David Emerson, PhD

Senior Research Scientist
Phone: +1 (207) 315-2567, ext. 303
Fax: +1 (207) 315-2329

For media inquiries, please contact sprofaizer@bigelow.org


B.A., Human Ecology, College of the Atlantic, 1981

Ph.D., Microbiology, Cornell University, 1989

Research Interests

Dr. Emerson’s research is focused in the area of geomicrobiology – the study of microbes that literally give life to some of Earth’s most important geological processes. Specifically, he studies oxygen-dependent iron-oxidizing bacteria in environments as varied as undersea volcanoes, saltmarshes, and freshwater wetlands. The fundamental reasons for these studies range from understanding the potential for these organisms to exist on other planets, to learning how they extract energy from iron, to analyzing their in influence on other biogeochemical cycles that affect greenhouse gas emissions. The practical implications of his work have to do with the beneficial potential of these microbes for removing pollutants from groundwater, mitigating their nuisance potential as agents of biofouling and corrosion in water distribution systems, as well as the use of biogenic iron oxides in a variety of applications. He is interested in applying the basic knowledge his laboratory has gained toward solving applied problems, and does consulting for industry.

Associate Director of the CCMP for bacteria

The Provasoli-Guillard National Center for Culture of Marine Phytoplankton (NCMA) is a world-renowned bioresource center for marine phytoplankton that has been in existence at Bigelow since 1981. It has over 2,500 strains of phytoplankton, primarily eukaryotes, and supplies over 3,000 strains/year to the scientific community. I am helping to expand the NCMA to include marine bacteria and archaea. I am also working on developing genome-based standards for evaluation of marine microbial communities based on molecular methods. If you have a strain you would like to deposit or one you would like to see in the collection please email me.

Personal Pages


In the Emerson Lab we study iron-oxidizing bacteria in marine and freshwater environments. Our work ranges from exploring the community of iron-oxidizing bacteria at the Loihi Seamount, to isolation of novel iron-oxidizing bacteria from marine and freshwater environments, to studying the role of iron-oxidizing bacteria in steel corrosion.

Overview of Research in the Emerson Lab

Work in my laboratory centers around a unique property of some microbes to control the biological iron cycle. We have discovered several new groups of bacteria that are capable of capturing enough energy to grow by oxidizing Fe(II) (ferrous iron) to Fe(III) (ferric iron). These bacteria are adapted to growing at very low oxygen levels, which is important, because at higher O2 levels, the chemical oxidation of Fe(II) becomes so rapid it outcompetes biological oxidation. These Fe-oxidizing bacteria (FeOB) grow and are abundant in freshwater and brackish wetlands, water wells and distribution systems, hydrothermal vents in the ocean, and other marine environments where Fe(II) is present. We have isolates of FeOB from the freshwater iron seeps, the rhizosphere, deep ocean hydrothermal vents, and coastal settings. Highlights of this work include pioneering efforts on the growth and isolation of novel Fe-oxidizing bacteria from both freshwater and marine environments. The discovery of the Zetaproteobacteria, a new class in the phylum Proteobacteria, that has a cosmopolitan distribution around the globe, but is restricted to marine environments with high concentrations of Fe(II). Furthermore, we have shown that marine and freshwater FeOB belong to very distinct lineages, sharing few genes in common, yet having very convergent lifestyles in terms of niche preference, physiology, as well as unique morphotypes. We have sequenced genomes from several pure cultures of FeOB, as well as over 30 single cell genomes that represent important environmental strains that cannot be grown in the laboratory. This latter work has opened up new metabolic possibilities for FeOB, and allows more detailed study of their evolution allowing us to delve into the antiquity of these organisms that form unusual mineral structures that are recognized in the fossil record. We have shown FeOB may initiate biocorrosion of steel and could help structure a biocorrosion microbiome. We have made significant progress in identifying possible genes involved in neutrophilic iron oxidation, and this work is bringing us closer to understanding the mechanism of iron oxidation. Other recent discoveries include the finding that FeOB are abundant and the iron cycle is very active in tundra wetlands on the North Slope of Alaska, and the discovery of a 10 meter tall 'iron tower' associated with a hydrothermal vent site in the Pacfic Ocean. The work in my lab is funded through the National Science Foundation, NASA, and the Office of Naval Research. We have has significant sequencing support from the DOE's Joint Genome Institute.

