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We are proud to support the following C-DEBI projects.
Esther Singer
(Katrina Edwards Laboratory, University of Southern California)
Metagenomic signatures in seafloor rocks and subsurface sediments
6/15/11 - 6/14/13, $64,000
The seafloor and subsurface microbial world represents a
significant portion of life on our planet. The influence on
its proximate ambience and global processes, such as element
cycles, has potentially been largely underestimated and not
always been precisely evaluated. I am interested in the nature
of deep biosphere microorganisms in rocks from the Loihi seamount,
Hawai’i, the East Pacific Rise, and the Juan de Fuca
Ridge, as well as in sediments from North Pond (Mid-Atlantic).
In order to assess microbial diversity, metabolic activity,
adaptation strategies and biogeographical signatures in the
deep subseafloor biosphere, metagenomics by pyrosequencing
will be used to complement previous research efforts with
the most in-depth and precise data that is available to date.
Benjamin Tully
(John Heidelberg Laboratory, University of Southern California)
Deep phylogenetic and metagenomic analysis of microbial diversity
associated with ferromanganese nodules collected from the
South Pacific Gyre
8/16/11 - 8/15/13, $64,000
The importance of microbial mediation in the biogeochemical
cycles of the ocean is well documented. A major source of
marine metallic minerals exists as ferromanganese (polymetallic)
nodules in the deep ocean (4,000-5,000 m deep). Composed predominantly
of iron, manganese, copper, nickel, and zinc, these nodules
play a key role in governing the biogeochemical availability
of many of these metals in the global ocean. While it is assumed
that microorganisms mediate some of the processes that form
nodules, it is poorly constrained as to which organisms mediate
these processes or how these processes in turn may support
microbial metabolisms. We propose using fingerprinting and
sequencing methods to examine the microbial community diversity
of organism associated with ferromanganese nodule collected
from the South Pacific Gyre. Further, because many of the
microbial organisms present in the deep-sea are novel and
uncultivated, we plan to perform metagenomic analysis to link
phylogenetic identity with physiology, with the goal of generating
(near-)complete environmental genomes. The proposed research
will be the first attempt to determine how the microbiology
of deep oceanic nodules shape and are shaped by the environment.
Roman
Barco (Katrina Edwards Laboratory, University of Southern
California)
Proteomic profiling of neutrophilic, iron-oxidizing Mariprofundus
ferrooxydans, strain PV-1, grown under different iron
sources
8/16/11 - 8/15/13, $64,000
The aim of this proposal is to gain a better understanding
of what subsets of proteins are actually being expressed during
neutrophilic, microbial iron (Fe)-oxidation. The recently
isolated Mariprofundus ferrooxydans, strain PV-1,
will be used as a marine model organism to investigate proteomic
differences under different Fe substrates: aqueous Fe2+ and
solid Fe0. Two-dimensional gel electrophoresis (2D-GE) and
shotgun proteomic methods (LC-MS/MS) will be employed to obtain
results from the cultures grown under different conditions.
The research being proposed would constitute the foundation
for the development of diagnostic tools for the accordance,
distribution, and activity level of Fe-oxidation, a globally
important biogeochemical process at and below the ocean floor.
Luke McKay (Andreas Teske Laboratory, University
of North Carolina, Chapel Hill)
Constraints on microbial biogeography in hydrothermally active
sediments of Guaymas Basin: Energetic limits, physical stressors,
and upward compression of metabolic zones
5/1/12 - 4/30/13, $32,000
Subsurface hydrothermal temperatures and flow cause upward
compression of geochemical and metabolic zones in Guaymas
Basin seafloor sediments. The Guaymas hydrothermal system
can be viewed as an accessible seafloor analog to deep, geothermally
heated sedimentary microbial ecosystems. Using push core samples
collected by the Alvin submersible I am investigating
thermal limits and substrate concentration ranges and their
influence on microbial biogeography. This interdisciplinary
approach employs 16S rDNA clone libraries and CARD-FISH surveys
of Archaea and Bacteria, gas chromatographic coupled mass
spectrometry for substrate concentrations and isotopic values,
and the most extensive shallow thermal data from Guaymas Basin
to date, consisting of 113 temperature profiles. I plan to
identify the range of concentrations of methane, dissolved
inorganic carbon (DIC), sulfate, and sulfide, and isotopic
values for methane and DIC that characterize these sediments
and examine these data for biogeochemical process signatures
and their associated temperature ranges. I will investigate
how “real world” upper temperature boundaries
for microbial life in situ are affected by fluctuating temperature
regimes. Finally, I will determine the distribution of Bacteria
versus Archaea as influenced by depth, temperature, and substrate
availability. This research intends to answer questions regarding
the limits and extent of key microbial processes (anaerobic
carbon remineralization, and methane and sulfur cycling) that
are essential for subsurface life.
