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We are proud to support the following C-DEBI projects.
The distribution of the 14 small
research grants funded to date have been across all
4 C-DEBI research
themes. Many have been associated with the initial
three focus drilling cruises, IODP Expedition 327, 329,
and 336, to the Juan
de Fuca Ridge Flank, South
Pacific Gyre and North
Pond, respectively, though a third of the proposals
has been associated with other drilling expedition sites
or not at all. |
By Research Theme |
By Study Site |
Brian
Glazer, University of Hawaii
Chemical sensor development for microbially-relevant scales
of concentration
gradients
Microbially-mediated redox cycling of oxygen, iron, manganese,
and sulfur exerts a strong influence on the behavior of various
organic and inorganic compounds in the deep subsurface biosphere
and has been relevant to the co-evolution of the earth and
life through geologic time scales; sensors that enable improved
understanding and characterization of processes involving
such redox-reactive chemical species are of key relevance
to the C-DEBI mission. The work proposed is to attempt new
methods of solid-state voltammetric microelectrode fabrication
to enable new sensor configurations and environmentally-relevant
experiments. We aim to: (i) make in vitro working
electrodes smaller than previously available for increasing
spatial resolution with respect to characterizing single-to-several
cell scale processes in laboratory experiments, and (ii) make
in situ working electrodes effectively larger than
previously available for increasing sensitivity and thus lowering
detection limits for characterization of redox reactive chemical
species in field studies. Successes in each objective will
significantly enhance upcoming lab and field work at Juan
de Fuca Ridge CORKs and North Pond.
Gerardo
Iturrino, Lamont-Doherty Earth Observatory
Development of telemetry system for the Deep Exploration Biosphere
Investigative Tool (DEBI-t)
Scientists and engineers from the Center for Dark Energy
Biosphere Investigations at the University of Southern California
(USC), Lamont-Doherty Earth Observatory (LDEO) of Columbia
University, Jet Propulsion Laboratory (JPL), and Photon Systems
Inc. have been developing a Deep Exploration Biosphere Investigative
tool (DEBI-t) for deployment at Deep Sea Drilling Project
(DSDP) Hole 395A in the Mid-Atlantic Ridge during IODP Expedition
336. The LDEO Borehole Research Group (BRG) has been developing
a multi-function telemetry module (MFTM) that will allow the
DEBI-t transmit data to a surface data acquisition system.
The MFTM will allow combining the DEBI-t with other logging
tools such as gamma ray and temperature sondes and transmit
data in real time via a 7-conductor wireline cable to a surface
data acquisition system onboard the JOIDES Resolution.
NEW!
Karen Lloyd, University of Tennessee, Knoxville
Using single cell genomics to determine the roles of uncultured
microbes in the deep subsurface carbon cycle
One of the major challenges in the study of deep subsurface
microbiology is determining the geochemical processes performed
by uncultured microorganisms. These microorganisms are often
abundant and diverse, but have been identified only by taxonomic
marker genes. The proposed work will attempt to address this
issue by sequencing whole genomes from individual cells of
key groups of uncultured Archaea. This will link metabolic
functions and phylogenetic identities to each other as well
as to key environmental factors such as the source of organic
matter. By accessing samples from the recently approved Baltic
Sea Basin IODP expedition, we will compare whole genomes from
individual cells across multiple glacial and interglacial
periods. The Archaea that are the target of this study have
been shown to be present at all depths of deep marine sediments,
irrespective of geochemical or sediment regime. However, individual
microorganisms may harbor genetic adaptations specific for
a given environment. We will identify these genes in a few
fully-sequenced genomes, and then quantify these genes in
the sediments to determine whether a given adaptation is widespread.
In this way, we hope to find new links between microbial phylogeny
and function in deep subsurface prokaryotic communities.
