|
We are proud to support the following C-DEBI projects.
The distribution of the 14 small
research grants funded as of May 2012 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 |
Victoria Orphan, Joshua Steele,and
Anne Dekas (California Institute of Technology)
Microbe-mineral interactions in oligotrophic subseafloor habitats
5/1/11 - 4/30/13, $49,974
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.
Alberto Robador
(University of Hawaii)
Temperature and pressure as microbial physiological variables
in low-energy deep subseafloor habitats
5/1/11 - 4/30/13, $49,239
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.
Radu Popa, Amy Smith, Gilberto
Flores (Portland State University) and Martin Fisk (Oregon
State University)
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
6/1/11 - 5/31/13, $49,418
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.
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
7/1/11 - 6/30/12, $24,997
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.
Brian Glazer
(University of Hawaii)
Chemical sensor development for microbially-relevant scales
of concentration
gradients
8/1/11 - 7/31/12, $49,999
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.
Heath Mills
and Brandi Reese (Texas A&M University)
Expedition 329: Expanding metabolic potential by characterizing
anaerobic lineages in aerobic sediments
9/1/11 - 8/31/12, $49,970
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.
Michael Rappé
and Sean Jungbluth (University of Hawaii)
Metagenomics, metatranscriptomics, and single-cell genomics
of microbial communities inhabiting Juan de Fuca Ridge flank
borehole fluids
9/15/11 - 9/14/12, $49,204
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.
Adina Paytan (University
of California, Santa Cruz)
Phosphorous sources and cycling in the deep biosphere –
fueling life in the dark
10/1/11 - 9/30/13, $50,000
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.
Craig Moyer (Western Washington University)
Zetaproteobacteria and associated microbial communities
from the Okinawa Trough subsurface biosphere
2/1/12 - 1/31/13, $50,000
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.
Karen Lloyd (University of Tennessee, Knoxville)
Using single cell genomics to determine the roles of uncultured
microbes in the deep subsurface carbon cycle
2/1/12 - 1/31/13, $50,000
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.
Carol Arnosti (University of North Carolina, Chapel Hill)
Measuring microbial extracellular enzymes that hydrolyze deeply
buried organic matter: An analytical challenge and opportunity
2/15/2012 - 2/14/2013, $49,891
In subsurface environments, heterotrophic microbial communities
access complex organic matter in order to survive. The rates
and means by which they remineralize deeply buried organic
carbon are still topics of speculation, due to a lack of methods
for measuring specific carbon-degrading activities of these
communities. The paucity of information, in turn, is related
to technical limitations of standard methods, including methods
for measuring microbial enzymatic activity, the initial step
in degradation of high molecular weight organic matter. To
date, there are only 2 publications (Coolen et al., 2000;
2002) on microbial enzyme activities in sediments at depths
greater than ca. 20 cm. The proposed project will adapt a
technique developed by the P.I. to measure microbial enzyme
activities in surficial sediments so that it can be used routinely
(also aboard ship) in deep subsurface sediments. Initial experiments
suggest that using fluorescently labeled macromolecules, enzymatic
hydrolysis rates and substrate structural specificities can
be determined in deep subsurface sediments. Once the method
has been thoroughly tested and standardized, it can be combined
in the future with targeted investigations of heterotrophic
metabolism and gene expression in order to obtain a more complete
picture of the controls on heterotrophic life in subsurface
environments.
Jennifer Biddle (University of Delaware)
The deep biosphere of the Iberian Margin: microbiological
studies for IODP Expedition 339, Mediterranean Outflow
2/15/12 - 1/31/13, $50,000
IODP Expedition 339 is scheduled to begin coring sediments
in the area of the Meditteranean Outflow on November 17, 2011.
This expedition is primarily focused on paleooceanography
and we are the only currently confirmed microbiological participants,
accepted as shore-based researchers. We propose to study the
microbial population in these sediments using sequencing and
cultivation based approaches in order to examine what microbes
are present, their activity and how they relate to the depositional
environment created by the Meditternaean outflow waters. Cultivations
will focus on iron, sulfur and methane metabolisms. Sequencing
efforts will aim to describe what bacteria and archaea are
present and will attempt to use QPCR-based methods to determine
the relative abundances of each domain. Both cultivation and
sequencing approaches will be used to tie microbial presence
to depositional environment of the sediment, in an attempt
to tie microbial ecology with paleooceanography. This study
will offer the first and only look at deep sediments from
this active margin and allow for comparison to other well-studied
margin environments.
