As the world faces global change and resource limitation, understanding the planet’s microbes becomes necessity. Microbes drive the biogeochemistry that runs the planet, and are central to human endeavors, from food to health to industry. Viruses that infect microbes (phages) profoundly shape microbial populations and processes by acting as both major predators and sources of new genes. I work to understand viral impacts on globally important microbial processes. As an empiricist, I test hypotheses through direct systems-level studies of natural populations, complemented by developing and studying model phage-host systems in the lab. I seek to generate the data required for predictive ecosystem modeling. The globalscale of the TARA OCEANS collected viral archive provides unprecedented windows into viral ecology, having captured nearly all viral particles [ref. 6] with minimally-biased preparations [refs. 3, 4] and remarkable multitrophic (identity and gene expression) ‘Ecosystems Biology’-scale contextualization afforded by the broader Consortium efforts. Beyond the large-scale community genomic sequencing (70 are already funded), this work will take place in the context of extensive innovative and cutting methods developed specifically to elucidate nutrient-virus-host interactions from the single-cell [ref. 1] to population-genomic [refs. 2, 5, 6] scales.
- Allers, E., et al., phageFISH: Detecting viral infection of microbial hosts at the single−cell level. 2012. in review.
- Deng, L., et al., Contrasting strategies of viruses that infect photo- and heterotrophic bacteria revealed by viral-tagging. 2012. in review.
- Duhaime, M., et al., Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Environ Microbiol, 2012. in press.
- Hurwitz, B.H., et al., Comparative evaluation of methods to concentrate and purify wild ocean virus communities through replicated metagenomics. Environ Microbiol, 2012. in press.
- Ignacio-Espinoza, J.C. and M.B. Sullivan, Phylogenomics of T4 cyanophages: Lateral gene transfer in the “core” and origins of host genes Environ Microbiol, 2012. in press.
- John, S.G., et al., A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environmental Microbiology Reports, 2011. 3(2): p. 195-202.
1 postdoc working on ecology and evolution of ocean viruses
For application, please send your CV to Matthew.