Amanda Martino (Christopher House Laboratory,
Pennsylvania State University)
Working around drilling contamination in deep cores: Costa
Rica Margin
6/1/12 - 5/31/13, $32,000
Most microbiology work in marine subsurface sediments has been focused in the upper 100-200 meters of sediment. This is because the switchover from APC to XCB coring generally occurs around this depth, which leads to large increases in drilling-induced contamination. Molecular studies in deeper samples are greatly hindered by interference from these contaminating microbes. The work proposed here would provide two methods of obtaining useful microbiological information from these deeper samples, even in the presence of contamination. It would also provide a thorough molecular characterization of the subsurface community of the Costa Rica Margin down to 780 meters below seafloor.
Joseph Russell (Jennifer Biddle Laboratory,
University of Delaware)
Genomic analyses and microbial cultivations in unexplored
sub-seafloor ridge flank and continental margin environments
7/1/12 - 6/30/13, $32,000
Investigations are proposed to explore the microbial inhabitants
of both the sediment and basalt crust underneath “North
Pond”, a sediment deposit ringed by basalt outcrops
on the western edge of a young ridge flank associated with
the Mid-Atlantic Ridge system. This will be done using a cultivation-based
approach supported by collaborators’ molecular data.
Cultivations will focus on Fe, S, and CH4
redox metabolisms, as well as heterotrophs. A similar approach
will be used to explore the sediments of the continental margin
associated with the Mediterranean Outflow. Enrichments and
cultivation of isolates will be pursued, as well as deep 454-pyrosequencing
and q-pcr analyses in order to understand the diversity and
activity of the microbial population in this margin environment
underlying waters of high productivity. This study aims to
assess the cultivability and physiological tolerances of in-situ
subsurface microbial populations as well as compare new data
from North Pond and Mediterranean Outflow with existing data
from similar environments such as Juan de Fuca Ridge and the
Peru Margin to understand the extent of microbial adaptation
to distinct geographical niches.
Delphine Defforey (Adina Paytan Laboratory,
University of California, Santa Cruz)
Nature of labile and refractory phosphorus pools fueling life
in deep sub-seafloor sediments
7/1/12 - 6/30/13, $32,000
Phosphorus (P) is an essential nutrient that can be limiting
in some environments. Yet, many components of its cycle remain
unclear, including P uptake and cycling in deep-sea sediments.
These are critical, since a significant portion of Earth’s
prokaryotes thrives in deep marine sediments, which are thought
to mainly contain low bioavailable P in mineral phases. This
suggests that microorganisms possess mechanisms to utilize
recalcitrant P pools. Little is known about the specific nature
of those compounds and the microbial mechanisms used. This
study aims to identify the specific P compounds within the
sedimentary labile and refractory P pools that "fuel"
the deep biosphere using 31P-NMR.
NEW!
Kiana Frank (Peter Girguis Laboratory, Harvard
University)
Key variables for modeling rates of microbially mediated
sulfate reduction
7/1/12 - 6/30/13, $32,000
Despite sulfate reduction’s ubiquity in marine systems,
relatively little is known about how environmental or ecological
factors influence rates of sulfate reduction. While numerous
studies have considered how sulfate reduction and methanogenesis
compete for reductants in natural and human-made systems,
less is known about how temperature or metabolite concentration,
such as sulfate and sulfide concentrations, affects rates
of sulfate reduction. Here we use a factorial experimental
design to evaluate the effects of key variables on sulfate
reduction kinetics in sulfide deposits recovered from hydrothermal
vents in the Main Endeavor Field, Juan de Fuca ridge. Microbial
sulfate reduction rates were measured by 35S tracer techniques
over a range of environmentally relevant chemical conditions
(pH, H2S, SO42-, and organic carbon concentrations) and temperatures
(4, 50 and 90°C). Maximum sulfate reduction rates were
observed at 50°C, and sulfate reduction rates had significant
positive correlations with increasing sulfide, pH and sulfate.