Alfred Spormann (Stanford University)
Genomic biology and population structure of dehalogenating
Chloroflexi in deep sea sediments
3/1/12 - 2/28/13, $49,989
The physiological basis of microbial life in the deep biosphere
is unknown and one of the last frontiers in microbial biology
and biogeochemistry. One challenge is to find useful model
microorganisms that have key features of deep biosphere microbes
including utilizing low amounts of free energy, low substrate
turnover rates, long periods of starvation, but are also amenable
to basic laboratory studies. We propose to investigate by
genomic methods dehalogenating Chloroflexi, in particular
Dehalococcoides (Dhc), as a dominant group of microbes
found in some deep sea sediments. From studies of Dehalococcoides
involved in reductive dechlorination of choroethenes in anthropogenically
polluted surface environments we know that these microbes
are restricted to a unique catabolism, which is the reductive
dehalogenation of organohalogens with H2
mediated by reductive dehalogenases, encoded by rdh
genes. Based on our previous findings we hypothesize that
dehalogenating Chloroflexi found in deep sea sediments
conserve energy by reductive dehalogenation of naturally occurring
organohalogens. Moreover, the deep sea sediment dehalogenating
Chloroflexi are under different selective pressure
compared to their surface relatives, which should be reflected
in different genomic features. We propose molecular and genomic
studies of sediment samples obtained from Eastern Equatorial
Pacific and Peru Margin, Leg 201, South Pacific Gyre (IODP
329) Costa Rica (IODP 344) and the Loihi Seamount, Hawaii
to determine the genome of single Dhc cells, to analyze the
structure of rdh genomic islands, to determine population
structure of Dhc in these sediments, and to determine rdh
molecular diversity. We expect that the results of these comparative
studies will provide novel insights into the ecophysiology
and population structure of slow growing deep sea microbes.
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
4/1/12 - 3/31/13, $49,919
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.
NEW!
William Orsi, Virginia Edgcomb (Woods Hole Oceanographic Institution),
Jennifer Biddle (University of Delaware)
The distribution and activity of marine subsurface fungi
7/1/2012-6/30/2013, $49,441
Little is known about which microorganisms have the most
impact on biogeochemical cycles in the subsurface, and practically
nothing is known about microbial eukaryotes (mEuks) in these
ecosystems. During the first year of the C-DEBI funded postdoctoral
fellowship project “World-wide Exploration of Microbial
Eukaryote Diversity and Activity in the Marine Subsurface”
we produced the first survey of active subsurface mEuks across
a globally distributed sample collection of sediments from
up to 48 meters below seafloor (mbsf). The data reveal a dramatic
increase in fungal diversity with increasing sediment depth.
Unique communities of fungi inhabit different locations and
are selected for as a result of geographic isolation and differential
responses to in situ geochemical conditions. These
findings support the hypotheses that the diversity of subsurface
fungi increases substantially with sediment depth, and that
fungi may play an important role in large scale elemental
cycling and organic substrate turnover in the marine subsurface.
We propose to test these hypotheses by 1) surveying fungal
diversity across five depths from Iberian Margin sediments
spanning 10-120 mbsf, and 2) sequencing metatranscriptomes
for analysis of fungal derived message RNA coding for functional
proteins in Peru Margin (IODP site 1229) sediments from 5
and 50-mbsf.
NEW!
Everett Salas (Photon Systems) and Jason Sylvan (University
of Southern California)
Quantification and spatial heterogeneity of microbial
biomass in subsurface igneous marine basement
8/1/12 - 7/31/13, $49,417
This project aims to quantify microbial biomass in subsurface
oceanic crust collected during Integrated Ocean Drilling Program
Expedition 330 to the Louisville Seamount Chain. No data currently
exists on biomass in subsurface ocean crust, despite the fact
that models predict microbial biomass in oceanic crust may
be equal to or greater than in marine sediments. We will combine
recent advances in cell counts using Nycodenz gradient separation
of cells from rocks and subsequent quantification via flow
cytometry with spatial analysis of microbial biomass using
deep UV native fluorescence imaging. The bulk cell counts
provide direct quantification of microbial biomass with meter
scale resolution while deep UV native fluorescence provides
information on the centimeter scale heterogeneity of microbial
biomass in oceanic crust. The data generated will be analyzed
for correlation with porosity, degree of oxidation, density
and elemental composition of the samples to determine if subsurface
microbial biomass in ocean crust can be predicted from known
variables. Additionally, comparison of the deep UV analysis
with an accepted methodology will help ground truth this new
tool. This will be the first quantitative analysis of biomass
in subsurface oceanic crust and will provide data to use in
models quantifying subsurface biomass.
NEW!