Applied Research

The primary focus of my lab is on the basic science behind FeOB; however we are becoming increasingly interested in putting that knowledge to practice in solving myriad problems, primarily in the water industry, associated with FeOB, as well as developing novel beneficial applications for the reactive biogenic iron oxides these bacteria produce. I am on the Joint Task Force on 'Iron and Sulfur Bacteria/ for the 'Standard Methods for the Examination of Water and Wastewater'; I co-authored the forthcoming chapter on 'Iron-oxidizing Bacteria' for the American Water Works Association (AWWA) 'Manual of Water Supply Practices', and recently wrote a review article for AWWA Journal on FeOB. I also do consulting for industry.

Associate Director of the CCMP for bacteria

The Provasoli-Guillard National Center for Culture of Marine Phytoplankton (CCMP) is a world-renowned bioresource center for marine phytoplankton that has been in existence at Bigelow since 1981. It has over 2,500 strains of phytoplankton, primarily eukaryotes, and supplies over 3,000 strains/year to the scientific community. I am helping to expand the CCMP to include marine bacteria and archaea. This important group of microbes includes a very diverse array of heterotrophic and lithotrophic bacteria and archaea. Representatives can grow at both coldest and hottest temperatures for life and use a bewildering number of different substrates for growth. They are of fundamental interest to understanding marine ecosystem processes, in maintaining ocean health, and of commercial importance in biotechnology. If you have a strain you would like to deposit or one you would like to see in the collection please email me (demerson at bigelow.org).


