Simons Postdoctoral Fellowships in Marine Microbial Ecology – Awardees

2017 Awardees

Natalie Cohen, PhD.
Education: University of North Carolina at Chapel Hill, Ph.D., Marine Sciences
Institution: Woods Hole Oceanographic Institution (laboratory of Mak Saito)

Project: Linking trace metal availability with phytoplankton metal metabolism

Trace metals are essential for marine phytoplankton to perform cellular processes including photosynthesis, nitrogen assimilation, and carbon fixation; however, we are currently limited in our understanding of how trace metal distributions influence phytoplankton metal-dependent cellular metabolism in large regions of the open ocean. In particular, it is unclear how shifts in metal availabilities influence metal-containing protein (metalloprotein) usage, and how metal allocations to biochemical pools may vary by taxa. The goal of this proposal is to examine the relationships among trace metal distributions, metalloprotein abundance, and biomarkers of trace metal status in eukaryotic phytoplankton using geochemical, metatranscriptomic and metaproteomic approaches across diverse ocean provinces.

This goal will be addressed through the following research objectives: 1) comparing phytoplankton metalloprotein expression patterns from contrasting water masses of the subtropical and equatorial Pacific Ocean, 2) investigating how metal-dependent metabolism is influenced by the addition of iron or cobalt-dependent vitamin B12 in the North Atlantic Ocean, and 3) evaluating correlative patterns in trace metal distributions and metalloprotein abundance through the Tara Oceans repository of metatranscriptomic, trace metal and environmental metadata.

The first objective will be explored through eukaryotic metaproteomes obtained along a longitudinal transect of the subtropical and equatorial Pacific Ocean, differing in nitrate, iron, cobalt and nickel concentrations. Biomarkers of iron and cobalt-containing-B12 stress will quantified along the transect, and taxa-specific metalloprotein abundances will be analyzed to determine whether diverse phytoplankton rely on distinct trace metal strategies. The second objective will be examined through mesocosm incubation experiments performed on an upcoming research cruise to the subtropical Atlantic Ocean, where trace metal stress seasonally occurs. Combinations of macronutrients (nitrate, phosphate and iron) and micronutrients (iron and B12) will be added to surface seawater to determine how metal-dependent metabolic processes are influenced by changes in metal availability among diverse North Atlantic Ocean phytoplankton assemblages. The third and final objective will be investigated by utilizing the global Tara Oceans metadata and identifying correlative relationships between metalloprotein transcript abundances and trace metal concentrations. These analyses will elucidate how diverse phytoplankton from biogeochemically distinct biomes have structured their metabolism as a function of seawater trace metal regime.


Keisuke Inomura, Ph.D.
Education: Massachusetts Institute of Technology, Ph.D., Climate Physics and Chemistry
Institution: University of Washington (laboratory of Curtis Deutsch)

Project: Predicting ecological niches of diverse nitrogen fixers in the global ocean

Nitrogen fixers alter marine biogeochemistry and ecosystems by adding bioavailable nitrogen. The ocean hosts diverse physiological types of nitrogen fixers; multicellular bundle, unicellular and symbionts. How the physiological traits of each nitrogen fixer shape its ecological niche and geographic distribution is not clear. Here I propose to extend a cellular resource allocation model to include four different nitrogen fixers and then incorporate them into a three-dimensional ocean ecosystem model. I will analyze how physiological traits control the niche of each functional type. I will predict the abundance and distribution of each functional type and rate of nitrogen fixation, and compare to the available observations. This study would improve our quantitative understanding of nitrogen fixers and the rates of nitrogen fixation, contributing to our understanding of ecosystems and biogeochemistry.

Chana Faye Kranzler, Ph.D.
Education: Hebrew University of Jerusalem, Ph.D., Environmental Science
Institution: Rutgers University (laboratory of Kimberlee Thamatrakoln)

Project: Driving marine biogeochemical cycles through phytoplankton host-virus interactions

Marine phytoplankton contribute over 50 percent of the total primary productivity on Earth, making them an important component of the global carbon cycle. Diatoms, eukaryotic phytoplankton that contribute 40 percent of the marine primary productivity, are unique in their obligate requirement for silicon for cell wall formation and growth. As the largest group of siliceous organisms in the ocean, diatoms represent the critical link between the carbon and silicon cycles. Thus, identifying and understanding the factors that regulate diatom growth and mortality is crucial for assessing how these ecologically dominant organisms influence community productivity, biological pump efficiency, and silicon biogeochemistry. Viral infection and subsequent host demise has been shown to significantly impact other phytoplankton groups, but the role that diatom-infecting viruses play in regulating diatom populations is completely unknown. Historically thought to be immune to infection due to the physical protection afforded by their silica cell wall, the identification, isolation and cultivation of diatom host-virus model systems has opened the door for detailed mechanistic studies. Specifically, I plan to combine laboratory-based studies with analysis of targeted field samples of natural diatom populations to determine the effect that viral infection has on both silica production (i.e., cell wall formation) and silica remineralization (the process by which silica returns to a dissolved, bioavailable form). As the most abundant entity in the ocean, viruses play a critical role in shaping microbial ecosystems and driving global biogeochemical cycles. Drawing upon tools from the fields of molecular and cell biology, viral ecology, biogeochemistry and microbial oceanography, this research will explore how viruses impact one of the most globally important and ecologically dominant organisms in the modern ocean.

