Research Team

Matthew B. Sullivan

Ecology and Evolutionary Biology Department

University of Arizona, Tucson, AZ, USA

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, including “host” genes viruses steal that are central to photosynthesis and metabolism that likely drive viral niche-differentiation [refs. 7, 8]. 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 to generate the data required for predictive ecosystem modeling [reviewed in ref. 2]. The globalscale of the Tara Oceans collected viral archive provides unprecedented windows into viral ecology, having captured nearly all viral particles [ref. 11] with minimally-biased preparations [refs. 5, 6, 12, 13] and remarkable multitrophic (identity and gene expression) ‘Ecosystems Biology’-scale contextualization afforded by the broader Consortium efforts.

Beyond the large-scale community genomic sequencing (104 now sequenced), this work is taking place in the context of extensive innovative and cutting-edge methods developed specifically to elucidate nutrient-virus-host interactions from the single-cell [ref. 1, 2, 3] to population-genomic [refs. 4, 7, 9, 10] scales.

Relevant publications

  1. Allers, E. et al. (2013). Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses. Environmental Microbiology. 8:2306-18.
  2. Brum, J. R. & M. B. Sullivan. (2015). Rising to the challenge: accelerated pace of discovery transforms marine virology. Nature Reviews in Microbiology. 13: 147-59.
  3. Dang, V. & M.B. Sullivan. (2014). Emerging methods to study bacteriophage infection at the single-cell level. Frontiers in Microbiology. 5: 724.
  4. Deng, L. et al. (2014). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature. 513:242-5.
  5. Duhaime, M. et al. (2012). Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Environmental Microbiology. 14:2526-39.
  6. Hurwitz, B.H. et al. (2012). Comparative evaluation of methods to concentrate and purify wild ocean virus communities through replicated metagenomics. Environmental Microbiology. in press.
  7. Hurwitz, B. L. et al. (2014). Depth stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome. ISME J in press.
  8. Hurwitz, B. L. et al. (2013). Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biol 14:R123.
  9. Hurwitz, B. L. et al. (2014). Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. PNAS 111:10714-10719.
  10. Ignacio-Espinoza, J.C. and M.B. Sullivan, Phylogenomics of T4 cyanophages: Lateral gene transfer in the “core” and origins of host genes Environmental Microbiology, 2012. in press.
  11. 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.
  12. Solonenko, S.A. et al. (2013). Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics. 14:320.
  13. Solonenko, S.A. & M. B. Sullivan. (2013). Preparation of metagenomic libraries from naturally occurring marine viruses. In E. F. Delong (ed.), Methods in Enzymology: Microbial community "omics": Metagenomics, metatranscriptomics, and metaproteomics Elsevier.

The scientific activities of the Tara Oceans expedition, led by EMBL senior scientist Eric Karsenti, present an unprecedented effort that resulted in 35,000 samples containing millions of small organism collected in more than 210 ocean stations, chosen for their climatic significance or biodiversity.