Funded Graduate Student Fellowship Projects

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

Roman Barco, University of Southern California (Katrina Edwards)
Proteomic profiling of neutrophilic, iron-oxidizing Mariprofundus ferrooxydans, strain PV-1, grown under different iron sources

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.

NEW! Delphine Defforey, University of California, Santa Cruz (Adina Paytan)
Nature of labile and refractory phosphorus pools fueling life in deep sub-seafloor sediments

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.

Joseph Russell, University of Delaware (Jennifer Biddle)
Genomic analyses and microbial cultivations in unexplored sub-seafloor ridge flank and continental margin environments

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.

Esther Singer, University of Southern California (Katrina Edwards)
Metagenomic signatures in seafloor rocks and subsurface sediments

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, University of Southern California (John Heidelberg)
Deep phylogenetic and metagenomic analysis of microbial diversity associated with ferromanganese nodules collected from the South Pacific Gyre

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.

> See more on our graduate student fellowship program.