et al., Using QIIME to analyze 16S rRNA gene sequences from microbial
communities. Curr Protoc Microbiol, 2012. Chapter 1: p. Unit 1E 5.
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Kelley, D.S., et al., A serpentinite-hosted ecosystem: the Lost City hydrothermal field.
Science, 2005. 307(5714): p. 1428-34.
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Lin, L.H., et al., Long-term sustainability of a high-energy, low-diversity crustal biome.
Science, 2006. 314(5798): p. 479-82.
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Sherwood Lollar, B., et al., Isotopic signatures of CH4 and higher hydrocarbon gases
from Precambrian Shield sites: A model for abiogenic polymerization of hydrocarbons.
Geochmica et Cosmochimica Acta 2008. 72.
11.
Horsfield, B., et al., Living microbial ecosystems within the active zone of catagenesis:
Implications for feeding the deep biosphere. Earth and Planetary Science Letters, 2006.
246(1): p. 55-69.
12.
Menez, B., V. Pasini, and D. Brunelli, Life in the hydrated suboceanic mantle. Nature
Geoscience, 2012. 5(2): p. 133-137.
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Hayes, J.M. and J.R. Waldbauer, The carbon cycle and associated redox processes
through time. Philos Trans R Soc Lond B Biol Sci, 2006. 361(1470): p. 931-50.
14.
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from: http://publications.iodp.org/preliminary_report/313/313pr_4.htm.
15.
Ruppel, C. Catching Climate Change in Progress: Drilling on Circum-Arctic Shelves and
Upper Continental Slopes; San Francisco, California, 10–11 December 2011. in Scientific
Drilling for Climate Related Objectives on Arctic Ocean Margins. 2011. San Francisco,
CA: EOS.
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Parkes, R.J., et al., Temperature activation of organic matter and minerals during burial
has the potential to sustain the deep biosphere over geological time scales. Organic
Geochemistry, 2007. 38: p. 845-852.
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Progress and Challenges for the Future, ed. U. Harms, C. Koeberl, and M.D. Zoback.
2007, Springer: Berlin-Heidelberg. 163-212.
18.
Moore, G.F., et al., Structural Setting of the Leg 190 Muroto Transect. Proc. ODP, Init.
Repts College Station, TX (Ocean Drilling Program), 2001. 190.
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Glass, E.M., et al., Using the metagenomics RAST server (MG-RAST) for analyzing
shotgun metagenomes. Cold Spring Harb Protoc, 2010. 2010(1): p. pdb prot5368.
A.2 - DECADAL GOALS
37
Overall Summary of Deep Life
Deep Life exerts a vital influence on Earth's subsurface carbon fluxes and reservoirs. It exploits
Earth's deep energy at the intersection between abiotic and biotic realms. The Deep Life
Community will map the abundance and diversity of subsurface marine and continental
microorganisms in time and space as a function of their phylogenomic and biogeochemical
properties, and their interactions with deep carbon. By integrating in situ and in vitro
assessments of biomolecules, cells, communities, process rates and subsurface habitats using
advanced measurement, imaging, and cultivation technologies, we will describe the
environmental limits to deep life, its survival, metabolism and reproduction. The resulting data
will inform experiments and models that seek to measure Deep Life’s impact on the carbon
cycle, to constrain biologically-mediated structural alteration of deep reservoirs of carbon and
other elements, and to define the deep biosphere’s relation to the surface world.
Decadal Goals:
DEEP LIFE: The Deep Life Community will explore the evolutionary and functional
diversity of Earth’s deep biosphere and its interaction with the carbon cycle.
I. Determine the processes that define the diversity and distribution of deep life as it
relates to the carbon cycle. Examples of research focus include:
•
•
•
Conduct a global 3-D census over time of biological diversity (Bacteria, Archaea,
Eukarya, viruses) in continental and marine deep subsurface environments.
Investigate whether specific mechanisms govern microbial evolution and dispersal in the
deep biosphere.
Determine what ecological rules explain deep microbial community structure, e.g. spatial
and temporal scales of community turnover, the role of the rare biosphere, and the effects
of limited dispersal.
II. Determine the environmental limits of deep life. For example we will:
•
•
•
Probe and test life’s response to physical and chemical extremes using observation,
experimentation in the laboratory and in the field, and modeling.
Explore what genomes can tell us about the limits and possible origins of life.
Establish a bio-energetic framework for understanding the limits and adaptation of life in
the deep subsurface.
III. Determine the interactions between deep life and carbon cycling on Earth. For example
we will:
•
•
•
Determine the principal pathways of carbon transformations in the subsurface and
quantify the rates of these reactions.
Characterize transitions between abiotic and biotic realms.
