Dr. Feng Chen

Dr. Feng Chen

Dr. Feng Chen

Research Interests

  • The role of marine viruses on microbial mortality and diversification
  • Population dynamics of virio- and bacterio-plankton in the marine environment
  • Microbial genomics and proteomics
  • Microalgae for biofuels and clean coal

Research Area: Marine microbial ecology

Research Specialties: Molecular ecology of marine viruses, bacteria and microalgae; cyanobacteria and cyanophage; roseobacterial phage; gene transfer agent; microbial genomics and functional genomics; Taxonomy and physiology of microalgae.

Research Overview

Molecular ecology of viruses in the sea. 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. My laboratory uses cyanobacteria/cyanophage and roseobacter/roseophage as two model systems to study the complex interaction between bacteria and their phages. Specific gene markers, including photosynthetic genes psbA and RuBisCO, ITS, viral capsid genes and DNA polymerase gene, have been developed in my lab to monitor the population dynamics of both host and phage populations in the aquatic environments. These studies will deepen our understanding on how viruses interact with microbial hosts in the natural environment.

Picocyanobacteria in the estuarine ecosystem. Picocyanobacteria are important phytoplankton and primary producer in the ocean. Although extensive work has been done for picocyanobacteria (i.e. Synechococcus and Prochlorococcus) in the coastal and oceanic waters, little is known about the composition of picocyanobacterial community in the estuarine ecosystem like Chesapeake Bay. We have isolated and identified unique picocyanobacteria adapted to the Chesapeake estuary. The vast majority of estuarine picocyanbacteria belong to the novel clades of Synechococcus. We also isolated many cyanophages that infect estuarine Synechococcus. Recently, the genomes of two estuarine Synechococcus and eight cyanophages have been sequenced (with the support of Moore Foundation). These genomic sequences will allow us to explore the ecology and evolution of viruses and hosts.

Isolation and selection of microalgae for biofuels and clean coal. Extensive collection of cyanobacteria and microalgae from diverse aquatic environments have been isolated and maintained in my laboratory. We have developed a rapid screening method for testing the physiology or environmental tolerance of microalgae. Many algal strains in our collections have shown a great potential for biofuel development and clean coal application.

Selected publications 2006-present

Chi, Y.X., F. Chen, and Y. Takiguhi. 2015. Effect of nitrogen on biomass and lipid production of a marine microalga Nannochloropsis oceanica IMET1. Green Sustain. Chem. DOI: 10.4236/gsc.2015.52013
Xu, Y., N. Jiao, F. Chen*. 2015. Heterogeneous cyanobacteria endure cold winter in the coastal estuary. J. Phycol. DOI: 10.1111/jpy.12318

Zhan, Y.C., A. Buchan, and F. Chen. 2015. Unexpected genetic diversity of N4 like phages in the natural environment. Appl. Environ. Microbiol. doi:10.1128/AEM.00832-15.

Huang, S.J., S. Zhang, N.J. Jiao, and F. Chen. 2015. Marine cyanophages demonstrate biogeographic patterns throughout the global ocean. Appl. Environ. Microbiol. 81:441-452.

Huang, S.J., Y.Q. Liu, A. Hu, X.B. Liu, F. Chen, T.D. Yao, and N.Z. Jiao. 2014. Genetic diversity of picocyanobacteria in Tibetan lakes: assessing the endemic and universal distributions. Appl. Environ. Microbiol. 80:7640-7650

Zheng, L., F. Zhang, F. Chen. 2013. High throughput screening of CO2-tolerating microalgae using GasPak bags. Aquat. Bios. 9:23.

Marsan, D., K.E. Wommack, J. Ravel, F. Chen. 2013. Draft genome sequence of Synechococcus sp. strain CB0101 isolated from the Chesapeake Bay estuary. Genome Anno. 2: e01111-13. doi: 10.1128/genomeA.01111-13

Wang, D.M., K. Ning, J. Li, D. Han, H. Wang, X.W. Zeng, X.Y. Jing, J.Q. Hu, X.Z. Chang, A.H. Wang, W. Wang, J. Jia, L. Wei, Y. Xin, Y.H. Qiao, R.R. Huang, J. Chen, B. Han, R.T. Hill, Y. Zohar, F. Chen, Q. Hu, and J. Xu. 2013. Nannochloropsis phylogenome reveals evolution of microalgal oleaginous traits. PLoS Genet. 10: e1004094.  

