People | Matthew T. Cottrell

• B.A., Biology, Columbia University in the City of New York, 1986.
• M.S., Marine Environmental Science, State University of New York at Stony Brook, 1989.
• Ph.D., Marine Science, University of Texas at Austin, 1995.

Microbial ecology of the oceans. Bacterial diversity and the structure of bacterial communities. Controls on bacterial community structure, including substrates supporting growth, grazing and viral attack. Innovative approaches for assessing the link between bacterial community structure and function (Micro-FISH). Photoheterotrophic bacteria, including aerobic anoxygenic phototrophic (AAP) bacteria. Genomic approaches to probing the ecology of microbes, including the analysis of whole genome shotgun sequences. (Sargasso WGS).

• Relationship between bacterial community structure and DOM consumption
• Community structure of bacterial biofilms on stainless steel and their role in corrosion
• Abundance and diversity of aerobic anoxigenic phototrophic (AAP) bacteria

Click here for a complete list of publications.

Cottrell, M.T., and D.L. Kirchman. 2012. Virus genes in Arctic marine bacteria identified by metagenomic analysis. Aquat. Microb. Ecol. 66:107-116.

Christman, G.D., M.T. Cottrell, B.N. Popp, E. Geir, and D.L. Kirchman. 2011. Abundance, diversity, and activity of ammonia-oxidizing prokaryotes in the coastal Arctic Ocean in summer and winter. Appl. Environ. Microb. 77:2026-2034.

Lehours, A.C., M.T. Cottrell, O. Dahan, D.L. Kirchman, and C. Jeanthon. 2010. Summer distribution and diversity of aerobic anoxygenic phototrophic bacteria in the Mediterranean Sea in relation to environmental variables.  FEMS Microbiol. Ecol. 74:397-409.

Kirchman, D.L., Cottrell, M.T., and C. Lovejoy. 2010. The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes. Environ. Microbiol. 12:1132-1143.  doi:10.1111/j.1462-2920.2010.02154.x.

Cottrell, M.T., J. Ras, and D.L. Kirchman. 2010. Bacteriochlorophyll and community structure of aerobic anoxygenic phototrophic bacteria in a particle-rich estuary.  ISME J. 4:945-954.

Cottrell, M.T., and Kirchman, D.L.  2009.  Photoheterotrophic microbes in the Arctic Ocean in summer and winter.  Appl. Environ. Microbiol. 75:4958-4966.

Lami, R., M.T. Cottrell, B.J. Campbell, and D.L. Kirchman.  2009.  Light- dependent growth and proteorhodopsin expression by Flavobacteria and SAR11 in experiments with Delaware coastal waters. Environ. Microbiol. 11: 3201-3209.

Straza, T.R.A., M.T. Cottrell, H.W. Ducklow, and D.L. Kirchman.  2009.  Geographic and phylogenetic variation in bacterial biovolume as revealed by protein and nucleic acid staining.  Appl. Environ. Microbiol. 75:4028-4034.

Kirchman, D.L., V. Hill, M.T. Cottrell, R. Gradinger, R.R. Malmstrom, and A. Parker. 2009. Standing stocks, production and respiration of phytoplankton and heterotrophic bacteria in the western Arctic Ocean. Deep-Sea Res II 56:1237-1248. doi:10.1016/j.dsr2.2008.10.018

Elifantz, H., L.A. Waidner, V.K. Michelou, M.T. Cottrell, and D.L. Kirchman. 2008. Diversity and abundance of glycosyl hydrolase family 5 in the North Atlantic Ocean. FEMS Microbial Ecol. 63:316-327.

Cottrell, M.T., V.K. Michelou, N. Nemcek, G. DiTullio, and D.L. Kirchman. 2008. Carbon cycling by microbes influenced by light in the Northeast Atlantic Ocean. Aquat. Microb. Ecol. 50:239-250.

Campbell, B.J., L.A. Waidner, M.T. Cottrell, and D.L. Kirchman. 2008. Abundant proteorhodopsin genes in the North Atlantic Ocean. Environ. Microbiol. 10:99-109.