Heath Mills
and Brandi Reese, Texas A&M University
Expedition 329: Expanding metabolic potential by characterizing
anaerobic lineages in aerobic sediments
The sediments within South Pacific Gyre (SPG) represent the
most biologically inactive sediments on the planet, despite
dissolved oxygen, nitrate, phosphate and inorganic carbon
being present throughout the entire sediment column. Detection
and characterization of lineages associated with potential
cryptic biogeochemical cycles (e.g., a microbial process that
is not reflected in the geochemical signature due to populations
utilizing the metabolic products from another population in
the reverse redox reaction) within the subsurface biosphere
may indicate that the SPG is more metabolically active than
previously predicted through geochemical assessments. Presence
of anaerobic respiring populations within aerobic, energy-limited
SPG sediments would expand our understanding of activity in
the deep biosphere, extent and limits of life, and the evolution
and survival of life. The overall objective of this work is
to use culture independent and dependent techniques to provide
the most complete assessment of the SPG subsurface microbial
ecology. The central hypothesis is that anaerobic populations
have remained viable and potentially metabolically active
within these sediments despite the low energy availability
and presence of oxygen.
NEW!
Craig Moyer, Western Washington University
Zetaproteobacteria and associated microbial communities
from the Okinawa Trough subsurface biosphere
This expedition represents the first time that subsurface
microbial samples have been collected from a hydrothermal
system using modern microbially-motivated ocean drilling techniques
with the aim of obtaining direct evidence for a functionally
active, metabolically diverse subvent biosphere in relation
to the hydrothermally active mounds located in the Okinawa
Trough. This proposal seeks to expand on our post-cruise results
with the focus directed towards a metagenomic community analysis
using two different avenues of next-gen sequencing. We are
motivated by the recent discovery of unique and possibly endemic
populations of subsurface Zetaproteobacteria phylotypes.
We are also motivated by our initial cultivation results of
multiple enrichments that were obtained using both microaerophilic
and anaerobic FeOB culturing conditions and that we were able
to detect up to 13% Zetas, by qPCR analysis, in two habitats
with very different fluid flow regimes. We propose to use
pyrosequencing of 16S genes to assay community diversity and
massively-parallel sequencing to reconstruct genomes of the
most abundant community members, focusing on these two habitat
extremes. We hypothesize that this approach will allow insights
into the physiology of these FeOB communities thereby demonstrating
key features that they use to survive, compete and grow in
the deep “tepid” biosphere.
NEW!
Beth Orcutt, Bigelow Laboratory for Ocean Sciences, and Peter
Girguis, Harvard University
Primary productivity in young, oxic oceanic crust: Rates of
activity and autotrophic groups in subsurface and seafloor-exposed
basalts from North Pond, Mid-Atlantic Ridge
Oceanic crust comprises the largest aquifer system on Earth,
and the entire volume of the ocean circulates through the
ocean crust on the order of every 105 - 106
yrs, making this ‘subsurface ocean’ within the oceanic crust
a site of geologically rapid chemical exchange between the
crust and the oceans, which has significant ramifications
on global chemical cycles. Knowledge of metabolic reactions
occurring in the oceanic crust is sparse, as accessing this
environment is technologically challenging. It has been suggested
that autotrophic carbon fixation metabolisms could occur in
the basaltic oceanic crust; however, there are no published
empirical evaluations of the rates of autotrophy or the microbial
groups potentially responsible for autotrophy in this environment.
We propose to apply state-of-the-art molecular techniques,
as well as traditional stable isotopic tracer incubations,
to constrain potential rates of carbon fixation and to characterize
the associated microbial community in a suite of seafloor-exposed
and subsurface basalts. Our methods will involve time series
incubations with stable isotopes, evaluation of stable carbon
isotope incorporation into organic matter over time, and subsequent
investigation of active microbial groups through taxonomic
and functional gene analysis of 13C-labeled DNA. We will focus
on seafloor-exposed and subsurface basalts collected from
the North Pond location on the western Mid-Atlantic Ridge
during IODP Expedition 336 and a future expedition in 2012.
Victoria Orphan, California
Institute of Technology (Joshua Steele, Anne Dekas)
Microbe-mineral interactions in oligotrophic subseafloor habitats
The in situ interactions between microorganisms
and minerals in sediments are an important, yet poorly understood
area of research. Microbe-mineral interactions in the deep
subseafloor have the potential to influence microbial activity,
by serving as a localized source of nutrients or carbon, in
addition to providing oxidized or reduced species for energy-yielding
redox chemistry. Here, we propose to conduct shipboard sediment
incubations using carbon-13 and nitrogen-15 tracers, combined
with a recently developed magnetic and density-based separation
protocol for enriching specific mineral fractions from sediments.
