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Grants List

Grants

Courtesy of Gregory Dick and Chris German

University of Michigan, Department of Geological Sciences

Unveiling the microbial communities that underpin deep-sea biogeochemistry

To investigate and model the dynamics of whole microbial communities that inhabit distinct geochemical provinces in the deep sea associated with seafloor volcanic activity. The research aims to improve understanding of how these microbial communities regulate the flow of energy and nutrients from beneath the seafloor into the deep ocean and how these communities respond to natural environmental perturbations.

Title: Unveiling the microbial communities that underpin deep-sea biogeochemistry
Date Awarded: Oct 2010
Amount: $1,718,987
Term: 37 months
Grant ID: GBMF2609
Funding Area: Science, Marine Microbiology Initiative

Abstract:

Deep-sea hydrothermal vents are submarine hot springs that occur along the mid-ocean ridges on the seafloor around the world. At these vents, hot water enriched in chemicals such as sulfur, hydrogen and iron is injected into the deep sea, providing energy that sustains famously dense and diverse chemosynthetic ecosystems and serving as a significant source of elements and nutrients that play a key role in the broader chemistry and biology of the oceans. At the foundation of these vent ecosystems are microorganisms. Though too small to be seen by the naked eye, microbes have a big impact on the chemistry and biology of this extreme environment. First, they convert chemical energy from the vents into forms that can be used by animals. Second, they modify the elements that are coming out of vents, influencing their fate and the ultimate chemical and biological impact on the oceans. This interplay between vent chemistry and microbiology is being studied at two deep-sea vent systems: Guaymas Basin in the Gulf of California and the Mid-Cayman Rise in the Caribbean.

Our project addresses two over-arching questions: (1) how does vent chemistry fuel chemoautotrophic growth and thus shape microbial communities, and (2) How do microorganisms influence the form and ultimate fate of key vent inputs such as iron and manganese, for which vents are the major oceanic source? Of particular interest is the rising portion of hydrothermal plumes, which hosts important biogeochemical processes but is challenging to sample due to its dynamic nature. To overcome this challenge, we are developing a system that collects discrete samples and preserves them in situ for geochemical and microbiological characterization. These samples are being studied by metagenomics, metatranscriptomics, bulk geochemistry and synchrotron X-ray spectroscopy to track the co-evolution of microbiology and geochemistry in rising deep-sea hydrothermal plumes. A major goal is to define the energy metabolism and characterize gene expression patterns of dominant plume microorganisms under varying geochemical conditions. This data is being synthesized through integration into physical and biogeochemical models that explicitly represent the role of microorganisms in hydrothermal plume biogeochemistry.

Read more:

Anantharaman, K., J. A. Breier, C. S. Sheik, & G. J. Dick. (2013). Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria. Proc Natl Acad Sci U S A, 110(1), 330-335. doi: 10.1073/pnas.1215340110

Baker, B. J., R. A. Lesniewski, & G. J. Dick. (2012). Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume. ISME J, 6(12), 2269-2279. doi: 10.1038/ismej.2012.64

Baker, B. J., C. S. Sheik, C. A. Taylor, S. Jain, A. Bhasi, J. D. Cavalcoli, & G. J. Dick. (2013). Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. ISME J. doi: 10.1038/ismej.2013.85

Dick, G. J., K. Anantharaman, B. J. Baker, M. Li, D. C. Reed, & C. S. Sheik. (2013). The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Front Microbiol, 4, 124. doi: 10.3389/fmicb.2013.00124

Lesniewski, R. A., S. Jain, K. Anantharaman, P. D. Schloss, & G. J. Dick. (2012). The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs. ISME J, 6(12), 2257-2268. doi: 10.1038/ismej.2012.63

Li, M., S. Jain, B. J. Baker, C. Taylor, & G. J. Dick. (2013). Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume. Environ Microbiol. doi: 10.1111/1462-2920.12182

Sheik, C. S., S. Jain, & G. J. Dick. (2013). Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics. Environ Microbiol. doi: 10.1111/1462-2920.12165

Toner, Brandy, Matthew Marcus, Katrina Edwards, Olivier Rouxel, & Christopher German. (2012). Measuring the Form of Iron in Hydrothermal Plume Particles. Oceanography, 25(1), 209-212. doi: 10.5670/oceanog.2012.19

Zeng, T., W. A. Arnold, & B. M. Toner. (2013). Microscale characterization of sulfur speciation in lake sediments. Environ Sci Technol, 47(3), 1287-1296. doi: 10.1021/es303914q

Products: 

Bioinformatics scripts and protocols - https://github.com/Geo-omics/scripts      

 

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