Quantify how these processes interact with the surface world.
A.3 - FUNDING THAT SUPPORTS ONE OR MORE OF DEEP LIFE’S DECADAL GOALS
A.3.1 - Funded Projects:
Bartlett, D. Deep Trench single-cell genomics. National Science Foundation, 9/1/08-8/31/13,
$658,000
38
Bartlett, D. Active microbial populations at depth. NASA, 8/10/10-8/9/14, 686,212
Bartlett, D. Deep-sea Trench Landers. The Prince Albert II of Monaco foundation, 1/1/1212/31/14, $600,000
Boetius,
A.
Gottfried-Wilhelm
Leibniz
Award
2009,
2009-2016,
Deutsche
Forschungsgemeinschaft, 2.5 M€ (approx. 30% will be invested towards DL research)
Boetius, A. ERC-Adv. Investigator Grant ABYSS; 3.5 Mio€, appr. 30% spent on questions
addressing carbon cycling and microbial biodiversity at the boundary between surface and
subsurface life in polar realms.
Boetius, A. DeBeer D. EU ESONET/EMSO seafloor observatories network; 500k€; 2008-2012
LOOME mudvolcano observatory
Colwell, F.S., Microbiological Studies of Geological Systems Exposed to Supercritical CO2,
DOE-NETL, 4/1/12-11/30/13. $97,000
Colwell, F.S., Experimental Characterization of Microbial Communities in Geological Materials
Exposed to Hydrofracturing Fluids, DOE-NETL, 1/1/13-11/30/13. $80,000
Daniel, I. (PI), Hazael, R. (Co-I), Picard, A. (Co-I), Foglia, F. (Co-I), 6 days ESRF beamtime
06/2013, $63,000
Daniel, I. (PI), Reynard, B. (Co-I), Andreani, M. (Co-I). Lyon Institute of the Origins equipment
grant 2013-2015, $368,000
Daniel, I. (PI), Feuillie, C. (Co-I), Pedreira Segade, U. (Co-I), Michot, L. (Co-I), Serpentines
and the origin of the genetic material, CNRS-CNES interdisciplinary program, 2009 - 2016,
$252,000
Daniel, I. Institut Universitaire de France. 2009-2013, $158,000
D’Hondt, S. (PI), Radiolytic hydrogen and microbial life in subseafloor sediment and basalt,
NASA Astrobiology: Exobiology and Evolutionary Biology, 2011-present, $173,246.
D’Hondt, S. (PI), Quantification of contamination potential in South Pacific Gyre sediment,
Consortium for Ocean Leadership/USSSP, 2011-present, $15,000.
D’Hondt, S. (PI) and A.J. Spivack (Co-PI), Collaborative Research: IODP Expedition 329
Objective Research on Supply of H2 by Water Radiolysis in Subseafloor Sediment of the South
Pacific Gyre, NSF Ocean Drilling, 2011-present, Collaboration with R. Murray (Boston
University), URI portion is $185,507.
D’Hondt, S. (PI). U.S. Science Support Program Salary for IODP Expedition 329, USSSP/IODP,
2010-present, $196,127.
D’Hondt, S. (PI), and J. Sauvage (Co-PI), IODP Expedition 337 Shimokita Coalbed Biosphere
USSSP Support for Justine Sauvage, Consortium for Ocean Leadership, 2012-2013, $12,000.
D’Hondt, S. (PI), and E.A. Walsh (Co-PI). Microbial Community Composition of the Bering Sea
Site U1344, Consortium for Ocean Leadership/USSSP, 2010-present, $15,000.
D’Hondt, S. (Co-I), Sogin, M. (Co-I). Microbial Community Structure of Subsurface Marine
Environments. 8/1/13-12/30/13. $250,000
39
Edwards, K.J. (PI), J. Cowen (Co-PI), S. D’Hondt (Co-PI), A. Fisher (Co-PI) and G. Wheat (CoPI), Center for Dark Energy Biosphere Investigations, Science and Technology Centers:
Integrative Partnerships program, 2010-2015, $25M (URI portion is $1.25M).