Stilianos Louca, Ph.D.
Education: University of British Columbia, Vancouver, Ph.D., Mathematical Biology
Institution: California Institute of Technology (laboratory of Victoria Orphan)

Project: Multi-layered biogeochemical models, from genes to microbial communities

Microorganisms are the most ancient and the most diverse life-form on Earth. Through their metabolic activity, millions of different microorganisms are driving global biochemical fluxes and have been shaping the ocean’s chemistry for billions of years. Yet, we understand very little about how microbial metabolism affects marine biogeochemistry, partly because the enormous diversity of microbial communities makes it hard to model them mathematically. Despite the millions of extant microbial species, most global elemental fluxes are driven by a core set of genes for energy transduction, each found within multiple microbial clades. It is conceivable that the dynamics of these genes at ecosystem scales may, to a certain approximation, be modeled independently of the taxa hosting each gene. A gene-centric description of microbial metabolic networks, if accurate, would greatly simplify the modeling of marine ecosystems. The precise distribution of genes across genomes, and co-occurrences of genes with traits not directly related to energy transduction, such as susceptibility to viruses, may constitute “higher order” corrections to gene-centric models. The importance of such corrections is currently unknown. Understanding how genes and genomes interact with their environment to drive biochemical fluxes, is needed for constructing accurate models of the ocean. I will use sediment and biofilm microcosms to investigate the effects of geochemical conditions and microbial community structure on microbial metabolism. I will use DNA sequencing, isotope labeling techniques and substrate enrichments to investigate how the microcosms respond to stimuli. This will give insight into the dynamics of the microbial metabolic networks and allow comparison of these dynamics to various aspects of microbial community structure.

Xuefeng Peng, Ph.D.
Education:Princeton University, Ph.D., Geosciences
Institution: University of California, Santa Barbara (laboratory of David Valentine)

Project: Impact of Marine Fungi on Global Biogeochemical Cycling of C and N

My research as a Simons Postdoctoral Fellow aims at elucidating the potentially significant role marine fungi play in the global biogeochemical cycling of carbon (C) and nitrogen (N). Compared to their terrestrial counterparts, marine fungi are vastly understudied partly because of their cell biology and feeding strategies. As osmotrophs, fungi feed by secreting extracellular enzymes into the environment to depolymerize food substrates before transporting the digested monomers and nutrients back into the cell for growth. Such a lifestyle has largely defined fungi primarily as biomass degraders, and hence they should play an important role in remineralization in global biogeochemical cycles.

Recent evidence has suggested that fungi in marine sediments could be responsible for a significant portion of nitrate removal and the production of nitrous oxide (N2O, a potent greenhouse gas). Moreover, fungi’s ability to degrade large particles in the water column, along with their spore-forming life cycles, provides them a special position in the microbial food web, which remineralizes organic matter in the mixed layer and reduces particle export. However, most of our knowledge describing marine fungi’s ecological and geochemical roles remains qualitative. Little is known about the marine fungi’s activity and their quantitative contribution to geochemical cycles of C and N.

We propose to determine the fungal activity in organic matter degradation and N2O production in coastal and estuarine sediments, coastal seawater and an open ocean oxygen minimum zone. Incubation experiments targeting fungal populations will be performed to quantify their contribution to C and N turnover in marine sediments and water columns. We aim to link fungal abundance and diversity to their activities using next-generation sequencing, which will employ a novel method I developed that effectively extracts fungal DNA and RNA from complex microbial communities and environments. Additionally, we will isolate novel marine fungal strain responsible for C and N turnover.

Wei Qin, Ph.D.
Education: University of Washington, Department of Civil and Environmental Engineering, Ph.D., Environmental Microbiology
Institution: University of Washington, School of Oceanography (laboratory of Anitra Ingalls)

Project: Adaptive significance of marine ammonia-oxidizing archaeal membrane lipids

Marine ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant organisms in the ocean and are now recognized to exert a major control over the oxidation state of nitrogen in marine environments. Marine AOA also make a significant contribution to carbon fixation through chemosynthetic pathways, the production of the greenhouse gases nitrous oxide and methane, and the provision of vitamin B12 to B12-dependent populations in oceanic systems. Marine AOA synthesize the glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids with crenarchaeol, containing a unique cyclohexane ring as the characteristic component. The GDGT membrane lipids form the basis for one of the most commonly employed proxies, the TEX86 proxy, which is used for sea surface temperature reconstructions from the Jurassic to present. Despite widespread application of the TEX86 paleothermometer, mounting evidence suggests that we do not understand the fundamental controls on GDGT distributions in living AOA.

In this project I will investigate the major physiological and environmental controls and the adaptive significance of GDGT compositional plasticity in marine AOA. I will use the most recent technological advances in lipid analysis and high throughput sequencing to evaluate the variation in GDGT distributions among AOA ecotypes across large spatial scales in the ocean. In addition, by combining laboratory and field studies, I will test the influence of environmental and biotic variables on GDGT distributions in pure cultures and natural communities of marine AOA. Finally, I will determine the physical structures and mechanical properties of marine AOA membranes by isolating and characterizing the nanoscale lipid patches with different GDGT compositions and cyclization. Together these studies will determine the fundamental principles controlling the ecophysiology of AOA, advance understanding of their remarkable adaptive capacity in the marine environments, and refine our interpretation of TEX86 records.

 

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