Elifantz, H., A.I. Dittel, M.T. Cottrell, and D.L. Kirchman. 2007. Dissolved organic matter assimilation by heterotrophic bacterial groups in the western Arctic Ocean. Aquat. Microb. Ecol. 50:39-49. 

Lami, R., M.T. Cottrell, J. Ras, O. Ulloa, I. Obernosterer, H. Claustre, D.L. Kirchman, and P. Lebaron. 2007. High abundances of aerobic anoxygenic photosynthetic bacteria in the South Pacific Ocean. Appl. Environ. Microbiol. 73:4198-4205.

Malmstrom, R.R., Straza, T.R.A., M.T. Cottrell, and D.L. Kirchman. 2007. Diversity, abundance, and biomass production of bacterial groups in the western Arctic Ocean. Aquat. Microb. Ecol. 47:45-55.

Recent Oceanographic Cruises

My work over the last few years has included research expeditions to the Arctic, Pacific and Atlantic Oceans. Some of the cruises, such as the Western Arctic Shelf- Basin Interactions (SBI) cruises have included scientists from many universities. In other cases, like the Hatteras cruise, Kirchman's group and I have taken the lead and other scientists have joined us to contribute expertise in areas such as phytoplankton biology and biogeochemistry. In either case our work has focused on microbial community structure, heterotrophic metabolism and the contribution of photoheterotrophic microbes to the microbial food web. Check out the links below to see some photos, movie clips and cruise descriptions.

• Arctic Shelf Basin Interaction - (SBI, 2002/2004)
• Mid-Atlantic Bight - (HATTERAS, 2003)
• Hawaii Ocean Times Series Station - (HOGS, 2004)
• North Atlantic Spring Bloom - (NASB, 2005)

Micro-FISH Visitors

Scientists have visited the lab from around the world to learn our approach to assaying bacterial community structure and function using microautoradiography and fluorescence in situ hybridization (Micro-FISH). If you are interesting in coming to Lewes to learn about Micro-FISH and our semi-automated microscopy system, send me an email <mattcottATudelDOTedu>.

Toshi Nagata and his student Taichi Yokogawa, Kyoto University, Japan

John Hobbie, Marine Biological Labroatory, Woods Hole, USA

Byron Crump, Center for Environmental Science Horn Point Laboratory, USA

Josep Gasol and his student Laura Alonso, Institute of Marine Sciences, Barcelona, Spain

Christian Tamburini, Marine Laboratory of Microbiology, Geochemistry and Ecology, Marseille, France

Phillipe Lebaron, Oceanographic Observatory, Banyuls sur Mer, France

Academic collaborators and a commercial firm specializing in environmental bioremediation have used my MicrobeCounter software to setup their own semi-automated microscopy systems for bacterial direct counts, fluorescence in situ hybridization (FISH) and Micro-FISH.

Toshi Nagata, Kyoto University, Japan

David Hutchins, University of Southern California, USA

Eric Hince, Geovation Technologies, USA

Software Development

Mac OS X

Manual Counter for bacterial direct counts (MS Excel VBA works on Windows as well)
Place a laptop next to your microscope and use the space bar to score cells. Counts are automatically recorded in an Excel spreadsheet along with counting statistics. Our lab group gets the most out of this application when we take our small microscope on oceanographic cruises.

Ping Script queries the satellite internet connection while at sea on the USCGC Healy (Perl)
This is a nifty little script that prompts me when the satellite connection on the Healy becomes active outside of scheduled hours. When you are at sea for more than a month you take advantage of every email opportunity to keep in touch with the folks back home.

Batch Blast performs a batch blast of FASTA formatted nucleotide sequences using NCBI BLAST running on our dual processor Macintosh G4 (Unix shell script with iHook GUI).

Custom databases, such as the ARB database are invaluable in the analysis of environmental whole genome shotgun sequence databases (Sargasso WGS).

CEOE MapIt! generates maps for oceanographers using sampling locations as input (HTML GMT cgi)

The Generic Mapping Tool (GMT) is a wonderful application with a very steep learning curve for the infrequent user. This cgi script presents a user-friendly Web based interface that oceanographers can use to rapidly generate cruise maps. Modeled after the USGS Woods Hole Science Center Web site.