Foglia, F. (Co-I), McMillan, P.F. (Co-I), Hazael, R. (Co-I), Forsyth, T. (Co-I), Simeoni, G. (CoI), Appavou, M-S. (Co-I), Meersman, F. (Co-I), Intra-cellular and trans-membrane H2O diffusion
and chemical exchange processes at high pressure, 9 days FRMII and ISIS neutron days 20122013, $94,600
Hinrichs, K.-U., Gottfried-Wilhelm Leibniz Award 2011, 2011-2018, Deutsche
Forschungsgemeinschaft, 2.5 M€ (approx.. 50% will be invested towards DL research)
Hinrichs, K.-U., DARCLIFE, European Research Council, 2010-2015. 2.908 M€
Hinrichs, K.-U., Timothy Ferdelman, Michael Friedrich, Sabine Kasten, MARUM-GB2:
Biogeochemical processes fueling sub-seafloor life: Transformation of C, S, Fe; 2012-2017,
Deutsche Forschungsgemeinschaft. 537 k€ (multiple Co-Is, only Hinrichs Lab portion indicated)
Hinrichs, K.-U., Molecular-isotopic studies of microbial processes and organic matter in the
subseafloor coalbed biosphere of Shimokita (IODP Exp. 337), 2012-2015, Deutsche
Forschungsgemeinschaft, 231.75 k€
Hornbach, M. (PI), F.S. Colwell (Co-PI), Gas Hydrate Dynamics on the Alaskan Beaufort
Continental Slope: Modeling and Field Characterization. DOE - Office of Fossil Energy,
10/1/12-9/30/15. $1,105,000
Itavaara, M. Deep Metapathway 2012-2015. Finnish Academy grant. 560.000 euros.
Kieft, T. Determination of Regional Fluid Flow and gas flux rates for a continental plateau using
cosmogenic and radiogenic noble gas isotopes., 03/01/12 – 02/28/14, NSF Hydrology Program
$24,820
Kieft, T. (Co-I), Onstott, T. (Co-I), ETBC: Collaborative Research: Deep Crustal Biosphere
Microbial Cycling of Carbon. National Science Foundation. 10/01/10 – 09/30/13, $638,590
Morgan-Smith, D. Pressure Resuscitation of the Deep Subsurface Biosphere. C-DEBI
postdoctoral fellowship with M. Schrenk (ECU) and D. Bartlett (SIO). $58,000.
Schrenk, M. (Co-I), Brazelton W., (Co-I). Metagenome- and Metatranscriptome- enabled
Investigations of Carbon and Hydrogen Flux through the Serpentinite-hosted Subsurface
Biosphere. DOE Joint Genome Institute, Community Sequencing Program.
Stepanauskas, R. (PI), Emerson, D. (Co-I), Itavaara, M. (Co-I), Kieft, T. (Co-I), Lau, M. (Co-I),
Moser, D. (Co-I), Moyer, C. (Co-I), Onstott, T.C. (Co-I), Orcutt, B. (Co-I), Wommack, E. (CoI), Bomberg, M. (Co-I). Enigmatic life underground: Large-scale single cell genomics of deep
subsurface microorganisms. DOE Joint Genome Institute, Community Sequencing Program.
Stepanauskas, R., Illumina MiSeq Grant.
http://www.illumina.com/landing/miseqgrant/index.ilmn. $150,000
A.3.2 - Pending Leveraged proposals
Cardace, D. How Deep Does Life Go? NSF-CAREER. $399,997..
40
Colwell, F.S., Biogeochemistry of Carbon Sequestration in Columbia River Basalts, Subcontract
from Pacific Northwest National Laboratory; $24,000
Daniel, I. X-ray Proposal for 5-6 days beamtime at the ESRF
D’Hondt, S. (PI), and J. Sauvage (Co-PI), Microbial Energetics in Subseafloor Hydrocarbon
Reservoirs, Shimokita Peninsula, Consortium of Ocean Leadership, pending, $12,000.
D’Hondt, S., J.B. Kirkpatrick, A. Abrajevitch, F. Colwell, H. Cypionka, B. Engelen, S.
Gallagher, C. Hubert, F. Inagaki, J. Kallmeyer, Y. Morono, R.W. Murray, B. Opdyke and R.
Pockalny. Nature and origin of subseafloor life in Mesozoic sediment of the Scott Plateau,
Integrated Ocean Drilling Program (IODP) Ancillary Program Letter 830 (submitted April 1,
2013).
Huber, J.A (PI), Stepanauskas, R. (Co-I). Deciphering metabolic and evolutionary processes at
the upper temperature limits of life in subseafloor archaea using single cell genomics" NASA
Exobiology and Evolutionary Biology Program. $649,581.
Kelley, K., D. Cardace, and S. Carey.. Acquisition of a Fourier-Transform Infrared Spectrometer
for igneous petrology, volcanology, and geobiology research. NSF-EAR IF, $155,522.
Kieft, T. (PI), Mike Pullin (Co-PI) Characterization of dissolved organic carbon in deep crustal
fracture water using solid state nuclear magnetic resonance analysis, Environmental Molecular
Sciences Laboratory (EMSL) at DOE’s Pacific Northwest National Lab, proposal for facility
access.
