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Assistant Professor
07/2011 |
RESEARCH
My research focuses on how microbial communities impact biogeochemistry and global change. Specifically, I use the tools of molecular microbial ecology (examining nucleic acid and protein biomarkers, e.g. through metagenomics, environmental microarrays, etc.) to examine microbial community interactions with their environments, in both terrestrial and marine habitats. To gain a systems-level understanding of these communities and processes, I collaborate heavily with biogeochemists, modelers, and others. My two current projects examine (i) microbial roles in carbon gas emissions from thawing permafrost, and (ii) microbial degradation of pollutants at the Great Barrier Reef.
I am starting a lab group in the SWES department and am actively recruiting motivated undergraduates, graduates and postdocs to join me in this collaborative endeavor to better understand how microbial communities support and drive earth systems, and how they respond to anthropogenic change. If you're interested, email me. To see our currently open postdoc position, on the bioinformatics of meta-omic datasets in thawing permafrost systems, please visit http://www.ecogenomic.org/workace.
EDUCATION
Postdoctoral Researcher, Interdisciplinary Microbial Ecology, University of Arizona, Ecology and Evolutionary Biology Department, Saleska Lab , Dec. 2008 – Aug. 2011
Ph.D., Microbial Oceanography, Massachusetts Institute of Technology and Woods Hole Oceanographic Institute Joint Program, DeLong Lab, 2008
B.A., (i) Integrative Biology and (ii) Molecular and Cell Biology: Genetics, University of California at Berkeley, 1998
PROFESSIONAL EXPERICNCE
8/2011-present: Assistant Professor, Soil, Water and Environmental Sciences Department, University of Arizona
12/2008-8/2011: Postdoctoral Research Scientist, Ecology and Evolutionary Biology Department, University of Arizona
PUBLICATIONS
Rich, V, Pham V, Eppley J, Shi Y, DeLong EF. 2011. Time-series analyses of Monterey Bay coastal microbial picoplankton using a ‘genome proxy’ microarray. Environmental Microbiology. 13: 116-134.
Rich, V, Konstantinidis K, DeLong EF. 2008. Design and testing of “genome proxy” microarrays to profile marine microbial communities. Environmental Microbiology, 10: 506-521.
- Faculty of 1000 “Must Read” paper, 4 Feb 2008.
DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science. 311:496-503.
- Faculty of 1000 “Recommended” paper, 17 Feb 2006
Horz, H-P, Rich V, Avrahami S, and Bohannan BJ. 2005. Methane-oxidizing bacteria in a California upland grassland soil: diversity and response to simulated global change. Applied and Environmental Microbiology. 71(5): 2642-2652.
In preparation
Preston, CM, Suzuki, M, Rich V, Heidelberg J, Chavez F, DeLong EF. Detection and distribution of two novel form II RuBisCos in the Monterey Bay.
TEACHING EXPERIENCE
University of Arizona
- Co-instructor for Global Change, a mixed undergraduate and graduate class in the Geosciences and the Ecology and Evolutionary Biology Depts., taught by Drs. Julie Cole and Scott Saleska. Fall 2009. Guest Lecturer in Fall 2010.
- Guest Lecturer for Marine Biology, a majors and non-majors class in the Ecology and Evolutionary Biology Department, taught by Dr. Katrina Mangin. Spring 2011.
- Guest Lecturer for Biology of the Oceans, a mixed undergraduate and graduate class in the Ecology and Evolutionary Biology Department, taught by Dr. Matt Sullivan. Fall 2008, 2010, 2011.
University of Washington at Seattle, 1/00 – 6/02
- Lecturer and Teaching Associate, for the Friday Harbor Lab’s “Research Apprenticeship on Acetabularia Morphogenesis and Development”. Our apprenticeship received the best reviews of any at FHL, and we returned to offer a second iteration. Fall 2000, Spring 2002.
- Teaching Associate and Assistant Lab Coordinator, for U.W.’s Biology 201, “Introductory Biology: Genetics and Biochemistry”. Winter 2000, Spring 2000, Spring 2001.
- Teaching Associate, for U.W.’s Biochemistry 442, “Cellular and Molecular Biology”. Spring 2000.
FUNDING
Department of Energy (DOE), Genomic Science program, Biological Systems Research on the Role of Microbial Communities in Carbon Cycling
"Genes, isotopes, and ecosystem biogeochemistry: dissecting methane flux at the leading edge of global change” co-PIs: Scott Saleska and Virginia Rich. CIs: Gene Tyson, Patrick Crill, Jeff Chanton, Changsheng Li, Steven Frolking. Amount: $2.9 million. Duration: 2010 – 2013.