Jiao, N., G.J. Herndl, D.A. Hansell, R. Benner, G. Kattner, S.W. Wilhelm, D.L. Kirchman, M.G. Weinbauer, T.W. Luo, F. Chen, and F. Azam. 2011. The microbial carbon pump and the oceanic recalcitrant dissolved organic matter pool. Nat. Rev. Microbiol. (in press).

Huang, S., S.W. Wilhelm, H.R. Harvey, K. Taylor, N.Z. Jiao, and F. Chen. 2011. Novel lineages of Prochlorococcus and Synechococcus in the global oceans. ISME J (in press).

Huang, S., K. Wang, N.Z. Jiao, and F. Chen. 2011. Genome sequences of four Synechococcus siphoviruses: a new insight into the diversity of marine cyanophage. Environ. Microbiol. (in press).

Weinbauer, M., F. Chen, S. Wilhelm. 2011. Virus mediated redistribution and partitioning of carbon in the global oceans. pp. 54-55. In: Jiao et al. (ed). Microbial Carbon Pump in the Ocean. Science/AAAS, Washington, DC.

Kan, J. T.E. Hanson, and F. Chen. 2011. Synchronicity between population structure and proteome profiles: A metaproteomic analysis of Chesapeake Bay bacterial communities. In: Frans J. de Bruijn (ed.). Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Wiley-Blackwell, New Jersey.

Huang, S., Y.Y. Zhang, F. Chen, N.Z. Jiao. 2011. Complete genome sequence of a marine roseophage provides evidence into the evolution of gene transfer agent in alphaproteobacteria. Virology Journal 8:124 (doi:10.1186/1743-422X-8-124).

Jiao, N., G.J. Herndl, D.A. Hansell, R. Benner, G. Kattner, S.W. Wilhelm, D.L. Kirchman, M.G. Weinbauer, T.W. Luo, F. Chen, and F. Azam. 2010. Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean. Nature Rev. Microbiol.8: 593-599.

Cai, H.Y., K. Wang, S.J. Huang, N.Z. Jiao, and F. Chen. 2010. Shift of picocyanobacterial populations between winter and summer in Chesapeake Bay. Appl. Environ. Microbiol. 76: 2955–2960.

Huang, S.J., S. Wilhelm, N.Z. Jiao, and F. Chen. 2010. Ubiquitous cyanobacterial podoviruses in the global oceans unveiled through viral DNA polymerase gene sequences. ISME J. 4: 1243-1251.

Fu, Y., D.M. MacLeod, R.B. Rivkin, F. Chen, A. Buchan, and A.S. Lang. 2010. High diversity of Rhodobacterales in the sub-arctic North Atlantic Ocean and gene transfer agent protein expression in isolated strains. Aquat. Microb. Ecol. 59:283-293.

Zhao, Y.L., K. Wang, H-W. Ackermann, N. Z. Jiao, F. Chen. 2010. Searching for a “hidden” prophage in a marine bacterium. Appl. Environ. Microbiol. 76: 589–595.

Sparks, W., J. Hough, T. A. Germer, F. Chen, S. DasSarma, et al. 2009. Detection of circular polarization in light scattered from photosynthetic microbes. Proc. Natl. Acad. Sci. 106:7816-7821.

Zhao, Y.L, K. Wang, N.Z, Jiao, and F. Chen. 2009. Genome sequences of two novel phages infecting marine roseobacters. Environ. Microbiol. 11:2055-64.

Zhao, Y., K. Wang, C. Budinoff, A. Buchan, A. Lang, N. Jiao, and F. Chen. 2009. Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake Bay. ISME J. 3: 364-373.

Sparks, W. B., J. H. Hough, L. Kolokolova, T. A. Germer, F. Chen, S. DasSarma, P. DasSarma, F. Robb, N. Manset, I.N. Reid F. Duccio Macchetto William Martin. 2009. Circular polarization in scattered light as a possible biomarker. J. Quant. Spectro. Radia. Trans. 110: 1771-1779.