  • Vesenka, J. J. Havu, and D. Emerson. 2017. A model for sheath formation coupled to motility in Leptothrix ochracea. Geomicrobiology J. In Press.
  • He, S., R.A. Barco, D. Emerson, and E.E. Roden. 2017. Comparative genomic analysis of neutrophilic iron(II) oxidizer genomes for candidate genes in extracellular electron transfer. Frontiers in Microbiology. 8:1584. Doi: 10.3389/fmicb.2017.01584.
  • Mori, J.F., J.J. Scott, K.W. Hager, C.L. Moyer, K. Kusel, and D. Emerson. 2017. Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov. ISME J. Advance online publication, doi:10.1038/simej.2017.132
  • Emerson, D., J.J. Scott, A. Leavitt, E. Fleming, and C. Moyer. 2017. In situ estimates of iron-oxidation and accretion rates for iron-oxidizing bacterial mats at Lō’ihi Seamount. Deep-Sea Research Part 1. 126: 31-39. http://dx.doi.org/10.1016/j.dsr.2017.05.011
  • Scott, J.J., B.T. Glazer, and D. Emerson. 2017. Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lō’ihi Seamount. Environmental Microbiology. In Press.
  • Mumford, A., I.J. Adaktylou, and D. Emerson. 2016. Peeking under the iron curtain: Development of a microscosm for imaging colonization of steel surfaces by Mariprofundus sp. DIS-1, an oxygen tolerant Fe-oxidizing bacterium. Applied and Environmental Microbiology. Doi:10.1128/AEM.01990-16
  • Chan, C.S., S.M. McAllister, A.H. Leavitt, B.T. Glazer, S.T. Krepski, and D. Emerson. 2016. The architecture of iron microbial mats reflects the adaptation of chemolithotrophic iron oxidation in marine and freshwater environments. Frontiers in Microbiology. 7:796. Doi: 10.3389/fmicb.2016.00796
  • Chan, C.S., D. Emerson, and G.W. Luther III. 2016. The role of microaerophilic Fe-oxidizing microorganisms in producing banded iron formations. Geobiology. Doi: 10.111/gbi.12192
  • McBeth, J.M., and D. Emerson. 2016. In situ microbial community succession on mild steel in estuarine and marine environments: exploring the role of iron-oxidizing bacteria. Frontiers in Microbiology. 7:767. Doi: 10.3389/fmicb.2016.00767.
  • Henri, P., C. Rommevaux-Jestin, A. Godfroy, F. Lesongeur, A. Mumford, D. Emerson, B. Menez. 2016. Structural iron(II) of basaltic glass as an energy source for Zetaproteobacteria in an abyssal plain environment off the Mid-Atlantic Ridge. Frontiers in Microbiology. 6:1518 doi: 10.3389/fmicb.2015.01518
  • Emerson, D. 2016. The irony of iron – biogenic iron oxides as an iron source to the ocean. Frontiers in Microbiology. 6:1502 doi: 10.3389/fmicb.2015.01502
  • Emerson, D., and C. Lydell. 2016. Inventory of cultivatable populations of S-cycling, fermentative, Fe-reducing, and aerobic heterotrophic bacteria from saltmarsh sediments. bioRxiv doi: http://dx.doi.org/10.1101/048611
  • Kappler, A, D. Emerson, J.A. Gralnick, E.E. Roden, and E.M. Muehe. 2016. Geomicrobiology of Iron, In: Ehrlich’s Geomicrobiology, 6th edition. H.L. Ehrlich, D.K. Newman, and A. Kappler (editors). CRC Press, Boca Raton, FL. Pp 343-399.
  • Emerson, D., J. Scott, J. Benes, and W.B. Bowden. 2015. Microbial iron oxidation in the Arctic tundra and the implications for biogeochemical cycling. Applied and Environmental Microbiology. 81:8066-8075. DOI:10.1128/AEM.02832-15
  • Sanders, J.G., A.C. Beichmann, J. Roman, J.J. Scott, D. Emerson, J.J. McCarthy, and P.R. Girguis. 2015. Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. Nature Communications. 6:8285 DOI: 10.1038/nrcommms9285 (abstract & PDF)
  • Barco, R.A, D. Emerson, J.B. Sylvan, B.N. Orcutt, M.E. Jacobson-Meyers, G.A. Ramirez, J. D. Zhong, and K.J. Edwards. 2015. The proteomic profile of an obligate iron-oxidizing chemolithoautotroph reveals new insight into microbial iron oxidation. Applied and Environmental Microbiology. 81:5927-5937. DOI:10.1128/AEM.01374-15 (abstract)