CURRENT RESEARCH PROJECTS
1. How do microbial communities in thawing northern peatlands mediate methane flux?
Saleska Lab (Univ. of Arizona), Tyson Lab (Univ. of Queensland), Crill Lab (Stockholm Univ.), Chanton Lab (Florida State Univ.), Li and Frolking Labs (Univ. of New Hampshire), and Abisko Research Station in Sweden
Approach: We are working with biogeochemists and modelers to intensively monitor the carbon gas fluxes and isotope compositions at an existing long-term field site at the southern edge of the discontinuous permafrost zone, while tracking microbial community composition and metabolic activity. A collaborative modelling component of our project examines scaling of biogeochemical and molecular inferences from the soil column and plot level to the ecosystem and region.
2. How do near-shore microbial communities “buffer” reef systems from terrestrial pollutants?
Tyson lab (Univ. of Queensland), Sullivan Lab (Univ. of Arizona), and the Australian Institute for Marine Science
Approach: In tandem with a long-term water chemistry monitoring program at the Great Barrier Reef, we are examining the marine microbial community response to wet season influxes of high pollutant loading of pesticides, nutrients, and organic carbon. We are using both molecular microbial and culture-based methods to identify taxa shifts and key degradative metabolic pathways. A collaboration with a hydrodynamic modeller will allow us to discern current-based dispersion from potential microbial degradation, while our work with an ecosystem modeller will allow an integration of the chemical, microbial, and physical data to model total system processing of pollutants.
CURRENT COLLABORATORS
David Bourne, Australian Institute for Marine Science; Jason Bragg, Macquarie University; Jeff Chanton, Florida State University; Patrick Crill,U niversity of New Hampshire/ Stockholm University; Steve Frolking, University of New Hampshire; Candice Heath, University of Queensland; Suzanne Hodgkins, Florida State University; Changsheng Li, University of New Hampshire; Rhiannon Mondav, University of Queensland; Britta Schaffelke, Australian Institute for Marine Science; Matthew Sullivan, University of Arizona; Nathan Verberkmoes, Oak Ridge National Labs
FORMER RESEARCH PROJECTS
1. How do marine microbial communities change across environmental gradients of light, temperature, and nutrients?
Massachusetts Institute of Technology, and the Monterey Bay Aquarium Research Institute, DeLong Lab, Graduate Student, 01/04 – 09/08
1st Approach: As part of a collaborative effort to explore metagenomics data from microbial communities through the water column at the Hawai’i Ocean Time Series Station ALOHA, I examined the depth distribution of specific marine microbes.
Findings: Pelagic microbial communities are stratified with depth; taxa and metabolic genes are differentially distributed through the water column. This work was published in Science.
2nd Approach: To enable higher-throughput tracking of marine microbes, I developed a novel “genome proxy” microarray platform targeting uncultivated, dominant microbes in environments of interest.
Findings: The array was able to track microbes within >85% average nucleotide identity of those targeted, with a limit of detection of 1000 cells/ml seawater. Microarray signal was linearly related to target cell concentration with an R2 of 0.999 across six orders of magnitude. This work was published in Environmental Microbiology.
3rd Approach:I applied the “genome proxy” array to understand seasonal and depth distributions of marine microbial communities over four years in Monterey Bay, CA, in concert with an associated long-term physical-, chemical- and biological- monitoring program. Array and metagenomic data were cross-compared for several samples. This work was a major focus of the Monterey Bay Microbial Observatory.
Findings: Core groups of common and abundant taxa occurred at each depth in Monterey Bay, with abundances often peaking after strong upwelling events. We observed population shifts within several abundant taxa, in some cases clustering by depth or oceanographic season. Array data correlated to metagenomic data with an R2 of 0.85-0.91 across three samples. This work was published in Environmental Microbiology.
2. How does simulated global change affect grassland microbial communities?
Stanford University, Bohannan Lab, Rotating Graduate Student 1/03 – 12/03
Approach: We examined methane oxidizers at the Jasper Ridge Global Change Experiment (a national Long-Term Ecological Research site), through the particulate methane mono-oxygenase gene, and by measuring of in situ methane concentrations. Molecular evolutionary analyses helped map the potential functional constraints and selective pressures that gave rise to several novel clades.
Findings: Type II methanotrophs and three novel clades of potential methane-oxidizing microbes were identified at this site, whose lineages responded differently to multifactorial global change conditions. This work was published in Applied and Environmental Microbiology.
3. How does autotrophy vary with depth through the water column?
Monterey Bay Aquarium Research Institute, DeLong Lab, Collaborating Scientist 9/01 – 12/01, Intern 6/01 - 8/01
Approach: I screened the lab’s large-insert environmental genomic libraries and DNA depth profiles for functional genes involved in carbon fixation.
Findings: A novel monophyletic group of Form II RuBisCO was identified in the 750m Monterey Bay BAC library, representing potentially unknown autotrophy in the oxygen minimum zone. The manuscript is in preparation by the lead author.