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1. Microbial Metagenomics
Microbes play fundamental roles in all biology-associated processes on the planet. A powerful new tool in such studies is metagenomics wherein one uses high throughput DNA sequencing methods on DNA isolated directly from environmental samples. Metagenomics has the potential to revolutionize our understanding of the normally hidden yet incredibly important world of microorganisms. However this great potential comes with enormous challenges in the analysis of the sequence data, including (i) the fragmentary nature of sequence data, (ii) the sparse sampling of genomes, populations and communities, and (iii) the unknown phylogenetic diversity and ecological structure of the communities being sampled. We are now working on methodology for analysis of metagenomic data as part of a new collaborative project: Integrating Statistical Evolutionary, and Ecological Approaches to Metagenomics (iSEEM). The iSEEM Project, funded by the Gordon and Betty Moore Foundation, takes an integrated, interdisciplinary approach to metagenomic analysis. We will be working with the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) to make any methods we develop available to the broader community.
Collaborators: Jonathan Eisen (UC Davis) and Katie Pollard (UCSF)
2. Microbial Diversity in Mediterranean-climate regions
Microorganisms comprise much of Earth ’s biodiversity and play critical roles in biogeochemical cycling and ecosystem functioning, yet little is known about their spatial distribution. We are using beta-diversity analyses as a theoretical tool to answer questions about the relative importance of dispersal history and environmental heterogeneity in controlling the spatial scaling of microbial diversity. We are determining microbial beta diversity patterns by generating a spatially-explicit set of microbial diversity data, sampled on a global scale. These data are have been generated by surveying soils in the Mediterranean-climate regions of California, Chile, South Africa, and Australia, using molecular methods for microbial community characterization. A variety of statistical tools are being applied to this data set in order to determine the relative importance of the different processes generating and maintaining microbial beta diversity, and how these processes vary with region, spatial scale and taxonomic resolution.
Collaborator: Brendan Bohannan (University of Oregon)
3. Microbial Diversity in the Arctic
There is tantalizing evidence that polar soils could be some of the most diverse microbial communities on the planet. Total genomic diversity in prokaryotic communities calculated from the reassociation rate of DNA isolated from Spitsbergen soils suggests that the Arctic is exceptionally diverse. The presence of this putatively unusual, perhaps unique, biological community is likely a function of latitude and low temperatures. Yet in many global warming scenarios the highest latitudes are expected to warm most quickly. This community could be under threat from global warming and might disappear almost before we are able to properly understand it. We are currently characterizing microbial soil diversity in five Arctic habitats using a spectrum of molecular techniques. We wish to confirm our hypothesis of hyperdiversity and, assuming it is correct, devise a plan to rationally document and explore, not only the diversity itself but the forces that have brought this phenomenon to the Arctic.
Collaborators: Lise Øvreås, University of Bergen, Steve Coulson, University Centre in Svalbard, Tom Curtis, University of Newcastle, Bill Sloan, University of Glasgow.