Bongkeun  Song

Associate Professor

Email: [[songb]]
Phone: (804) 684-7411
Office: Andrews Hall 339
Department: Biological Sciences
Interests: Microbiome ecology and biogeochemistry
Fax: (804) 684-7399

  • B.S., Agriculture Biology, Dongguk University, Seoul, Korea.1994
  • M.S., Environmental Science, Rutgers the State University of New Jersey, New Brunswick, New Jersey, 1997
  • Ph.D., Environmental Science, Rutgers the State University of New Jersey, New Brunswick, New Jersey, 2000
Research Interests

Microorganisms are key players in biogeochemical cycles and bio-indicators of ecosystem function and environmental health. My primary areas of research focus on understanding the relationship between structure and function of microbial communities. I have studied various terrestrial and marine ecosystems in order to better understand how community structures correlate to microbial processes. These include microbial pathways in the biogeochemical nitrogen (N) cycle, metal transformation, biodegradation, and primary production. I have employed a variety of analytical, microbial, molecular and stable isotope techniques to identify and quantify the functional members of microbial communities of interest.

My current research emphasis:

  • Biotic and abiotic N cycling processes

  • Microbial regulation on greenhouse gas emission

  • Microbial interaction during harmful algal bloom

  • Oyster microbiomes and their function

  • Metagenomics and bioinformatics

  • Microplastic identification and quantification using Raman spectromicroscopy

Current Projects
  • NOAA Sea Grant: Enhancing commercial sustainability in the hatchery production of eastern oysters and clams, PIs: R. Carnegie, T. Hartley, S. Allen, K. Hudson, D. Kuhn, K. Reece, E. Rivest, M. Schwarz, E. Shadwick, J. Smith, B. Song, R. Snyder.
  • NSF Biological Oceanography: Alteration of carbon fluxes by intense phytoplankton blooms in a microtidal estuary, PIs: I. Anderson, M. Brush, K. Reece, B. Song.
  • NSF Chemical Oceanography: Collaborative Research: Cryptic nitrogen cycling in the anoxic subterranean estuary, PIs: B. Song, I. Anderson, C. Tobias.
  • New Zealand Government: Mitigation via chemical di-nitrogen formation: Exploring ways to remove nitrogen while bypassing nitrous oxide emission, PIs: A. McMillan, R. Phillips, B. Song, C. Tobias.
  • VA Sea Grant: Sustainability of microbial nitrogen removal in tidal creeks impacted by concentrated animal feeding operations in the VA Eastern Shore, PIs: M. Semedo, B. Song.
  • Hampton Road Sanitation District: Detection of microplastics in wastewater using Raman Microspectroscopy. PI: B. Song.
  • USDA-NIFA: Unveiling fungal contributions to soil nitrogen cycling for agroecosystems applying organic and inorganic fertilizers. PIs: B. Song, C. Crozier, R. Phillips, C. Tobias. 
Selected Publications

Van Duc, L., B. Song, H. Ito, T. Hama, M. Otani and Y. Kawagoshi (2018) High growth potential and nitrogen removal performance of marine anammox bacteria in shrimp-aquaculture sediment. Chromosphere, 196, 69-77.

Smyth, A., A. Murphy, I. Anderson, and B. Song (2017) Differential effects of bivalves on sediment nitrogen cycling in a shallow coastal bay. Estuaries and Coasts, DOI: 10.1007/s12237-017-0344-9.

Lisa J., A. Jayakumar, B. Ward, and B. Song (2017) nirS-type denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary. Environmental Microbiology Reports, doi: 10.1111/1758-2229.12594.

Arfken, A., B. Song, J. Bowman, and M. Piehler (2017) Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach. PLOS One 12: e0185071.

Conroy, B. J., D. K. Steinberg, B. Song, A. Kalmbach, E. J. Carpenter, R. A. Foster (2017) Mesozooplankton grazing of cyanobacteria in the Amazon River plume and western tropical North Atlantic. Frontiers in Microbiology, doi: 10.3389/fmicb.2017.01436.