  • Scott, J.A., J.A. Brier, G.W. Luther III, and D. Emerson. 2015. Characterization of microbial iron mats at the Mid-Atlantic Ridge and evidence that Zetaproteobacteria are unique to marine iron-oxidizing habitats. PLoS ONE. 10(3): 30119284. Doi: 10.1371/journal.pone.0119284 (abstract & PDF)
  • Sanchez-Alberola, N., S. Campoy, D. Emerson, J. Barbe, and I. Erill. 2015. A SOS regulon under control of a non-canonical LexA-binding motif in the Betaproteobacteria. J. Bacteriol. 197:2622-2630. (abstract)
  • Emerson, D., and de Vet, W. 2015. The role of iron-oxidizing bacteria in engineered water ecosystems. Journal of the American Water Works Association. http://dx.doi.org/10.5942/jawwa.2015.107.0004 (abstract & PDF)
  • Field, E.K., C.C. Harris, A.E. Lyman, A. Sczyrba, T. Woyke, R. Stepanauskas, and D. Emerson. 2015. Single cell genomics reveals metabolic potential of uncultivated marine Zetaproteobacteria at Loihi Seamount. ISME J. 9:857-870. (abstract)
  • MacDonald, D.J., A.J. Findlay, P. Hredzak-Showalter, S.M. McAllister, S.T. Krepski, S.G. Cone, J. Scott, S.K. Bennett, C.S. Chan, D. Emerson, and G.W. Luther III. 2014. Using in situ voltammetry as a tool to search for iron oxidizing bacteria: from fresh water wetlands to hydrothermal vent sites. Environmental Science: Processes and Impacts. 16:2117-2126.(abstract)
  • Fleming, E.J., I. Cetinic, C.S. Chan, D.W. King, and D. Emerson. 2014 Ecological succession among Fe-oxidizing bacteria. ISME J. 8:804-815. DOI:10.1038/ismej.2013.197 (abstract)
  • Lee, J.S., J.M. McBeth, R.I. Ray, B.J. Little, and D. Emerson. 2013. Iron cycling at corroding carbon steel surfaces. Biofouling: The Journal of Bioadhesion and Biofilm Research. 29: 1243-1252. (abstract & PDF)
  • Emerson, D., E. Field, O. Chertkov, K.W. Davenport, L. Goodwin, C. Munk, M. Nolan, and T. Woyke. 2013. Comparative genomics of freshwater Fe-oxidizing bacteria: Implications for physiology, ecology, and systematics. Frontiers in Microbiology. 4:254. Doi: 10.3389/fmicb.2013.00254 (abstract & PDF)
  • Krepski, S.T, D. Emerson, P.L. Hredzak-Showalter, G. Luther III, and C.S. Chan. 2013. Morphology of biogenic iron oxides records microbial physiology and environmental conditions: towards interpreting iron microfossils. Geobiology. 11:457-471. (abstract)
  • Fleming, E.J., R.E. Davis, S.M. McAllister, C.S. Chan, C.L. Moyer, B.M. Tebo, and D. Emerson. 2013. Hidden in plain sight: discovery of sheath-forming, Fe-oxidizing Zetaproteobacteria at Loihi Seamount. FEMS Microbiological Ecology. 85:116-127 (abstract) (Selected Chief Editor's Choice for this issue)
  • McBeth, J.M., E.J. Fleming, and D. Emerson. 2013. The transition from freshwater to marine iron-oxidizing lineages along a salinity gradient on the Sheepscot River, Maine USA. Environ. Microbiol. Reports. 5:453-463 doi:10.1111/1758-2229.12033 (abstract)
  • Emerson, D. W. Bellows, J.K. Keller, A. Sutton_Grier, and P.J. Megonigal. 2013. Anaerobic metabolism in tidal freshwater wetlands: II. Effects of plant removal on Archaeal microbial communities. Estuaries and Coasts. 36:471-481. (abstract)
  • Emerson, D. 2012. Biogeochemistry and microbiology of microaerobic Fe(II) oxidation. Biochem. Soc. Trans. 40: 1211-1216. (abstract)
  • Brier, J.A., D. Gomez-Ibanez, E. Reddington, J. Huber, and D. Emerson. 2012. A precision multi-sampler for deep-sea hydrothermal microbial mat studies. Deep-Sea Res. Part I. 70:83-90. Doi: 10.1016/j.dsr.2012.10.006
