Feng Chen Assistant Professor chenf@umbi.umd.edu (410) 234-8866

Research Interests

My current research interests focus on three main areas: 1) the role of marine viruses on microbial mortality and diversification; 2) population dynamics of virio- and bacterio-plankton in the Chesapeake Bay over time and space; 3) microbial genomics and community proteomics: a goal to understand microbial function and microgeochemical processes in nature.

Bacteria and bacteriophage are the two most abundant biological components in the sea. Viral lysis of bacteria and production of phage particles occurs continuously in seawater. Marine viruses are known to play a key role on regulating microbial biomass and production. However, little is known about the role of marine viruses on microbial population structure, genetic diversification, and genomic evolution. Our lab uses cyanobacteria and cyanophage as a model system to study the complex interaction between bacteria and their phages. Specific gene markers, including photosynthetic genes psbA and RuBisCO, ITS, viral capsid gene (g20), and DNA polymerase gene, have been developed in our lab to co-monitor the populations of both cyanobacteria (Synechococcus) and cyanophage in the Chesapeake Bay. With more than three-year data from the Bay, we are able to address the questions like: How diverse are cyanobacteria and cyanophage in the Bay? How does the phage-host system change temporally and spatially?

To highlight some exciting research achievements, the first cyanophage genome was sequenced and characterized in our lab. We first applied the SYBR Gold nucleic acid stain to enumerate viruses and bacteria in seawater [SYBR Gold protocol]. We have successfully applied community-based proteomics (2-D gel and LC-MS/MS) to characterize estuarine microbial communities, and link the protein characterization to the Sargasso Sea metagenomic database. A unique group of picocyanobacteria (Marine Cluster B Synechococcus) and their phages were found and isolated from the Chesapeake estuary. Based on our 3-yr survey in the Bay, we found that the majority of bacterioplankton exhibited repeatable seasonal patterns. Moreover, Chesapeake Bay bacterioplankton exhibited stronger seasonal than spatial variations.

Selected Publications

Kan, J., B. Crump, K. Wang, and F. Chen. 2006. Bacterioplankton community in Chesapeake Bay: Predictable or random assemblages. Limnol. Oceanogr. (in press).

Chen, F., K. Wang, J. Stewart, R. Belas. 2006. Induction of prophages from a marine roseobacterium, Silicibacter sp. TM1040: A genomic approach. Appl. Environ. Microbiol. (in press).

Chen, F., K. Wang, J, Kan, and M. Suzuki, E. Wommack. 2006. Diverse and unique picocyanobacteria found in the Chesapeake Bay. Appl. Environ. Microbiol. 72:2239-2243.

Bettarel, Y., J. Kan, K. Wang, S. Cooney, K. Williamson, F. Chen, E. Wommack, W. Coats. 2005. Isolation and characterisation of a small nuclear inclusion virus infecting the diatom Chaetoceros c.f. gracilis. Aquat. Microbial. Ecol. 40:103-114.

Kan, J., T. E. Hanson, J. M. Ginter, K. Wang, F. Chen. 2005. Metaproteomic analysis of Chesapeake Bay microbial communities. Saline Systems 1:7.

Lohr, J. E., F. Chen, and R. T. Hill. 2005. Genomic analysis of bacteriophage JL001: Insights into interaction with a sponge-associated alpha-proteobacterium. Appl. Environ. Microbiol. 71: 1598-1609.

Chen, F., K. Wang, J. Kan, D.S. Bachoon, J. Lu, S. Lau, and L. Campbell. 2004. Phylogenetic diversity of Synechococcus in the Chesapeake Bay revealed by ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) large subunit gene (rbcL) sequences. Aquat. Microb. Ecol. 36:153-164.

Kan, J. and F. Chen. 2004. Co-monitoring bacterial and dinoflagellates communities by denaturing gradient gel electrophoresis (DGGE) and SSU rDNA sequencing during a dinoflagellates bloom. Acta Oceanologia Sinica. 23:483-492.

Wang, K. and F. Chen. 2004. Genetic diversity and population dynamics of cyanophage communities in the Chesapeake Bay. Aquat. Microb. Ecol. 34:105-116, 2004.

Chen, F. and Lu, J. R. 2002. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Appl. Environ. Microbiol. 68:2589-2594.

Zhong, Y., F. Chen, J. R. Lu, L. Poorvin, S. Wilhelm, R. Hodson. 2002. Phylogenetic diversity of marine cyanophage isolates and natural virus communities as revealed by sequences of viral capsid assembly protein gene g20. Appl. Environ. Microbiol. 68:1576-1584.

Lau, S. C. K., K. K. W. Mak, F. Chen and P. Y. Qian. 2002. Bioactivity of bacterial strains isolated from marine biofilms in Hong Kong waters for the induction of larval settlement in the marine polychaete Hydroides elegans. Mar. Ecol. Prog. Ser. 226:301-310.

Lu, J.R., F. Chen and R. E. Hodson. 2001. Distribution, isolation, host specificity and diversity of marine cyanophages infecting Synechococcus spp. in Coastal Estuary. Appl. Environ. Microbiol. 67:3285-3290.

Chen, F., J. R. Lu, B. Binder, Y. C. Liu, and R. E. Hodson. 2001. Enumeration of viruses in aquatic environments using SYBR Glod stain: application of digital image analysis and flow cytometer. Appl. Environ. Microbiol. 67:539-545..

Bachoon, D., F. Chen, and R. E. Hodson. 2001. RNA recovery and detection of mRNA by RT-PCR from preserved prokaryotic samples. FEMS Microbiol. Lett. 201:127-132 .

Chen, F. and R. E. Hodson. 2001. In situ PCR/RT-PCR coupled with in situ hybridization for detection of functional gene and gene expression in prokaryotic cells. In: J. Paul (ed.) Methods in Marine Microbiology, Academic Press. pp.409-424.

Chen, F., B. Binder, R. E. Hodson. 2000. Flow cytometric detection of specific gene expression in prokaryotic cells using in situ RT-PCR. FEMS Microbiol. Lett. 184:291-295.

Chen, F., W. A. Dustman and R. E. Hodson. 1999. Detection of toluene dioxygenase gene and gene expression in Pseudomonas putida F1 in a toluene exposed seawater using in situ PCR and hybridization. Hydrobiologia 401:131-138.

Chen, F., J. M. Gonzalez, W. Dustman, M. Moran and R. Hodson. 1997. In situ reverse transcription: a new molecular approach to study microbial community structure. Appl. Environ. Microbiol. 63: 4907-4913.

Chen, F., and C. A. Suttle. 1996. Evolutionary relationships among large double-stranded DNA viruses that infect microalgae and other organisms as inferred from DNA polymerase genes. Virology 219:170-178.

Chen, F., and C. A. Suttle. 1995. Amplification of DNA polymerase gene fragments from viruses infecting microalgae Appl. Environ. Microbiol. 61:1274-1278.