Zhao, M.R. F. Chen, and N.Z. Jiao. 2009. Niche portioning of flavobacterial proteorhodopsin in the sea. Appl. Environ. Microbiol. 75: 529-533.

Short, S., F. Chen, S. Wilhelm. 2009. The Construction and Analysis of Marker Gene Libraries (Chapter 9). In: Suttle et al. (eds). Manual of Aquatic Viral Ecology. P82-91. Limnol. & Oceangr. Methods

Chen, F., K. Wang, S.J. Huang, H.Y. Cai, M.L. Zhao, N.Z. Jiao, and E. Wommack. 2009. Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences. Environ. Microbiol. 11: 2884-2892.

Eissler, Y., K. Wang, F. Chen, E. Wommack, W. Coats. 2009. Ultrastructural characterization of the lytic cycle of an intra-nuclear virus infecting the diatom Chaetoceros wighamii (Bacillariophyceae) from Chesapeake Bay, USA. J. Phycol. 45:787-797.

Zhang, Y.Y., N. Jiao, D.R. Colquhoun, R.U. Halden, and F. Chen. 2009. Protein modifications related to phage resistance in a marine roseobacter. Aquatic Microb. Ecol. 55:203-207.

Kan, J., S.E. Evans, F. Chen, M.T. Suzuki. 2008. Novel estuarine bacterioplankton in rRNA operon libraries from the Chesapeake Bay. Aquat. Microb. Ecol. 51:55–66.

Biers, E. J., K. Wang, C. Pennington, R. Belas, R., F. Chen, and M. A. Moran. 2008. Abundance and expression of gene transfer agent (GTA) genes in marine bacterioplankton. Appl. Environ. Microbiol. 74:2933-2939.

Wang, K. and F. Chen. 2008. Prevalence of highly host-specific cyanophages in the estuarine environment. Environ. Microbiol. 10:300-312 (also cover page).

Mohamed, N.M., E. Cicirelli, J. Kan, F. Chen, F., C. Fuqua, and R.T. Hill. 2008. Diversity and quorum sensing signal production of Proteobacteria associated with marine sponges. Environ. Microbiol. 10:75-86.

Kan, J., M. Suzuki, K. Wang, S.E. Evans, and F. Chen. 2007. High temporal but low spatial heterogeneity of bacterioplankton in the Chesapeake Bay. Appl. Environ. Microbiol. 73:6776-6789.

Jiao, N.Z., Zhang, Y., Zeng, Y.H., Wang, P.X., Liu, R., Tang, X.D., Chen, F., and Li, Q. 2007. Deviation in abundance and diversity of aerobic anoxygenic phototrophic bacteria in the ocean. Environ. Microbiol. 9:3091-3099.

Reid, I. N., W. B. Sparks, S. Lubow, M. McGrath, M. Livio, J. Valenti, K.R. Sowers, H.D. Shukla, S. MacAuley, T. Miller, R. Suvanasuthi, R. Belas, A. Colman, F.T. Robb, P. DasSarma, J.A. Müller, J.A. Coker, R. Cavicchioli, F. Chen, S. DasSarma. 2006. Terrestrial models for extraterrestrial life: methanogens and halophiles at Martian temperatures. Int. J. Astrobiol. 00 (0): 1–9.

Chen, F., K. Wang, J. Stewart, R. Belas. 2006. Induction of prophages from a marine reseobacterium, Silicibacter sp. TM1040: A genomic approach. Appl. Environ. Microbiol. 72:4995-5001.

Kan, J., B. Crump, K. Wang, and F. Chen. 2006. Bacterioplankton community in Chesapeake Bay: Predictable or random assemblages. Limnol. Oceanogr. 51:2157-2169.

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.

Kan, J., K. Wang, and F. Chen. 2006. Temporal variation and detection limit of an estuarine bacterioplankton community analyzed by denaturing gradient gel electrophoresis (DGGE). Aquat. Microb. Ecol. 42:7-18.

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