  • Roden, E.E., J.M. McBeth, M. Blothe, E.M. Percak-Dennett, E.J. Fleming, R.R. Holyoke, G.W. Luther, and D. Emerson. 2012. The microbial ferrous wheel in a neutral-pH groundwater iron seep. Front. Microbiol. 3:172. (abstract & pdf)
  • Singer E, Emerson D, Webb EA, Barco RA, Kuenen JG, et al. 2011. Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium. PLoS ONE 6(9): e25386. doi:10.1371/journal.pone.0025386 (abstract & pdf)
  • McAllister, S.M., R.E. Davis, B.M. Tebo, J.M. McBeth, D. Emerson, C.L. Moyer. 2011. Biodiversity and emerging biogeography of the neutrophilic iron-oxidizing Zetaproteobacteria. Appl. Environ. Microbiol. 77:5445-5457 doi:10.1128/AEM.00533-11. (abstract)
  • Fleming, E.J., A.E. Langdon, M. Martinez-Garcia, R.S. Stepanauskas, N. Poulton, D. Masland, D. Emerson. (2011) What’s new is old: resolving the identity of Leptothrix ochracea using single cell genomics, pyrosequencing and FISH. PLoS ONE 6(3): e17769. doi:10.1371/journal.pone.0017769.(abstract and pdf)
  • Edwards, K.J., B.T. Glazer, O.J. Rouxel, W. Bach, D. Emerson, R.E. Davis, B.M. Toner, C.S. Chan, B.M. Tebo, H. Staudigel, and C.L. Moyer. 2011. Ultra-diffuse hydrothermal venting supports Fe-oxidizing bacteria and massive umber deposition at 5000m off Hawai’i. ISME J. 5:1748-1758. (abstract & pdf)
  • McBeth, J.M., B.J. Little., R.I. Ray, K.M. Farrar, D. Emerson. (2010) Neutrophilic iron-oxidizing Zetaproteobacteria and mild steel corrosion in nearshore marine environments. Appl. Environ. Microbiol. 77(4): 1405-1412 (abstract)
  • Chan, C.S., S.C. Fakra, D. Emerson, E.J. Fleming, K.J. Edwards. (2011). Lithotrophic Fe-oxidizing bacteria form organic stalks to control mineral growth: implications for biosignature genesis. ISME Journal 5: 717-727 (abstract and pdf)
  • Emerson D., E.J. Fleming, J.M. McBeth. JM. 2010. Iron-Oxidizing Bacteria: An Environmental and Genomic Perspective. Annual Review of Microbiology. 64: 561-583. (abstract)
  • Emerson, D, and C. Moyer. 2010. Microbiology of Seamounts: Common patterns observed in community structure. Oceanography. 23: 148-163. (pdf)
  • Emerson, D. 2010. Leptothrix. Encyclopedia of Geobiology. (A. Kappler, ed). Springer-Verlag.
  • Emerson, D, and W. Wilson. 2009. Giving microbial diversity a home. Nature Microbiol. Rev. 7: 758. (abstract)
  • Emerson, D. 2009. Potential for iron-reduction and iron-cycling in iron oxyhydroxide-rich mats at Loihi Seamount. Geomicrobiology J. 26:639-647. (abstract)
  • Chan, C. S., Fakra, S, Edward, D.C., Emerson, D, and Banfield, J.F. 2009. Iron oxyhydroxide mineralization on microbial polymers. Geochimica Cosmochimica Acta. 73:3807-3818.
  • Smith, S.A, R.F. Unz, D. Emerson, and J.L. Clancy. 2009. Joint Task Group. Section 9240: Iron and Sulfur Bacteria. Standard Methods for the Examination of Water and Wastewater. www.standardmethods.org
  • Emerson, D, H. Liu, L. Agulto, and L. Liu. 2008 Identification and characterization of bacteria in the 21st century. Bioscience. 58: 925-936.
  • Druschel, G.K., D. Emerson, R. Sutka, P. Suchecki, and G.W. Luther. 2008. Low oxygen and chemical kinetic constraints on the geochemical niche of neutrophilic iron (II) oxidizing microorganisms. Geochemica Cosmochimica Acta. 72:3358-3370.
  • Cleland, D, P. Krader, and D. Emerson. 2008. Use of the DiversiLab Repetitive Sequence-Based PCR system for Genotyping and Identification of Archaea. J. Microbiol. Meth. 73:172-178.
  • Ma, S, Luther, G. W. Luther, J. Keller, A.S. Madison, E. Metzger, J.P. Megonigal, and D. Emerson. 2008. Solid-state Au/Hg microelectrode for the investigation of Fe and Mn cycling in freshwater wetland: implications for methane production. Electroanalysis. 20:233-239.
