Funded Postdoctoral Fellowship Projects

We are proud to support the following C-DEBI projects.

Anne-Kristin Kaster (Alfred Spormann Laboratory, Stanford University)
Ph.D. Max Planck Insititute for Terrestrial Microbiology, Marburg, Germany (2011)
Studying genomic and population biology of dehalogenating Chloroflexi in deep sea sediments by single cell sorting and single cell genome amplification
3/1/11 - 2/28/13, $120,000

Dehalogenating Chloroflexi, such as Dehalococcoides (Dhc), are members of the rare biosphere of deep sea sediments but were originally discovered as the key microbes mediating reductive dehalogenation of the prevalent groundwater contaminants tetrachloroethene and trichloroethene to ethane. Dhc are slow growing, highly niche adapted, strictly anaerobic microbes, that depend on a supporting microbial community for electron donor and cofactor requirements among other factors. Molecular and genomic studies on the key enzyme reductive dehalogenase encoded by rdh genes, have provided evidence for a rapid adaptive evolution of Dhc and rdh. However, the metabolic life style of Dhc in the absence of anthropogenic contaminants is still unknown. To understand the natural habitat of this unique and important microbial species it is important to analyse non-contaminated deep sea sediment samples by molecular and single cell genomic approaches in order to provide fundamental insights into life style, genomic population structure and evolution of Dhc. Derived correlations may help to assess biodegradative potential for reductive dehalogenation and to identify optimal engineering conditions leading to a more effective management of bioremediation strategies. In addition, this research will be able to answer questions about life within the poorly understood oligotrophic marine surface.

William Orsi (Virginia Edgcomb Laboratory, Woods Hole Oceanographic Institution; Jennifer Biddle, University of Delaware)
Ph.D. Department of Biology, Northeastern University (2010)
World-wide exploration of microbial eukaryote diversity and activity in the marine subsurface
5/1/11 - 4/30/13, $120,000

Practically nothing is known about microbial eukaryotes (mEuks) in the marine subsurface. mEuks are pivotal members of microbial communities because they regenerate nutrients and modify or remineralize organic matter through grazing on prokaryotic and other eukaryotic prey. Thus, mEuks help determine metabolic potentials of microbial communities and influence elemental cycling. Only one study has addressed mEuk diversity in the marine subsurface (Edgcomb et al. 2010), which suggested Fungi dominate the eukaryotic subsurface community and are active in sediments 35 mbsf at the Peru Margin. Thus, some mEuks may be specifically adapted to the deep subsurface and may play significant roles in the utilization and regeneration of organic matter and nutrients in deep-sea sediments.
   One objective of this study will be to further investigate whether Fungi are consistently the dominant group of mEuks in the marine subsurface by examining mEuk diversity in a broad range of subsurface samples from ODP expeditions spanning the world’s oceans. Deep sequencing of SSU rRNA in these samples will provide a proxy for mEuk diversity and activity in the marine subsurface. A second objective will be to ‘ground truth’ an mRNA isolation protocol for mEuks in marine subsurface sediments. Once established, this protocol will enable the third objective, which is the creation of a eukaryotic metatranscriptome from ODP site 1229. This metatranscriptome will provide insights into the functional role of mEuks in the marine subsurface and perhaps new insights into microbial evolution.

Jason Sylvan (Katrina Edwards Laboratory, University of Southern California)
Ph.D. Biological Oceanography, Rutgers University (2008)
Metagenomic insight from hydrothermally influenced rocks at East Lau Spreading Center and Valu Fa Ridge using 454-pyrosequencing and ion torrent sequencing
6/1/11 - 5/31/13, $120,000

This proposal aims to increase our understanding of how microbial communities residing on hydrothermally influenced seafloor rocks vary between rock type and between hydrothermal vent fields located on different host rock compostion. I will employ both proven and newly developed DNA sequencing technology (454 Titanium and the Ion Torrent Personal Genome Machine, respectively) to construct metagenomes from basalt, andesite, and extinct hydrothermal chimney samples collected at the East Lau Spreading Center and Valu Fa Ridge. My goal is to develop next generation sequencing procedures with these rocks for future use with subsurface basalt rocks I will collect on IODP Leg 330 to the Louisville Seamount Chain, December 2010-February 2011.

John Kirkpatrick (Steven D'Hondt Laboratory, University of Rhode Island)
Ph.D. Chemical Oceanography, University of Washington (2011)
Investigating a mysterious ammonium flux and its relation to the microbial community
8/1/11 - 8/31/12, $60,000

This project aims to address one of potentially many novel metabolisms present in the deep biosphere of which little or nothing is known. Considering energy-yielding pathways, several studies focusing on Gibbs energy calculations and known geochemical parameters in other extreme environments have shown hundreds of potentially life supporting redox couples; while these reactions may not be favorable under standard conditions, the deep biosphere is anything but standard. As microbial life can eke out a living using metabolisms right at the edge of possibility, the potential for not only novel organisms, but geochemically relevant ones, is tremendous.
   Specifically, we will be looking at a zone present in a few deep sediment cores, first noted by Schrum et al. (2009) which exhibit ammonium loss in the absence of typical oxidants (i.e. no oxygen, no nitrite). Uptake for biomass production doesn’t appear feasible, either – hence the mystery. Using genetic and isotopic tools, we hope to figure out what organisms may be unique to these zones and investigate the feasibility, previously proposed, of ammonium oxidation coupled to sulfate reduction. Our main sample set includes cores from the Bay of Bengal, though similar features have also been noted off the east coast of the U.S.; potentially, processes such as this could be of global importance.