Microbial assemblages from the mineral separates will be characterized
by microscopy and SIMS, enabling the assessment of variation
in microbial associations and activity for specific mineral
fractions across three sites in the South Pacific Gyre (Expedition
323) varying in the level overlying primary productivity and
organic matter deposition. We hypothesize that within these
oligotrophic, oxidized subseafloor environments, specific
minerals and clays adsorb organics near the seabed, which
in turn can serve as localized sites of enhanced heterotrophic
respiration and growth by particle associated microorganisms
within deeper sediment horizons. Determining the variation
in activity and diversity associated with different mineral
and clay fractions relative to the bulk sample are likely
to yield new insights into the metabolism and ecological strategies
of indigenous microbial assemblages.
Adina Paytan, University
of California, Santa Cruz
Phosphorous sources and cycling in the deep biosphere –
fueling life in the dark
Phosphorus (P) is an essential nutrient for all organisms,
yet it is the least mobile macro-nutrient in most sediments.
Phosphorous associated with organic matter, the principle
carrier of P to sediments, is converted to mineral phases
after burial, practically immobilizing the sedimentary P pool
and reducing P availability for microorganisms. Many processes
that determine P availability to the deep biosphere or its
sequestration in recalcitrant mineral forms occur in the sediment
simultaneously and measurement of P concentrations (organic
and inorganic) alone (in bulk sediment or using sequential
leaching extractions) is not sufficient for deciphering the
processes that control P bioavailability to the deep biosphere.
We propose to use a stable isotope tracing method to track
P cycling and transformations in sediments and within the
deep biosphere – the oxygen isotopes of phosphate
(δ18Op)
associated with various P pools in the sediment. The
use of δ18Op for the study of P cycling in the deep biosphere
(along with additional data) will shed light into the processes
that determine P availability and considerably improve our
understanding of P sources and cycling in the deep biosphere,
the mechanisms by which P is utilized, and changes in P availability
and mobility under a range of natural environmental conditions
within the deep biosphere.
Radu Popa, Portland
State University (Amy Smith, Gilberto Flores, Martin Fisk)
Genetic diversity and distribution of microbes colonizing
igneous minerals and glasses incubated in IODP Hole 1301A
on the eastern flank of the Juan de Fuca Ridge
The Integrated Ocean Drilling Program (IODP) Hole 1301A on
the eastern flank of Juan de Fuca Ridge (JFR) was used as
a long term sub-seafloor microbial observatory to determine
microbial colonization preferences for twelve silicate minerals
and glasses common in igneous rocks. Significant differences
in total cell density were found between mineral samples.
Fe(II)-rich olivine minerals had the highest density of culturable
organotrophic mesophiles as well as the only culturable organotrophic
thermophiles. Nine different phylotypes of mesophilic organotrophs
were present on the minerals and glasses, all of which are
closely related to known dissimilatory nitrate reducers, and
two known iron oxidizers. We hypothesize that neutrophilic
iron oxidizers are key players on olivine surfaces and thus
in basalts of JFR. Because most organisms are not culturable,
we cannot make inferences about differences in complexity
between microbial communities colonizing different minerals.
To achieve this we propose using 454 pyrosequencing and sequence
analysis of the hypervariable V4 region of the SSU rRNA, using
bacterial and archaeal primers and genomic DNA extracted from
our mineral samples. This work will significantly increase
the understanding of basalt endoliths, and help better decipher
their role in the biogeochemistry of subseafloor ecosystems
of JFR.
Michael Rappé, University
of Hawaii (Sean Jungbluth)
Metagenomics,
metatranscriptomics, and single-cell genomics of microbial
communities inhabiting Juan de Fuca Ridge flank borehole
fluids
We are investigating the deep biosphere of the subseafloor
basaltic crust on the eastern flank of the Juan de Fuca Ridge
by accessing pristine crustal fluids via Circulation Obviation
Retrofit Kit (CORK) sampling and instrumentation platforms.