Beth Orcutt (Bigelow Laboratory for Ocean Sciences)
The Dorado Outcrop low-temperature ridge flank environment:
Exploring the microbial ecology and biogeochemistry of sediments,
fluids, and basement in a globally significant but understudied
deep marine biosphere
12/1/12 - 11/30/13, $49,995
Although high-temperature ridge axis and ridge flank hydrothermal
systems have been studied for decades, little is known about
the geochemistry and microbiology of low-temperature venting
on the ridge flanks. Such low-temperature ridge flank systems
are globally abundant and are inferred to drive enormous fluxes
of fluid, heat and solutes – on a scale larger than
fluxes through high-temperature hydrothermal systems. The
Dorado outcrop on the eastern flank of the East Pacific Rise
represents an ideal system for studying microbial systems
associated with low-temperature venting, as it is characterized
by large estimated fluxes (103 – 104
L/s) and low temperatures (10-20°C) of venting fluids at a
small basement outcrop, thus providing a highly focused system
similar to the high-temperature counterparts at ridge axes.
Working in collaboration with colleagues that have recently
received funding to characterize the Dorado Outcrop geophysically
and geochemically, I propose to participate in this cruise-of-opportunity
to collect samples for coupled biogeochemical and molecular
microbiological analyses. This preliminary work at the Dorado
Outcrop is expected to provide a background of information
for evaluating whether this site is a suitable location for
a second generation C-DEBI focus site.
NEW!
Jan Amend and Roy Price (University of Southern California)
A Lost City-type hydrothermal system in readily accessible,
shallow water
12/1/12 - 11/30/13, $49,440
Diverse microbial communities associated with hydrothermal
vents thrive by taking advantage of the chemical disequilibria
established as hydrothermal fluids mix with seawater. Hydrothermal
vents discharge fluids that have evolved at high temperatures
and pressures far beneath the seafloor, and thus can be viewed
as “windows” into the subsurface biosphere. Serpentinite-hosted
hydrothermal systems have garnered much attention in recent
years, particularly since the discovery of the Lost City and
associated microorganisms. These sites have profound implications
for early Earth conditions and the origin of life. Our research
targets the Needle of Prony hydrothermal site (NPHS) in New
Caledonia, potentially a shallow-sea analog to the Lost City.
This site results from serpentinization, creating a reduced,
alkaline (pH ~11), warm (30 to 50 ºC) hydrothermal fluid that
mixes with surrounding seawater while precipitating a 35 m
high carbonate and brucite tower. Unlike the LCHF, serpentinization
at NPHS is caused by downward circulating meteoric water.
Thus, the discharging fluids are low salinity compared to
seawater, which may have important consequences for the microbial
communities at the site. Furthermore, the vents at the Prony
site occur within the photic zone, thus providing the opportunity
for not only chemosynthesis, but also photosynthesis in a
marine serpentinite-hosted system. While long-term investigations
are expected at the site, we will first establish baseline
data to confirm our hypothesis that the vent fluids and precipitates
at NPHS contain products of serpentinization (e.g., elevated
concentrations of H2, CH4, and low molecular weight hydrocarbons),
and similar microbial communities compared to the LCHF.
NEW! Chris House and Leah Brandt (Pennsylvania State University)
Investigating the active microbial community members as a function of temperature in a hydrothermal subsurface
2/1/13 - 1/31/14, $50,000
The deep, dark, marine subsurface biosphere has become an area of intense biogeochemical investigation because it represents a significant portion of Earth’s living biomass and, thus, influences global geochemical processes. A subset within the marine subsurface is hydrothermal vent systems, which support a unique community of life due to adaptations to high temperatures. IODP Expedition 331 to the deep, hot biosphere recovered a unique set of deep sediments because the samples are influenced by laterally migrating hydrothermal fluid and also geographically are located within a continental margin settings. We propose to use RNA analyses to investigate the active microbial community members within the subvent biosphere to determine whether they are functionally diverse and are potentially adapting to the increasingly high temperature conditions.