Julie Meyer (Julie Huber Laboratory, Marine Biological Laboratory)
Ph.D. Marine Biosciences, University of Delaware (2011)
Functional gene diversity and expression in ocean crust microbial communities
9/1/11 - 8/31/12, $59,911

The objective of this project is to determine the diversity, phylogeny, and expression of functional genes involved in carbon, hydrogen, and sulfur cycling in North Pond crustal fluids. These formation fluids are expected to be representative of the ubiquitous cold ocean crust habitat, where reactions between the water and mineral rock surfaces create substrates suitable for sustaining a potentially large reservoir of microbial life. Information regarding crustal microbial communities and the energy sources available for microbial metabolism has been limited by the inaccessibility of samples. IODP Expedition 336 will provide a unique opportunity to access deep subsurface formation fluids from North Pond, including sampling from multiple depth horizons within oceanic crust. My goal is to develop quantitative polymerase chain reaction assays to determine the expression of functional genes in order to increase our understanding of microbial metabolisms in deep subsurface environments.

Katherine Inderbitzen (C. Geoffrey Wheat Laboratory, University of Alaska)
Ph.D. Division of Marine Geology and Geophysics, University of Miami - RSMAS (2012)
Evaluating fluid circulation and geochemical constraints in a sedimented rift:
Integrated data analysis
3/1/12 - 2/28/13, $60,000

In the quest to discover both the extent and limits of microbial life in the subsurface oceanic crustal biosphere, we must first understand fluid circulation patterns and the evolution of rock/fluid composition as circulation occurs within permeable crust. Without knowing what processes dominate fluid chemical evolution and circulation on the flanks of the Juan de Fuca Ridge, it is difficult to make assumptions about the associated microbial biosphere’s distribution and character. This process-based project addresses this issue by integrating geochemical and geophysical data that will allow us to constrain ideal microbial niches within the crust by comprehending the roles of circulation and elemental exchanges at multiple scales. Such an integration is possible with the rich data sets (published and unpublished) from Middle Valley on the Juan de Fuca Ridge. This is not a ridge flank setting, yet Middle Valley exhibits fundamental processes of fluid flow, dissolution, and precipitation with more distinct chemical and thermal gradients than those found on ridge flanks. Thus it will be easier to define nuances of these processes here than elsewhere, where anomalies are difficult to distinguish. Questions addressed will include but are not limited to the following: How do differing scales of circulation affect pore fluid geochemistry and redox conditions in the subsurface? How does the presence/absence of a diagenetic boundary factor into potentially isolating fluids of with distinct compositions (and therefore microbial populations and function) from each other? Results from this study will be useful for characterizing the extent of microbial niches on other sedimented ridges as well as on ridge flanks in general.

NEW! Douglas LaRowe (Jan Amend Laboratory, University of Southern California)
Ph.D. Earth and Planetary Science, University of California, Berkeley (2005)
Bioenergetic profiles of microbial activity in the marine subsurface
4/1/12 - 3/31/13, $60,000

The goal of the proposed postdoctoral research project is to quantify the types and amounts energy that are available to microorganisms at the Juan de Fuca Ridge and North Pond – Mid Atlantic Ridge Focus Study Sites using data collected on IODP Expeditions 327, 336 and earlier expeditions. This will be accomplished by combining compositional data describing these environments with calculations that compare the energetics of potential metabolic processes. The hypothesis driving this proposal is that likely microbial processes can be deduced by calculating what the energetically favorable catabolic reactions are under a given set of conditions. The requisite thermodynamic calculations describing the catalytic activity of microbes will take into account the prevailing temperature, pressure, ionic strength, pH and other compositional conditions. Furthermore, a comprehensive set of organic and inorganic terminal electron acceptors and donors will be considered, including both the consumption of identifiable organic species and molecularly uncharacterized organic matter. Although this approach is tailored to Juan de Fuca and North Pond, the proposed research can be applied to the C-DEBI Study Site, the South Pacific Gyre, as well as other deep subsurface environments where geochemical data are available.

