Funded Postdoctoral Fellowship Projects

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

Katherine Inderbitzen, University of Alaska (C. Geoffrey Wheat)
Evaluating fluid circulation and geochemical constraints in a sedimented rift:
Integrated data analysis

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 Such an integration is possible with the rich data sets (published and unpublished) from Middle Valley on the Juan de Fuca Ridge.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.

Anne-Kristin Kaster, Stanford University (Alfred Spormann)
Studying genomic and population biology of dehalogenating Chloroflexi in deep sea sediments by single cell sorting and single cell genome amplification

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.

John Kirkpatrick, University of Rhode Island (Steven D'Hondt)
Investigating a mysterious ammonium flux and its relation to the microbial community

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.

NEW! Doug LaRowe, University of Southern California
Bioenergetic profiles of microbial activity in the marine subsurface

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.

Julie Meyer, Marine Biological Laboratory (Julie Huber)
Functional gene diversity and expression in ocean crust microbial communities

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.

William Orsi, Woods Hole Oceanographic Institution (Virginia Edgcomb; Jennifer Biddle, University of Delaware)
World-wide exploration of microbial eukaryote diversity and activity in the marine subsurface

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, University of Southern California (Katrina Edwards)
Metagenomic insight from hydrothermally influenced rocks at East Lau Spreading Center and Valu Fa Ridge using 454-pyrosequencing and ion torrent sequencing

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.

> See more on our postdoctoral scholar program.