Philips, B. Song, A. McMillan, G. Grelet, B. Weir, T. Palmada, and C. Tobias. 2016. Chemical formation of hybrid di-nitrogen calls fungal codenitrification into question, Scientific Reports, 6:39077, DOI: 10.1038/srep39077.

Murphy, A.E., Anderson, I.C., Luckenbach, M.W., Smyth, A.R., Song, B. (2016) Microbial nitrogen processing in commercial hard clam (Mercenaria mercenaria) aquaculture sediments: nitrogen removal versus recycling pathways, Limnology and Oceanography, DOI: 10.1002/lno.10305.

Stoliker, D.L., D.A. Repert, R.L.Smith, B. Song, D. R. LeBlanc, T. D. McCobb, C. H. Conaway, S. P. Hyun, D. B. Kent (2016) Hydrologic controls of groundwater discharge on abundance and activities of microbial communities responsible for nitrogen cycling processes in permeable lake sediments. Submitted in Environmental Science & Technology, 50: 3649-3657.

Philips, R., G. Grelet, A. McMillan, B. Song, B. Weir, T. Palmada, C. Tobias (2016) Fungal denitrification: Bipolaris sorokiniana exclusively denitrifies inorganic nitrogen in the presence and absence of oxygen. FEMS Microbiology Letters, 363, doi: 10.1093/femsle/fnw007.

Graham, E.B., J. E. Knelman, A. Schindlbacher, S. Siciliano, M. Breulmann, A. Yannarell, J. M. Beman, G. Abell, L. Pilipot, J. Prosser, A. Foulquier, J. C. Yuster, H. C. Glanville, D. Jones, R. Angel, J. Salminen, R. J. Newton, H. Bürgmann, L. J. Ingram, U. Hamer, H. M. Siljanen, K. Peltoniemi, K. Potthast, L. Bañeras, L., Hartmann, M., Banerjee, S., Yu, R.-Q., Nogaro, G., Richter, A., Koranda, M., Castle, S., Goberna, M., Song, B., Chatterjee, A., Nunes, O. C., Lopes, A., Cao, Y., Kaisermann, A., Hallin, S., Strickland, M. S., Garcia-Pausa, J., Barba, J., Kang, H.-J., Isobe, K., Papaspyrou, S., Pastorelli, R., Lagomarsino, A., Linström, E., Basiliko, N., Nemergut, D. R. (2016) Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Frontiers in Microbiology, doi: 10.3389/fmicb.2016.00214. 

Smith, R. L.*, J. K. Böhlke, B. Song, C. R. Tobias (2015) Role of anaerobic ammonium oxidation (anammox) in nitrogen removal from a freshwater aquifer. Environmental Science & Technology, 49: 169-177.

Lisa, J.A.1*, B. Song, C. R. Tobias, D. E. Hines1 (2015) Genetic and biogeochemical investigation of sedimentary nitrogen cycling communities responding to tidal and seasonal dynamics in Cape Fear River Estuary. Estuarine Coastal and Shelf Science, 167: A313-323.

Arfken, A.M.1, B. Song*, M. A. Mallin (2015) Assessing Hog Lagoon Waste Contamination in the Cape Fear Watershed Using Bacteroides 16S rDNA Pyrosequencing, Applied Microbiology and Biotechnology, 99: 7283-7293.

Arfken, A. M.1, B. Song*, J. S. Sung (2015) Comparison of airborne bacterial communities from hog farm and spray field. Journal of Microbiology and Biotechnology, 25: 709-717.

Hines, D. E.1, J. A. Lisa1, B. Song, C. R. Tobias, S. R. Borrett, (2015) Estimating the effects of seawater intrusion on an estuarine nitrogen cycle by comparative network analysis. Marine Ecology Progress Series, 524: 137-154.

Long, A. M.1, B. Song*, K. Fridey1, A. Silva1, (2015) Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils. FEMS Microbiology Ecology, 91(2): 1-9.

Repert, D. A.*, J. C. Underwood, R. L. Smith, B. Song (2014) Nitrogen cycling processes and microbial community structure in bed sediments to seasonal changes in the Yukon River at Pilot Station. J of Geophysical Research, 119: 2328-2344.