Second-generation CORKs installed within Integrated Ocean
Drilling Program boreholes provide unprecedented opportunities
to study the microbial ecology and biogeochemistry of fluids
circulating in the sediment-covered oceanic basement. In the
summers of 2008-2011, a unique large-volume sampling system
was used to collect some of the only large volume pristine
basement fluid samples available for microbiological studies
to date, from a 3.5 Myr-old basalt-hosted basement aquifer
that is covered by 260 m of sediment. On an annual scale,
the microbial community appears to be temporally dynamic;
however, some common community members are shared between
sample years. We will obtain nucleic acid sequence data from
the metagenome of two deep subsurface microbial community
samples (one each from field seasons 2010 and 2011) and the
metatranscriptome of one corresponding sample, as well as
amplify the genomes of a subset of single cells. Due to the
well-known difficulties in obtaining pristine sub-seafloor
ocean crustal fluids, these samples offer an unmatched opportunity
to investigate the community genomics of cells inhabiting
the deep subseafloor biosphere.
Alberto Robador,
University of Hawaii
Temperature and pressure as microbial physiological variables
in low-energy deep subseafloor habitats
The proposed work intends to specifically characterize the
temperature and pressure as microbial physiological variables
and explore quantitatively and qualitatively, the metabolic
capacities of single microbial cells in deeply buried habitats.
We hypothesize that the microbial physiological responses
to ambient temperatures may be used to characterize the nature,
in terms of the geographical origin, of the microorganisms
present in deeply buried habitats. A high pressure thermal
gradient system will be used to study the pressure and temperature
relationships of microbial metabolism in basaltic fluids.
Pulse-chase incubation experiments using radio- as well as
stable isotope labeled substrates will be performed in order
to quantify relevant metabolic processes rates under energy
limiting conditions and identify potential isotopic effects
during specific metabolic steps. In addition, voltammetric
measurements will be conducted to potentially quantify real-time
changes on manganese, iron and sulfur species of intermediate
oxidation state in samples incubated using the high pressure
thermal gradient system. Nanometer-scale secondary ion mass
spectrometry (NanoSIMS) will also be used in combination with
halogen in situ hybridization (HISH-SIMS) for simultaneous
quantification of cell-specific rates and phylogenetic identification
under different temperature and pressure regimes. We expect
that the physiological characterization of microorganisms
as a function of temperature and pressure in the basement
fluids will help to elucidate dispersal mechanisms that structure
microbial diversity.
Matt Schrenk,
East Carolina University, and D'Arcy Meyer Dombard, University
of Illinois-Chicago
Development of a stable isotope probing- metagenomics approach
to elucidate physiological traits associated with thermophilic
chemolithoautotrophy
The subseafloor biosphere associated with deep-sea hydrothermal
vents sustains a diverse range of chemical energy sources
capable of driving chemolithoautotrophic metabolism. Based
upon studies of microbial isolates, there are at least six
known pathways of carbon fixation, each with a unique phylogenetic
distribution, and specific requirements for energy, metal
cofactors, and reducing power. All of the newest pathways
have been elucidated in thermophilic and hyperthermophilic
microorganisms, particularly Archaea. As these studies require
the enrichment and isolation of pure cultures, which can be
challenging even in temperate environments, the overall diversity
of carbon fixation pathways, how, and why they vary under
different environmental conditions is unknown. We propose
that studying microbial carbon fixation in anaerobic, thermophilic
microcosm experiments by tracing 13-C labeled DIC into DNA
and subsequently sequencing its meta-genome, will elucidate
both who is fixing carbon at high temperatures and
how it is being fixed. This work will complement
phylogenomic and biogeochemical studies associated with CORK
observatories installed on the eastern flank of the Juan de
Fuca Ridge. Results of this work will provide critical data
to integrate with rate measurements of biogeochemical activities
and with cultivation independent genomic data derived from
the subseafloor biosphere.
> See more on our research
grants program.
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