Malinverno, A., (PI), Colwell, F.S. (Co-PI) IODP – Constraining Methane Cycling in
Continental Margins: A Combined Microbiological, Geochemical, and Modeling Approach
Proposal for ship time.
Pockalny, R., and S. D’Hondt, EarthCube RCN: EarthCube Building Blocks: Crowdsourcing
Geoscientific Data Curation, Collaboration with USC (prime sponsor: NSF), Submitted May 22
2013), URI portion = $133,745.
Ruppel, C. (PI), Colwell, F.S. (Co-PI). Alaskan Beaufort Margin: Investigating the Impact of
Warming Since the Last Glacial Maximum on Climate-Sensitive Sediments in the Arctic, IODP
– Proposal for ship time.
Schrenk, M. Microbial Activities in Serpentinized Rocks-Impacts upon Global and Regional
Carbon Exchange. DOE Early Career Research Program. $750,000.
Spivack, A.J. (PI), S. D’Hondt (Co-PI) and R. Pockalny (Co-PI), North Atlantic Meridional
Circulation during the Last Glacial Maximum: Density Structure and Pre-formed Nitrate,
submitted Feb 1 2013, $606,432.
Wildenshild, D. (PI), Colwell, F.S. (Co-PI) Development of a State-of-the-Art High-Resolution
Microtomography Facility Customized for Dynamic (4D) Imaging, NSF Major Research
Instrumentation, $1,332,000
Winter, R. Exploring the Dynamical Landscape of Biomolecular Systems by Pressure
Perturbation (FOR 1979 )", German Science Foundation (DFG) final decision pending
involving 9 research groups from Germany 2.4 M Euro funding for three years.
A.4 - DEEP LIFE COMMUNITY PUBLICATIONS
41
Anderson, R.E., Brazelton, W.J., Baross, J.A. The deep virosphere: assessing the viral impact on
microbial community dynamics in the deep subsurface. MSA volume "Deep Carbon", (R. M.
Hazen, ed.). Mineralogical Society of America and The Geochemical Society (Chantilly VA), pp
649-675. 2013.
Andreani, M., I. Daniel, and M. Pollet-Villard, Aluminum speeds up the hydrothermal alteration
of olivine. American Mineralogist, 2013. in press.
Bennett, S.A., Coleman, M., Huber, J.A., Reddington, E., Kinsley, J.C., McIntyre, C., Seewald,
J.S., and C.R. German. Trophic regions of a hydrothermal plume dispersing away from an
ultramafic-hosted vent-system: Von Damm vent-site, Mid-Cayman Rise. Geochemistry
Geophysics Geosystems. 14:317-327. 2013.
Brazelton, W.J.. P.L. Morrill, N. Szponar, M.O. Schrenk. Microbial communities associated
with subsurface geochemical processes in continental serpentinite springs. Appl. Environ.
Microbiol. 79(13):3906-3916. (2013).
Breier, J.A., Gomez-Ibanez, D., Reddington, E., Huber, J.A., and D. Emerson. A precision multisampler for deep-sea hydrothermal microbial mat studies. Deep-Sea Research Part I:
Oceanographic Research Papers.70:83-90. 2012
Briggs, B.R., F. Inagaki, Y. Morono, T. Futagami, C. Huguet, A. Rosell-Mele, T.D. Lorenson,
F.S. Colwell. Bacterial dominance in subseafloor sediments characterized by methane hydrates.
FEMS Microbiol. Ecol. 81: 88-98. 2012.
Campanaro, S, DePascale, F., Telatin, A., Schiavon, R., Bartlett, D. H. and Valle, G. The
transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR
mutant and its parental strain. BMC Genomics 13:567. 2012.
Colwell, F.S. , Dhondt, S. Nature and extent of the deep biosphere. MSA volume "Deep
Carbon", (R. M. Hazen, ed.). Mineralogical Society of America and The Geochemical Society
(Chantilly VA), pp. 547-574. 2013.
Daniel, I. and H.G.M. Edwards, Raman spectroscopy in Biogeology and Astrobiology, in Raman
Spectroscopy Applied to Earth Sciences and Cultural Heritage J. Dubessy, M.C. Caumont, and
F. Rull, Editors. The Mineralogical Society of Great Britain & Ireland. 2012.
Davydov, D. R., Sineva, E. V., Davydov, N. Y., Bartlett, D. H., and Halpert, J. R. 2013.
CYP261 enzymes from deep sea bacteria: A clue to conformational heterogeneity in
cytochromes P450. Biotechnology and Applied Biochemistry 60:30-40. 2013.
D’Hondt, S., Subsurface sustenance, News and Views, Nature Geoscience 6, 426–427,
doi:10.1038/ngeo1843. 2013.