Song, B.*, J. A. Lisa1, C. R. Tobias (2014) Linking DNRA community structure and activity in a shallow lagoonal estuarine system. Frontiers in Microbiology, 5: 460. doi: 10.3389/fmicb.2014.00460

Lisa, J. A.1*, Song, B., Tobias, C. R., Duernberger, K. A., (2014) Impacts of freshwater flushing on anammox community structure and activities in the New River Estuary, USA. Aquatic Microbial Ecology, 72: 17-31.

Song, B.*, Buckner, C. T.1, Hembury, D. J.1, Mills, R.A., Palmer, M. R., (2014) Impacts of volcanic ashes on anammox communities in deep sea sediments. Environmental Microbiology Reports, 6: 159-166.

Lisa, J. A., Song, B., Tobias, C. R., Duernberger, K. A., 2013. Impacts of freshwater flushing on anammox community structure and activities in the New River Estuary, USA. Aquatic Microbial Ecology, Accepted for publication.

Song, B., Buckner, C. T., Hembury, D. J., Mills, R.A., Palmer, M. R., 2013. Impacts of volcanic ashes on anammox communities in deep sea sediments. Environmental Microbiology Reports, Accepted for publication.

Kim, I.-S., Ekpeghere, K. I., Ha, S.-Y., Kim, B.-S., Song, B., Kim, J.-T., Kim, H.-G., Koh, S.,-C., 2013. Full-scale biological treatment of tannery wastewater using the novel microbial consortium BM-S-1. Journal of Environmental Sciences & Health, Part A-toxic/hazardous substances and environmental engineering, 49:355-364.

Giblin, A. E., Tobias, C. R., Song, B., Weston, N., Banta, G. T., Rivera-Monroy, V., 2013. The importance of dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen cycle of coastal ecosystems. Oceanography 26:124–131.

Borin, S., F. Mapelli, E. Rolli, B. Song, C. Tobias, M. Schmid, G. J. De Lange, G. J. Reichart, S. Schouten, M. Jetten, D. Daffonchio (2013) Anammox bacterial populations in deep marine hypersaline gradient systems. Extremophiles, 17: 289-299.

Long, A., J. Heitman, C. R. Tobias, Philips, R. and B. Song (2013) Co-occurring Anammox, Denitrification and Fungal Codenitrification in Agricultural Soils. Applied Environ Microbiol 79: 168-176.

Hines, D. E., Lisa, J. A., B. Song, C. R. Tobias, and S. R. Borrett (2012) A network model shows the importance of coupled processes in the microbial N cycle in the Cape Fear River Estuary. Estuarine Coastal and Shelf Science, 20: 45–75

Song, B. and C. R. Tobias (2011) Molecular and stable isotope methods to detect and measure anaerobic ammonium oxidation (anammox) in aquatic ecosystems. In research on nitrification and related processes (a volume of Methods in Enzymology), edited by Dr. Martin G. Klotz and Lisa Y. Stein. Volume 479, Burlington: Academic Press, Pg 63-89.

Luesken, F. A., Zhu, B., van Alen, T., Butler, M. K., Diaz, M. R., Song, B., den Camp, H. O., Jetten, M. M. M., and K. F. Ettwig (2011) PmoA primers for environmental detection of anaerobic methanotrophs. Applied Environ Microbiol 77: 3877-3880.

Hirsh, M. D., Long, Z. T and B. Song (2011) Anammox bacterial diversity in various aquatic ecosystems based on the detection of hydrazine oxidase genes (hzoA/hzoBMicrobial Ecol 61: 264-271.

Mallin, M. A., M. I. Haltom, B. Song, M. E. Tavares, and S. Dellies (2010) Bacterial source tracking guides management of boat head waste in a coastal resort area. J Environ Management 91: 2748-2753.

López-Legentil, S, P. M. Erwin, J. R. Pawlik, and B. Song (2010) Effects of sponge bleaching on ammonia oxidizing Archaea: Distribution and relative expression of ammonia monooxygenase genes associated with the barrel sponge Xestospongia muta. Microbial Ecol 60: 561-571.