However, sulfate reduction rates did not correlate to exogenous
dissolved organic carbon, implicating exogenous hydrogen or
endogenous organic matter as the reductant (or even sulfur
disproportionation). This research presents an opportunity
to better understand the key variables that influence the
rates of microbial sulfate reduction in hydrothermal environments
and provides a framework for modeling sulfate reduction in
mid-ocean ridge systems.
NEW!
Amy Smith (Rick Colwell
Laboratory, Oregon State University)
Modeling rates of olivine bioweathering in ocean
crust
9/24/12 - 9/23/13, $32,000
Microbes may play a major role in the oxidation and dissolution of silicate minerals in igneous ocean crust and may significantly influence geochemical cycling of elements in the ocean. Microbiological and molecular analyses of igneous minerals and glasses incubated in ocean crust indicate that microbial iron oxidation may be a common physiological trait among bacteria in ocean crust with seawater influx, and that olivine may be a major energy source for primary production in the deep, dark igneous biosphere (Smith et al., 2011). I will measure rates of olivine oxidation and weathering in the laboratory using previously isolated model organisms from IODP Hole 1301A on the eastern flank of the Juan de Fuca Ridge to generate a working model of global subseafloor weathering rates based on iron oxidation. C-DEBI’s central research theme “Activity in the deep biosphere: function and rates of global biogeochemical processes” would be directly addressed as a result of this work since this study will aid in assessing the role of microbial life in ocean crust weathering and their impact on geochemical cycling in the oceans through iron mineral-based chemolithotrophy.
NEW!
Sean Jungbluth (Mike Rappe
Laboratory, University of Hawaii)
Ridge flank crustal fluid microbial community genomics, expression, and phylogeny
12/1/12 - 12/1/13, $31,980
Our understanding of microbial life within the seafloor of the dark ocean is still in its infancy; particularly, with respect to the largely inaccessible sediment-covered ocean crust. Despite our profound lack of access, some experts argue that the upper ocean basement is among the most suitable subseafloor environment for microbial life. I have been exploring the deep biosphere of the subseafloor crust on the eastern flank of the Juan de Fuca Ridge by retrieving pristine crustal fluids via sampling and instrumentation platforms known as Circulation Obviation Retrofit Kit (CORK) observatories. Microbiological analysis of crustal fluids has been largely successful and, through C-DEBI support, I am currently applying next-generation sequencing techniques to these rare samples. These efforts include analysis of (1) 16S rRNA genes as a phylogenetic marker from an expansive catalogue of borehole fluid and related samples and (2) whole-community DNA and RNA collected via filtration of large (>70 liters) volumes of crustal fluids in order to characterize the metagenome and metatranscriptome of deep subseafloor crustal fluid-hosted microbial communities.
NEW! Kristin Woycheese (D'Arcy Meyer-Dombard Laboratory, University of Illinois at Chicago)
Comparative analysis of serpentinizing fluids in Turkey and the Philippines: Insights and the “genetic legacy” of deep subsurface microbes
5/16/13 - 5/15/14, $32,000
Serpentinization, an exergonic process by which hydrogen and methane are generated from ultramafic rocks via hydrous alteration, is proposed to support chemolithotrophic growth of microorganisms in subsurface environments (McCollum and Bach 2009). Surface expression of these fluids provides cost-effective and convenient access to deep subsurface microbial communities. This study investigates deep subsurface microbial communities associated with terrestrial serpentinization seeps in Turkey and the Philippines, and aims to address three fundamental questions: Do serpentinizing fluid seeps in terrestrial habitats preserve the “genetic legacy” of deep subsurface communities, particularly with regards to H2-based carbon fixation, and heterotrophic lifestyles such as methanotrophy, SO42- reduction, and Fe3+ reduction? Can this genetic legacy be resurrected upon subsequent exposure to deep subsurface temperatures and pressures? Is lateral gene transfer an evolutionarily favorable survival mechanism for microbial communities that must rapidly adapt to surface conditions (i.e., is transposase activity high at transition zones, e.g. Brazelton et al. 2012)? To address these questions, metagenomic- and transcriptomic-based analysis of communities isolated from fluids and sediment will be conducted. Fluid geochemistry will also be characterized, to aide in the determination of relevant metabolisms. Cultivation of surface samples at high pressure and temperature will be achieved using a high pressure environmental chamber at the University of Illinois at Chicago. The proposed research will increase understanding of the connectivity, relatedness, evolution, and adaptation of subsurface serpentine-hosted microbial communities.
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