D’Hondt, S., F. Inagaki, C Alvarez Zarikian and the IODP Expedition 329 Scientists, IODP
Expedition 329: Life and habitability beneath the seafloor of the South Pacific Gyre, Scientific
Drilling 15, 4-10. 2013.
Dunlea, A.G., R.W. Murray, R.N. Harris, M.A. Vasiliev, H. Evans, A.J. Spivack, and S.
D’Hondt, Assessment and Use of NGR Instrumentation on the JOIDES Resolution to Quantify
U, Th, and K Concentrations in Marine Sediment, Scientific Drilling 15, 57-63. 2013.
Edwards K.T., K. Becker, and F. Colwell. The Deep, Dark Energy Biosphere: Intraterrestrial
Life on Earth. Ann. Rev. Earth Planet Sci. 40: 551-568. 2012.
42
Eloe, E.A., Shulse, C. N., Fadrosh,D. W., Williamson, S. J., Allen, E. E. and Bartlett, D. H.
Compositional differences in particle-associated and free-living microbial assemblages from an
extreme deep-ocean environment. Environ. Microbiol. Reports. 3: 449–458. 2011.
Eloe, E.A., Fadrish, D. W., Novotny, M., Zeigler Allen, L., Kim, M., Lombardo, M.-J., YeeGreenbaum, J., Yooseph, S., Allen, E. A., Lasken, R., Williamson, S. J., Bartlett, D. H. Going
deeper: metagenome of a hadopelagic microbial community. PLoS ONE. 6: e20388. 2011.
Eloe, E.A., Malfatti, F., Gutierrez, J., Hardy, K., Schmidt, W. E., Pogliano, K., Pogliano, J.,
Azam, F. and D. H. Bartlett. Isolation and characterization of the first psychropiezophilic
Alphaproteobacterium. Appl. Environ. Microbiol. 77:8145-8153. 2011.
Feuillie, C., et al., A novel SERRS sandwich-hybridization assay to detect specific DNA target.
PLoS ONE, 6(5): p. e17847. 2011.
Feuillie, C., et al., Enzyme-free detection and quantification of double-stranded nucleic acids.
Analytical and Bioanalytical Chemistry, 404(2): p. 415-422. 2012.
Feuillie, C., et al., Adsorption of ribonucleotides to Fe-Mg-Al rich swelling clays. Geochimica
Cosmochimica Acta, 2013. in press.
Hofstetter, S., Winter, R., McMullen, L. M., Gänzle, M. G., In Situ Determination of Clostridium
Endosphore Membrane Fluidity during Pressure-Assisted Thermal Processing in Combination
with Nisin or Reutericyclin, J. Appl. & Environm. Microbiology 79: 2103-2106 . (2013).
Hinrichs, K.-U. and F. Inagaki, Downsizing the deep biosphere. Science, 338(6104): p. 204-05.
2012.
Jones, A.P., Baross J.A. (eds) Reviews in Mineralogy and Geochemistry, Volume 75, Carbon in
Earth, vol. Mineralogical Society of America, Geochemical Society, pp 547-574. (2013).
Kallmeyer, J., Pockalny, R., Adhikari, R., Smith, D.C., D’Hondt, S. Global distribution of
subseafloor sedimentary biomass, Proceedings of the National Academy of Science 109(40),
16213-16216. 2012.
Kapoor, S. Triola, G., Vetter, I., Erlkamp, M., Waldmann, H., Winter, R., Revealing
Conformational Substates of Lipidated N-Ras Protein by Pressure Modulation, Proc. Natl. Acad.
Sci. U.S.A. 109: 460-465. (2012).
Kapoor, S., Werkmüller, A., Goody, R. S., Waldmann, H., and Winter, R., Pressure Modulation
of Ras-Membrane Interactions and Intervesicle Transfer, J. Am. Chem. Soc. 135 6149-6156
(2013).
Kellermann, M.Y., et al., Autotrophy as a predominant mode of carbon fixation in thermophillic
anaerobic methane-oxidizing microbial communities. Proceedings of the National Academy of
Sciences of the United States of America, 109(47): p. 19321-26. 2012.
Lavalleur, H.J., F. Colwell. Microbial characterization of basalt formation waters targeted for
geological carbon sequestration. FEMS Microbiol. Ecol. DOI: 10.1111/1574-6941.12098. 2013.
Lever, M.A., et al., Evidence for microbial carbon and sulfur cycling in deeply buried ridge flank
basalt. Science, 339(6125): p. 1305-08. 2013.