NEW! Benjamin Harrison (Jake Bailey Laboratory, University of Minnesota)
Ph.D. Geochemistry, California Institute of Technology (2011)
Buried alive: microbial responses to sediment flux with implications for the deep biosphere
4/1/12 - 3/31/13, $55,614

The fate of microbial cells in the marine subsurface in response to changes in sedimentation rate as well as discrete burial events is poorly constrained, but potentially critical to our understanding of modern subsurface communities and their impact on the ancient rock record. In order to better understand the impact of sedimentation on the subsurface microorganisms, the proposed research primarily aims to measure transgression of community signatures across a marine/terrestrial sedimentary unconformity on IODP leg 337. The sampling locality off the coast of Japan presents a unique opportunity for studying the transport of marine organisms to depth within the sediment column. These primary environmental samples will be supplemented by requests of turbidite-impacted archival materials from ODP leg 204 and IODP leg 308 selected to investigate vertical migration of microbial communities in response to rapid burial. The results will be compared to a suite of mesocosm experiments exposed to active sedimentation as well as a set of lacustrine samples exhibiting sedimentary transitions, measuring both the active community and coeval changes in sediment mineralogy and chemistry. From these observations I hope to derive molecular and/or mineralogical signatures of microbial community response applicable to both modern and ancient samples, and better constrain the impact of physical sedimentation processes on the microbial diversity ultimately inherited by the deep biosphere.

NEW! Ulrike Jaekel (Pete Girguis Laboratory, Harvard University)
Ph.D. Marine Microbiology, Bremen University (2011)
Microbial transformations of recalcitrant organic carbon in the deep biosphere
10/1/12 - 9/30/13, $60,000

It has been long known that the oceanic crust is the largest aquifer on Earth. However, relatively little is known about how this aquifer influences biogeochemical cycles in the deep ocean. Recent studies suggest that in some seafloor settings, crustal aquifer fluids are replete with oxygen or nitrate, and provide the overlying sediments with additional oxidants. These environments provide a unique opportunity to examine how the availability of oxidants might influence sedimentary biogeochemical processes, in particular recalcitrant organic matter degradation. Specifically, deeper sediments at the North Pond appear to be replenished by oxygen through an upward flux of recharged crustal fluids. Thus, the North Pond represents an ideal natural laboratory to study the fate of recalcitrant organic carbon present in deep anoxic sediments that are being replenished with oxygen and other electron acceptors from below through recharged basement fluids. The proposed project will shed light on the degree to which the availability of oxidants supports the transformation of recalcitrant organic carbon by microbes in these deep subsurface sediments. The assessment of the metabolic potential of crustal microbial communities solidly aligns with the C-DEBI research themes, and our studies in particular are aimed at furthering our understanding of metabolic activity in the deep subseafloor biosphere and the limits of life across the range of habitats encompassing the subsurface biosphere.

NEW! Danielle Morgan-Smith (Matt Schrenk Laboratory, East Carolina University)
Ph.D. Oceanography, Old Dominion University (2012)
Pressure resuscitation of the deep subseafloor biosphere
11/1/12 - 10/31/13, $56,824

Repositories contain thousands of kilometers of cores from hundreds of sites, sampled at great expense and effort, which are currently sitting unused. We will use pressure as a selection factor to grow and isolate endemic piezophilic microbes from these cores. The goal is to establish a method by which native deep biosphere organisms, which may be dormant or slowly growing in core repositories, can be revived as well as to establish stable isolates of subsurface piezophiles which can be used in further studies of physiology and metabolism. If this is successful, it will greatly expand the range of microbiological studies which can be performed on organisms from drill cores representing the largest microbial habitat known. The focus of this study will be subseafloor habitats hosted in ultramafic rocks, and associated with serpentinization, specifically at the Atlantis Massif and Hess Deep locations. Three parallel studies will be undertaken to answer questions of how best to revive these dormant piezophiles, how piezophilic populations change during core storage and under differing storage conditions, and how these populations compare between stored cores from different sampling locations and geochemical environments.

NEW! Brandon Briggs (Hailiang Dong Laboratory, Miami University)
Ph.D. Oceanography, Oregon State University (2012)
Development of a novel and in-situ method to image microbe-mineral associations
3/1/13 - 2/28/14, $60,000

Diverse metabolic reactions occur in marine sediments that directly affect the sedimentary environment and alter the physical and chemical state.  For example, pyrite and carbonate are formed during the process of anaerobic oxidation of methane. However, microbe-mineral interactions are poorly understood in marine sediments and as such the knowledge about the consequences of microbial metabolisms on the sediment geochemistry is lacking.  This lack of knowledge is in part because observations from sedimentary environments are typically based on bulk community and geochemical analysis, where several grams of sediment are mixed for the analysis. The bulk analysis of microbial distributions and mineralogy does not reflect a scale that is relevant to the heterogeneous nature of sediment for microbial communities.  Furthermore, direct observations of microbial associations to these minerals have not been described. Therefore, methods need to be used that can identify the microbe and the surrounding mineralogy. The proposed work aims to increase our understanding of the micron-scale distributions of microbes in deep marine sediment and the mineralogy associated with those distributions.  I will develop a new technique that combines fluorescent in-situ hybridization, electron microscopy, and mineralogical identification on both frozen and freshly preserved sediment samples; thus, allowing the identification of both microbial types and their surrounding mineralogy.  This information aids in the understanding of the extent of life and provides clues into possible respiration on solid phase minerals in deep subsurface environments.

> See more on our postdoctoral scholar program.