NEW! Joaquin Martinez Martinez (Bigelow Laboratory for Ocean Sciences)
Viral genetic richness and functions that shape the microbial community at the Juan de Fuca Ridge
2/1/13 - 1/31/14, $49,999
Abundant physicochemical data for high-temperature ridge axis and ridge flank hydrothermal systems have been available for decades. Recently, several studies have explored the microbiology of these systems, mostly the bacterial and archaeal components. However, relatively few studies have estimated abundance and diversity of viruses in hydrothermal vent systems. Two of these studies focused on samples from the main Endeavour Field at the Juan de Fuca Ridge. Yet, despite the known importance of viruses in shaping microbial communities in aquatic and terrestrial systems, information about viral diversity and the way viruses interact and affect ecology and evolution within hydrothermal habitats and the deep biosphere remains very limited. I propose to employ state-of-the-art molecular techniques in combination with bioinformatic tools to investigate the diversity of viruses and their unicellular hosts in samples collected from the deep biosphere of the Juan de Fuca Ridge flank, a focus site of C-DEBI. The samples for this study were collected from the IODP Hole U1362B CORK observatory in 2011 by Dr. Beth Orcutt. The results from these analyses are expected to provide clues regarding the way viruses affect microbial diversity and evolution, and the prevalence of different infection strategies occurring at the Juan de Fuca Ridge flank.
NEW! Scott Wankel (Woods Hole Oceanographic Institution) and Wiebke Ziebis (University of
Southern California)
Autotrophy and heterotrophy supported by microbial nitrogen cycling in sediments underlying the oligotrophic ocean: A stable isotope study of North Pond porewaters
2/1/13 - 1/31/14, $50,000
Basic questions remain regarding the nature of life in the deep subsurface biosphere. For example, with the realization that oxygen and/or nitrate entirely penetrate sediments underlying vast areas of oligotrophic ocean, our understanding of subsurface biogeochemistry requires some reevaluation. In contrast to the importance of sulfur and methane cycling in continental margin sediments, evidence suggests nitrogen may be an important driver, of both autotrophic and heterotrophic processes, in the subsurface underlying these immense regions of the ocean; yet, the specific role of nitrogen in supporting subsurface microbial activity remains largely unexplored. Porewaters from IODP Expedition 336 to North Pond (North Atlantic Ocean), which demonstrate NO3- accumulation with depth, strongly implicate the process of nitrification as both an autotrophic sink of O2 and a source of NO3- supporting heterotrophy via denitrification where O2 is absent; however, the relative magnitude of these and other nitrogen metabolic processes is unclear. This project addresses this gap through measurement of N (and O) stable isotopes of porewater NO3- and NH4+ together with direct rate measurements of key nitrogen cycling processes. Together with geochemical modeling, this approach will yield a direct perspective on subsurface carbon and nitrogen cycles and their potential impact on global elemental cycles.
NEW! Andrew Steen (University of Tennessee Knoxville)
Novel peptidases in subsurface sediments: Activities and substrate specificities
3/1/13 - 2/28/14, $49,970
Recent evidence indicates that a large fraction of microbial cells in the deep subsurface may be organoheterotrophs, capable of metabolizing complex organic compounds. However, direct geochemical investigation of the ability of deep subsurface communities to degrade macromolecules has been lacking. Here, I propose to investigate the kinetics of six extracellular peptidases (protein-hydrolyzing enzymes) in subsurface sediments of the White Oak River estuary, NC. Previously published reports of extracellular peptidase activity have measured only a single peptidase, leucyl aminopeptidase. This is a major limitation, because leucyl aminopeptidase represents a tiny fraction of the total diversity of peptidases, and because genomic data and preliminary measurements indicate that other classes of peptidase are far more important in subsurface sediments. Furthermore, I will assess the substrate specificity of diverse sediment peptidases using a novel, quantitative approach based on competitive inhibition experiments. Measurements of extracellular peptidase activities will reveal the geochemical potential for protein metabolism in subsurface communities, and measurements of substrate specificities will yield insights into the chemical nature and ecological function of those peptidases. Together, these experiments will begin to reveal the mechanisms by which subsurface heterotrophs access complex organic matter, and will facilitate the development of novel enzymological methods relevant to the dark biosphere.
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Costantino Vetriani (Rutgers University)
Heterotrophy in deep-sea reducing environments: Physiology and metabolism of aerobic hydrocarbonoclastic bacteria
3/1/13 - 2/28/14, $49,972
We propose to use a combination of culture-dependent and independent approaches to investigate aerobic hydrocarbonoclastic bacteria as a model system for heterotrophic processes in deep-sea reducing environments. These microorganisms live at the interphase between reducing environments and bottom seawater and oxidize subseafloor-generated hydrocarbons to fatty acids. The relevance of the proposed research to the C-DEBI themes lies in the contribution of hydrocarbonoclastic bacteria to the recycling of buried organic matter, effectively linking the subsurface environment to the ocean. Our experimental strategy includes the identification and quantitation of genes and gene transcripts encoding for key enzymes in the oxidation of medium- and long-chain n-alkanes. The proposed study will provide a link between diversity and function in deep-sea aerobic hydrocarbonoclastic bacteria as well as insight into the evolution of different hydrocarbon oxidation pathways.
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