43
Lin, Y.S., et al., Towards constraining H2 concentration in subseafloor sediment: A proposal for
combined analysis by two distinct approaches. Geochimica et Cosmochimica Acta, 77(0): p. 186201. 2012.
Lin, Y.S., et al., Assessing production of the ubiquitous archaeal diglycosyl tetraether lipids in
marine subsurface sediment using intramolecular stable isotope probing. Environmental
Microbiology, 15(5): p. 1634-46. 2013.
Lomstein, B.A., A.T. Langerhuus, S. D’Hondt, B.B. Jørgensen and A.J. Spivack, Spore
abundance, microbial growth and necromass turnover in deep subseafloor sediment, Nature 484,
101–104, doi:10.1038/nature10905. 2012.
Lloyd, K.G., Schreiber L., Petersen D.G., Kjeldsen K., Lever M.A., Stepanauskas R., Richter M.,
Kleindienst S, Lenk S, Schramm A, Jorgensen BB. Predominant archaea in marine sediments
degrade detrital proteins. Nature 496:215-218. (2013).
Lucas, S., Han, J., Lapidus, A., Cheng, J.- F., Goodwin, L.A., Pitluck, S., Peters, L., Mikhailova,
N., Teshima, H., Detter, J. C., Han, C., Tapia, R., Land, M., Hauser, L., Kyrpides, N. C.,
Ivanova, N., Pagani, I., Vannier, P., Oger, P., Bartlett, D. H., Noll, K. M., Woyke T., and Jebbar,
M. Complete genome sequence of the thermophilic piezophilic heterotrophic bacterium
Marinitoga piezophila KA3. J. Bacteriol. 194:5974-5975. 2012.
Marteinsson, V.T., Runarsson, A., Stefansson, A., Thorsteinsson, T., Johannesson, T.,
Magnusson, S.H., Reynisson, E., Einarsson, B., Wade, N., Morrison, H.G., Gaidos, E. Microbial
communities in the subglacial waters of the Vatnajokull ice cap, Iceland. ISME J. DOI:
10.1038/ismej.2012.97. 2012.
Meersman, F., Daniel I., Bartlett D., Winter R., Hazael R., and P.F. McMillan. High pressure
biochemistry and biophysics. MSA volume "Deep Carbon", (R. M. Hazen, ed.). Mineralogical
Society of America and The Geochemical Society (Chantilly VA), pp. 607-648. 2013.
Möller, J., Schroer, M., Erlkamp, M., Grobelny, S., Paulus, M., Tiemeyer, S., Wirkert, F., Tolan,
M., and Winter, R., The Effect of Ionic Strength, Temperature, and Pressure on the Interaction
Potential of Dense ProteinSolutions: From Nonlinear Pressure Response to Protein
Crystallization, Biophys. J. 102: 2641-2648. (2012).
Nyyssönen, M., Bomberg, M., Kapanen, A., Nousiainen, A., Pitkänen, P., and M. Itävaara. 2012.
Methanogenic and sulphate-reducing microbial communities in deep groundwater of crystalline
rock fractures in Olkiluoto, Finland. Geomicrobiology Journal, 29:863–878, doi-link:
10.1080/01490451.2011.635759. 2012.
Oger, P.M., I. Daniel, and A. Picard, In situ Raman and X-ray spectroscopies to monitor
microbial activities under high hydrostatic pressure. High-Pressure Bioscience and
Biotechnology, 1189: p. 113-120. 2010.
Oger, P., Sokolova, T. G., Kozhevnikova, D. A., Chernyh, N. A., Bartlett, D. H., BonchOsmolovskaya, E. A., Lebedinsky, A. V. Complete genome sequence of the hyperthermophilic
archaeon Thermococcus sp. AM4 capable of organotrophic growth and growth at the expense of
hydrogenogenic or sulfidogenic oxidation of carbon monoxide. J. Bacteriol. 193:7019-7020.
2011.
44
Picard, A., et al., Monitoring microbial redox transformations of metal and metalloid elements
under high pressure using in situ X-ray absorption spectroscopy. Geobiology, 9(2): p. 196-204.
2011.
Picard, A., et al., The influence of high hydrostatic pressure on bacterial dissimilatory iron
reduction. Geochimica Cosmochimica Acta, 88: p. 120–129. 2012.
Prigozhin, M. B., Liu, A., Wirth, A. J., Kapoor, S., Winter, R., Schulten, K., and Gruebele, M.,
Misplaced Helix Slows Down Ultrafast Pressure-Jump Protein Folding, Proc. Natl. Acad. Sci.
USA 110: 8087-8092. (2013)
Røy, H., J. Kallmeyer, R.R. Adhikari, R. Pockalny, B.B Jørgensen and S. D’Hondt, Aerobic
microbial respiration in 86-million-year-old deep-sea red clay, Science 336 (6083), 922-925,
DOI: 10.1126/science.1219424. 2012.