  • S. Neubauer, D Emerson, and P. Megonigal. 2008. Microbial oxidation and reduction of iron in the root zones of wetland plants and mobility of heavy metals. In: Biophysico-Chemical Processes of Heavy Metals and Metalloids in Soil Environments. A. Violante, P.M. Huang and G. Stotzsky (eds). IUPAC. 339-371.
  • Weiss, J.V., Rentz, J.A., Plaia, T, Neubauer, S.C., Floyd, M.M., Lilburn, T., Bradburne, C. Megonigal, J.P., and D. Emerson. 2007. Identification of diverse neutrophilic Fe(II)-oxidizing bacteria isolated from the rhizosphere of wetland plants and description of Ferritrophicum radicicola gen. nov. sp. nov., and Sideroxydans paludicola sp. nov. Geomicrobiology J. 24:559-570.
  • Rentz, J.A., C. Kraiya, G.W. Luther III, and D. Emerson. 2007 Control of ferrous iron oxidation within circumneutral microbial iron mats by cellular activity and autocatalysis. Environ. Sci. Technol. 41:6048-6089.
  • Emerson, D., J.A. Rentz, T.G. Lilburn, R.E. Davis, H. Aldrich, C. Chan, and C.L. Moyer. 2007. A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities . PLOSOne. 2(8): e667. doi:10.1371/journal.pone.0000667
  • Emerson, D., and J. Tang. 2007. Media and Nutrition. In Manual of Methods for General and Molecular Microbiology, 3rd Edition. C.A. Reddy, et al [eds.] American Society of Microbiology Press. Pp 200-214.
  • Roden, E. R. and D. Emerson. 2007. Microbial Metal Cycling in Aquatic Environments. Manual of Environmental Microbiology, 3rd Ed. American Society of Microbiology Press. Washington, D.C. pp, 540-562.
  • Cleland D., K. Jastrzembski, E. Stamenova, J. Benson, C. Catranis, D. Emerson, and B. Beck. 2007. Growth characteristics of microorganisms on commercially available animal-free alternatives to tryptic soy medium. J. Microbiol. Methods. 69:345-352.
  • Neubauer, S.C., G. E. Toledo-Durán, D. Emerson, J.P.Megonigal. 2007. Returning to their roots: Iron-oxidizing bacteria enhance short-term plaque formation in the wetland-plant rhizosphere. Geomicrobiol. J. 24:65-73.
  • Scott, J.H., D.M. O’Brien, D. Emerson, H. Sun, G.D. McDonald, M. L. Fogel. 2006. An examination of the carbon isotope effects associated with amino acid biosynthesis . Astrobiology. 6:867-880
  • Emerson, D, J. Rentz, R. Davis, and C. Moyer. 2006. Role of a unique population of lithotrophic, Fe-oxidizing bacteria in forming microbial Fe-mats at the Loihi Seamount. Astrobiology. 6:148.
  • Plaia, T, M. Floyd, and D. Emerson. 2006. That which is most obvious is what we know the least: Investigation of a freshwater Fe-oxidizing microbial mat community. Astrobiology 6:206.
  • Pignone, M., K. Greth, J. Cooper, D. Emerson, and J Tang. 2006. Identification of Mycobacteria by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Journal of Clinical Microbiology. 44:1963-1970.
  • Kappler, A., D. Emerson, K. Edwards, J.P. Amend, J.A. Gralnick, P. Grathwohl, T. Hoehler, and K.L. Straub. 2005. Microbial activity in biogeochemical gradients – new aspects of research. Geobiology. 3:229-233.
  • Weiss, J.V., D. Emerson, and J.P. Megonigal. 2005. Rhizosphere iron(III) deposition and reduction in a Juncus effuses-dominated wetland. Soil Biol. Biochem. 69:1861-1870.
  • Floyd, M.M., J. Tang, M. Kane, and D. Emerson. 2005. Captured diversity in a culture collection: a case study of the geographic and habitat distribution of environmental isolates held at the American Type Culture Collection. Appl. Environ. Microbiol. 71:2813-2823.
  • Emerson, D. and M.M. Floyd. 2005. Enrichment and isolation of iron-oxidizing bacteria at neutral pH. Methods in Enzymology. 397:112-124