Matthew B. Sullivan, Ph.D.

Viral impacts on globally important microbial processes

 

As the world faces global change and resource limitation, understanding the planet's microbes becomes necessity. This is because microbes drive the biogeochemistry that runs the planet, and are centra

Matthew B. Sullivan, Ph.D.
 

Research Description

As the world faces global change and resource limitation, understanding the planet's microbes becomes necessity. This is because 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.

We work to understand viral impacts on globally important microbial processes. As empiricists, we test hypotheses through direct systems-level studies of natural populations, complemented by developing and studying model phage-host systems in the lab with the goal of generating the data required for predictive ecosystem modeling. Practically, we develop new ways to "see" viruses — in the microscope, in environmental sequence datasets, in experiments — i.e., we are learning how to "count" across different data types.

Given this quantitative toolkit, current research questions include:
1) What is a viral population or species?
2) How do viral assemblages change over space and time, and what drives these patterns?
3) How do bottom-up processes impact top-down predators?

Research Impact

This Investigator Award seeks to develop new ways to see viruses in diverse data types from both simplified laboratory experiments and complex natural communities. Broadly, three aims are envisioned:

Aim 1 – Explore methods for comprehensively characterizing 20 ocean viral communities beyond metagenomics.
Aim 2 - Develop 5 novel, ecologically-relevant isolates into model phages for hypothesis testing.
Aim 3 – Collaboratively advance predictive modeling, population and single-cell studies of wild communities, and informatics

This work directly addresses MMI goals to uncover principles that govern microbial interactions, and microbially-mediated nutrient flow in the environment. While many questions and hypotheses will be addressed by the proposed work, I highlight several scientific deliverables of broad community interest: (i) a map of ocean viral morphotype abundances at 20 dispersed global locations, (ii) improved knowledge of viral-encoded ‘unknown’ and ‘host’ sequences, (iii) ultrastructure of novel viral types, (iv) richly annotated viral protein clusters, invaluable for community metagenomic studies, (v) virus-host and virus-host-nutrient interaction data for predictive modeling, and (vi) significant advancement of single-cell and population-genomic analytical capabilities. Many of these approaches are new or yet-to-be-invented – so high-risk, high-reward – yet even partial success should greatly advance the field. Finally, to actively engage the science community and make new methods broadly available, interdisciplinary workshops will be hosted in 2015 (ASM Viromics Workshop) and 2017 (Environmental Virology Workshop 2).

Media Press

JGI News and Publications - Decoding Virus-Host Interactions in the Oxygen-Starved Ocean

ASU News - ASU experts follow gut reaction in autism treatment Study

UA News - Tiniest Catch: UA Scientists' Fishing Expedition Reveals Viral DIversity in the Sea

JGI News and Publications - Dyeing to Learn More About Marine Viruses

UA News - The Viruses You Don't Know About (Yet)

 
 

related links

Marine Microbiology Initiative Science University of Arizona, Sponsored Projects Services Back

Education

Ph.D., Biology
Massachusetts Institute of Technology/Woods Hole Oceanographic Institute, 2004

M.Phil., Biology
Queens University, United Kingdom, 1998

B.S., Marine Science
Long Island University, Southampton College, 1997

Awards

Fulbright Scholarship, 1998

Papers

Roux, S., A. K. Hawley, M. Torres Beltran, M. Scofield, P. Schwientek, R. Stepanauskas, T. Woyke, S. J. Hallam, & M. B. Sullivan. (2014). Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta- genomics.. doi: 10.7554/eLife.03125

Holmfeldt, K., C. Howard-Varona, N. Solonenko, & M. B. Sullivan. (2014). Contrasting genomic patterns and infection strategies of two co-existingBacteroidetespodovirus genera. Environ Microbiol. doi: 10.1111/1462-2920.12391

Deng, L., J. C. Ignacio-Espinoza, A. C. Gregory, B. T. Poulos, J. S. Weitz, P. Hugenholtz, & M. B. Sullivan. (2014). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature. doi: 10.1038/nature13459

Zhao, Y., B. Temperton, J. C. Thrash, M. S. Schwalbach, K. L. Vergin, Z. C. Landry, M. Ellisman, T. Deerinck, M. B. Sullivan, & S. J. Giovannoni. (2013). Abundant SAR11 viruses in the ocean. Nature, 494(7437), 357-360. doi: 10.1038/nature11921

Weitz, J. S., T. Poisot, J. R. Meyer, C. O. Flores, S. Valverde, M. B. Sullivan, & M. E. Hochberg. (2013). Phage-bacteria infection networks. Trends Microbiol, 21(2), 82-91. doi: 10.1016/j.tim.2012.11.003

Solonenko, S.A., J. C. Ignacio-Espinoza, A. Alberti, C. Cruaud, S. J. Hallam, K. T. Konstantinidis, G. W. Tyson, P. Wincker, & M. B. Sullivan. (2013). Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics, 14(320). doi: 10.1186/1471-2164-14-320

Prather, Kimberly A., Timothy H. Bertram, Vicki H. Grassian, Grant B. Deane, M. Dales Stokes, Paul J. DeMott, L. I. Aluwihare, Brian P. Palenik, F. Azam, John H.  Seinfeld, Ryan C. Moffet, Mario J. Molina, Christopher D. Cappa, Franz M. Geiger, Gregory C. Roberts, L. M. Russell, Andrew P. Ault, J.  Baltrusaitis, Douglas B. Collins, Craig E. Corrigan, Luis A. Cuadra-Rodriguez, C. J. Ebben, S. D. Forestieri, Timothy L. Guasco, S. P. Hersey, M. J. Kim, W. F. Lambert, R. L. Modini, W. Mui, B. E. Pedler, Matthew J. Ruppel, O. S. Ryder, N. G. Schoepp, R. C. Sullivan, & D. Zhao. (2013). Bringing the ocean into the laboratory to probe the chemical complexity of sea spray aerosol. Proc Natl Acad Sci U S A, 110(19), 7550-7555. doi: 10.1073/pnas.1300262110 

Ignacio-Espinoza, J.C., S. A. Solonenko, & M. B. Sullivan. (2013). The global virome: not as big as we thought? Curr Opin Virol, 3(5), 566-571. doi: 10.1016/j.coviro.2013.07.004

Hurwitz, B. L., & M. B. Sullivan. (2013). The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology. PLoS One, 8(2), e57355. doi: 10.1371/journal.pone.0057355.t001

Hurwitz, B. L., L. Deng, B. T. Poulos, & M. B. Sullivan. (2013). Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environ Microbiol, 15(5), 1428-1440. doi: 10.1111/j.1462-2920.2012.02836.x

Brum, J. R., R. O. Schenck, & M. B. Sullivan. (2013). Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses. ISME J, 7(9), 1738-1751. doi: 10.1038/ismej.2013.67

Affiliated Investigators