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N.N., Anderson, I.J., Cheng, J-F., Darling, A.,
Malfatti, S., Swan, B.K., Gies, E.A., Dodsworth, J.A., Hedlund, B.P., Tsiamis, G., Sievert, S.M.,
Liu, W-T., Eisen, J.A., Hallam, S., Kyrpides, N., Stepanauskas, R., Rubin, E., Hugenholtz, P.,
Woyke, T. Insights into the phylogeny and coding potential of microbial dark matter. Nature, in
press (2013).
Schrenk, M.O., Brazelton, W.J., Lang, S.Q. Serpentinization, Carbon, and Deep Life. Rev.
Mineral. Geochem. MSA volume "Deep Carbon", (R. M. Hazen, ed.). Mineralogical Society of
America and The Geochemical Society (Chantilly VA), pp.575-606. 2013.
Schroer, M. A., Markgraf, J., Wieland, D., Sahle, C., Möller, J., Paulus, M., Tolan, M., and
Winter, R., Nonlinear Pressure Dependence of the Interaction Potential of Dense Protein
Solutions, Phys. Rev. Lett. 106: 178102-1/4. (2011).
Schroer, M. A., Zhai, Y., Wieland, D., Sahle, C., Nase, J., Paulus, M., Tolan, M., and Winter, R.,
Exploring the Piezophilic Behavior of Natural Cosolvent Mixtures, Angew. Chem. Int. Ed. 50:
11413-11416. (2011).
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A.5 - POST DOCTORAL SUPPORT
William Brazelton
ECU
Melitza CrespoMedina
ECU
Priya Narasingarao
SIO
Rachael Hazael
UCL
Fabrizia Foglia
UCL
Dani Morgan-Smith
ECU
Maggie Lau
Princeton
Borja Linage
UFS
Malin Bomberg
VTT
Julie Revillaud
MBL
Woo Jun Sul
MBL
Schrenk
Schrenk
Bartlett
McMillan
McMillan
Schrenk/Bartlett
Onstott
van Heerden
Itavaara
Huber
Sogin
A.6 - MANAGEMENT PLAN
A.6.1 - MEMBERSHIP OF DEEP LIFE SCIENTIFIC STEERING COMMITTEE
Kai-Uwe Hinrichs – Co-Chair
Dean and Professor, Department of Geosciences and Head, Organic Geochemistry Group
MARUM Center for Marine Environmental Sciences, University of Bremen, Germany
Mitchell L. Sogin – Co-Chair
Director of the Josephine Bay Paul Center for Comparative Molecular Biology and
Evolution. Marine Biological Laboratory, Woods Hole MA
Professor, Molecular and Cellular Biology, Brown University, Providence RI
Douglas H. Bartlett
Professor, Scripps Institution of Oceanography, La Jolla, CA
Antje Boetius
Professor, HGF-MPG Group for Deep Sea Ecology and Technology
46
Alfred Wegener Institute for Polar and Marine Research in the Helmholtz Association,
Max Planck Institute for Marine Microbiology, Bremen Germany, Professor of
Geomicrobiology, University Bremen
Frederick S. Colwell
Professor, Oregon State University, Corvallis, OR
Isabelle Daniel
Professor, University Claude Bernard Lyon 1, Lyon, France
Steven D’Hondt
Professor, Graduate School of Oceanography, University of Rhode Island, Narragansett, RI
Fumio Inagaki
Group Leader/Senior Scientist Geomicrobiology Group, Kochi Institute for Core Sample
Research and Submarine Resources Research Project. Japan Agency for Marine-Earth
Science and Technology (JAMSTEC), Japan
Thomas L. Kieft
Professor, New Mexico Institute of Mining and Technology, Socorro, New Mexico
Matthew O. Schrenk
Assistant Professor, East Carolina University, Greenville, NC
Roland Winter
Professor, Technical University Dortmund, Germany
A.6.2 - STEERING COMMITTEE ACTIVITIES
Meeting schedule. The Co-Chairs Kai-Uwe Hinrichs and Mitchell L. Sogin have formed a
partnership to co-lead the Deep Life Scientific Steering Committee (SSC). As part of our efforts
to expand internationally, we have invited Fumio Inagaki of JAMSTEC to serve on the DLC
SSC. Drs. Hinrichs and Sogin will schedule Scientific Steering Committee meetings (a minimum
of one dedicated in-person DLC SSC meeting each year, quarterly video conferences, and inperson meetings linked to the 2014 and 2015 Deep Life Community Meeting and the 2015 DCO
“all-hands” meetings). Either Hinrichs or Sogin or (when possible) both will represent the DLC
at in person and teleconferencing DCO Executive Committee meetings. The entire Steering
Committee will participate in the planning of DLC annual meetings, workshops, and
organization of special sessions at national and international meetings and conferences.