López-Legentil, S., B. Song, S., M. DeTure, and D. G. Baden (2010) Characterization and localization of a hybrid non ribosomal peptide synthetase and polyketide synthase gene from the toxic dinoflagellate Karenia brevis. Mar Biotechnol 12: 32-41.

Dale, O. R., C. Tobias and B. Song (2009) Biogeographical distribution of diverse anaerobic ammonium oxidizing (ANAMMOX) bacteria in Cape Fear River Estuary. Environ. Microbiol. 11:1194-1207.

Song, B., E. Chyun, P. Jaffe and B. B. Ward  (2009) Molecular methods to detect and monitor  dissimilatory arsenate respiring bacteria (DARB) in sediments. FEMS Microbiol Ecology. 68: 108-117.

Chae, J.-C., B. Song and G. J. Zylstra (2008) Identification of genes encoding for hydrolytic dehalogenation in the metagenome derived from a denitrifying 4-chlorobenzoate degrading consortium. FEMS Microbiol. Lett. 281: 203-209.

Rich, J. J., O. R. Dale, B. Song, and B. B. Ward (2008) Anaerobic ammonium oxidation (anammox) in Chesapeake Bay sediments. Microbial Ecol. 55:311-320.

Lear G, B. Song, G.A. Gault, D. A. Polya, and J. R. Lloyd (2007) Molecular analysis of arsenate-reducing bacteria within Cambodian sediments following amendment with acetate. Appl. Environ. Microbiol. 73: 1041-1048.

Song, B and B. B. Ward. (2007) Molecular cloning and characterization of high affinity nitrate transporters in marine phytoplankton. J Phycol 43: 542-552.

Song, B. and B. B. Ward. (2005) Genetic Diversity of benzoyl-CoA reductase genes detected in denitrifying isolates and estuarine sediments. Appl Environ Microbiol 71: 2036-2045.

Allen, A. E., B. B. Ward and B. Song (2005) Characterization of diatom (Bacillariophyceae) nitrate reductase genes and detection of eukaryotic nitrate reductase genes from marine waters. J Phycol . 41: 95-104.

Song, B. and B. B. Ward. (2004) Molecular characterization of assimilatory nitrate reductase gene in marine green alga Dunaliella tertiolecta. J Phycol  40: 721-731.

Song, B. and B. B. Ward. (2003) Nitrite reductase genes in halobenzoate degrading denitrifying bacteria and related species. FEMS Microbial Ecology  43: 349-357.

Song, B., L. J. Kerkhof and M. M. Häggblom. (2002) Characterization of bacterial consortia capable of degrading 4-chlorobenzoate and 4-bromobenzoate under denitrifying conditions. FEMS Microbiol Lett  213: 183-188.

Song, B., N. J. Palleroni, L. J. Kerkhof  and M. M. Häggblom. (2001) Characterization of halobenzoate-degrading denitrifying bacteria belonging to the genera Azoarcus and Thauera and description of Thauera chlorobenzoica sp. nov. Int J Syst Evolut Microbiol 51: 589-602.

Song, B., N. J. Palleroni and M. M. Häggblom. (2000) Description of strain 3CB-1, a genomovar of Thauera aromatica, capable of degrading 3-chlorobenzoate coupled to nitrate reduction  Int J Syst Evolut Microbiol 50: 551-558.

Song, B., N. J. Palleroni and M. M. Häggblom. (2000) Isolation and characterization of diverse halobenzoate-degrading bacteria from soils and sediments. Appl Environ Microbiol 66: 3446-3453.

Song, B., M. M. Häggblom, J. Zhou, J. M. Tiedje and N. J. Palleroni. (1999) Taxonomic characterization of denitrifying bacteria that degrade aromatic compounds and description of Azoarcus toluvorans sp. nov. and Azoarcus toluclasticus sp. nov.. Int J Syst Bacteriol 49: 1129-1140.

Song, B., L. Y. Young, and N. J. Palleroni. (1998) Identification of denitrifier strain T1 as Thauera aromatica and proposal for emendation of the genus Thauera definition. Int J Syst Bacteriol 48: 889-894.