47
Liaison activities and resource management. Sogin will serve as the liaison to the DCO Data
Science Team and D’Hondt will serve as liaison to the DCO Engagement Team (See 4.7 DATA
SCIENCE, p. 21, and 4.8 ENGAGEMENT, p. 22.
The Co-Chairs will assume fiduciary
responsibility for managing DLC resources from the Sloan Foundation in consultation with SSC
members who will provide leadership in developing proposals that seek new resources for
scientific exploration that addresses the DLC Decadal Goals.
Expanding Deep Life Support. The DLC has articulated an ambitious science agenda that will
require resources that extend well beyond funding provided by the Sloan Foundation. The
collection of samples and their interrogation through cultivation, chemical characterization and
genomic analysis requires major investments that cannot be satisfied through the funding of
salaries for a few post doctoral and graduate students over the next two years. Instead the DLC
must extract information from its existing complex datasets and develop techniques and
strategies for taking deep life research to the next level. At the DLC May, 2013 meeting in
Portland ORE, with extensive community input the DL steering committee settled upon a
strategy that will enable generation of new information from which to leverage new research
proposals. As described under 4 - THE PROPOSED PROJECT: DEEP LIFE RESEARCH
AND
COORDINATION NETWORK, the DLC has set aside resources that will enable activities – both
scientific investigations and synthesis activities, that will serve a key role in developing new
proposals. The budget has set aside >45% of our direct costs to support DLC activities that lay
the groundwork for new proposals. Unlike grants from a funding agency or foundation, these
resources will have a short spending period of <= 6 months during which they should address the
following criteria: a) Requests for support must address unresolved questions related to deep life
and its decadal goals; b) Requests must identify the potential for attracting additional funding
48
resources and the description must outline a plan for seeking new research support; c) the
amount of support can range from $1000 to as large as ~$25,000 and can be submitted at any
time between January 1, 2014 and July 1, 2015; d) The supported activity must conclude within a
six-month time-frame. Other criteria that will contribute to an application’s success include: e)
the potential for leveraging other funding; f) fostering collaborative science; g) supporting
synthesis of knowledge across the different themes; h) support for projects too risky for funding
agencies; j) funding projects of opportunity that require immediate resources; i) projects that will
enhance international programs and collaborations.
By way of example, two days before the final draft for this this proposal was completed, Tom
Kieft and Mike Pullin of New Mexico Tech were approved for a Rapid Access (30-day) project
at the Environmental Molecular Sciences Laboratory (EMSL) at DOE’s Pacific Northwest
National Lab titled Characterization of dissolved organic carbon in deep crustal fracture water
using solid state nuclear magnetic resonance analysis. The project will use solid state NMR
(~200 hours instrument time) to structurally examine organic matter extracted from deep (0.7-3.5
km) fracture water in South Africa. The deep water samples were collected with partial support
from the DCO DL RHC project; the collaboration with EMSL is a direct result of the May 2013
DCO DL meeting in Portland. Kieft will have the opportunity to submit an application for DL
support that could lead to securing major funding (NSF, DOE, etc.) for expansion to other
analytical approaches (GC-MS, GC-Fourier transform-ion cyclotron resonance MS, etc.) and
other sites (continental and marine). This provides an example of how DLC resources can both
leverage recent awards from agencies and foundations as well as provide resources to support the
submission of new applications for expanded research capabilities.
49
The DLC will accept 3-4 page applications for such support without specific deadlines
throughout
2013-2015.
The
Deep
Life
section
on
the
DCO
website
(http://www.deepcarbon.net/content/deep-life) will disseminate this information and we will use
e-mail lists to notify members of the DLC of this opportunity. In addition we will share
announcements of these opportunities with allied research initiatives such as C-DEBI. The
Steering Committee (exclusive of members who participate in authorship of the proposed
activity under evaluation or who have an inherent conflict of interest) will review the merits of
proposals and render recommendations for funding to the Co-Chairs during in person meetings
or quarterly video-conferences. Decisions by the Steering committee for supporting an activity
will consider its impact on one or more DCO DL Decadal Goals; building the DL – DCO
community, the potential for leveraging other funding; their influence on fostering collaborative
science and synthesis of knowledge across the different themes; proposed activities too risky for
funding agencies; novel opportunities with immediate funding requirements; and activities that
will enhance international programs and collaborations.
50

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