David Emerson, PhD


Senior Research Scientist
Geomicrobiologist
Phone: +1 (207) 315-2567, ext. 303
Fax: +1 (207) 315-2329
demerson@bigelow.org

For media inquiries, please contact sprofaizer@bigelow.org



Education

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, coastal marine sediments, freshwater wetlands, and the Arctic tundra. 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. He has recently become involved in utilizing environmental DNA (eDNA) as an approach to link all life living in an ecosystem.

Current Research Projects

  • Arctic Iron Cycling (NSF)
    • This is a field-based project utilizing the Toolik Field Station in Alaska to study the role of Fe-oxidizing microbes in catalyzing a very active iron cycle in permafrost tundra, and to determine how this active iron cycle impacts the carbon cycle through interactions with biological methane production, and phosphorus retention.
  • Maine-eDNA. (NSF)
    • The goal of this project is to utilize eDNA to test the ability of environmental DNA (eDNA) science to resolve ecological patterns and processes at the diverse spatial, temporal and taxonomic scales of complex coastal systems in Maine, in order to evaluate its potential to be a transformative way to study and monitor ecosystems.
  • Fe-oxidizing bacteria as sources of nanomaterials (ONR)
    • We would like to understand the physiological and genetic basis for the production of nanoparticulate biogenic iron oxides in order to control the process for a range of potential applications.
  • Genome to phenome. (NSF)
    • Linking the remarkable diversity of bacteria and archaea to specific metabolisms remains a major challenge in microbiology. A primary goal of this project is to link physiological or phenotypic information of single cells of uncultivated bacteria or archaea to their genomic information combining fluorescent-based reporters of activity to single cell genomics via single cell sorting methodology.
  • Methane suppression in ruminants (Private funding)
    • This is a collaborative project with Bigelow colleagues to determine the efficacy of using algal products to suppress methanogenesis in ruminant animals.
  • Development of mock communities. (Bigelow internal)
    • We are developing mock communities constructed from the genomes of known bacteria and archaea as standards that can be used to assess data quality associated with high throughput or next generation genome sequencing methodologies.
  • Geoengineering (Unfunded)
    • I am interested in the potential of utilizing biogenic iron oxides distributed aerially as dust to provide iron fertilization to the third of the world ocean that is iron-limited, as a means of sequestering ppm levels of carbon dioxide from the atmosphere
  • Evolution of the Zetaproteobacteria (NASA)
    • Discovery of this novel class of Proteobacteria associated with Fe-rich ecosystems has led us into studies about their evolution and the use of Fe(II) as an energy source.

Recently completed

  • Iron cycling in coastal sediments (NSF).
    • This project systematically explored the role of iron-oxidizing bacteria in controlling iron fluxes from the sediment to the water column in coastal Maine ecosystems.
  • Impact of Fe-oxidizing bacteria on biocorrosion of steel (ONR)
    • Understanding the role that marine Fe-oxidizing bacteria may play in corrosion of steel, either acting alone or in environmental consortia.

Importance of this work with regard to Fe-oxidizing bacteria (FeOB).

FeOB play both nuisance and beneficial roles in human activities; they are major agents of biofouling and biocorrosion in industrial and domestic water distribution systems; they can aid in the removal of iron and other harmful metals and organics in water treatment systems.

Iron oxides are very reactive minerals that have high sorption capacities for P, as well as Ar, Cd, Pb, U, and other metals. FeOB have a variety of ways of controlling the deposition of the Fe oxides that likely influence their reactivity. Many FeOB produce unique microstructures, commonly in the form of sheaths or stalks, composed of an organo-mineral matrix, that undoubtedly influences these interactions in unique ways.

FeOB may have influenced the biogeochemistry of the early Earth through precipitation of iron oxides and the formation of banded iron formations (the world’s primary source of iron ore).

Since iron is one of the most common elements in planetary composition, it is possible that iron-based metabolisms may have arisen on other planets, the study of extant FeOB on Earth can help us understand the types of habitats we should look for on other planets and what sort of biomarkers we might expect to find.

Fe is the primary micro-nutrient limiting primary production in at least a third of the world’s ocean. Based on paleo-studies of CO2 levels in the atmosphere, atmospheric deposition of iron to the ocean via Aeolian dust, and the correlation to ice-ages, it has been proposed that fertilization of the global ocean with iron could enhance draw down of CO2 from the atmosphere, and remove enough CO2 from the atmosphere to exert a cooling effect. I have proposed that biogenic iron oxides could be an excellent source of iron for ocean fertilization. When dried these oxides produce a very fine powder (dust) that delivered to the atmosphere mimic the natural source of iron to the ocean, but in a more directed and potent way. If done on a global scale, distribution of these oxides could substantially reduce the amount of CO2 in the atmosphere.

Personal Pages

Laboratory

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).

Publications

  • MacDonald, B.L., D. Stalla, X. He, F. Rahemtella, D. Emerson, P.A. Dube, M.R. Maschmann, C.E. Klesner, T.E. White. Late-holocene hunter-gatherers harvested and thermally enhanced microbial biogenic iron oxides to produce rock art pigment. Scientific Reports, In Press.
  • Lopez, A., D. Albino, S. Beraki, S. Broomell, R. Canela, T. Dingmon, S. Estrada, M. Fernandez, P. Savalia, K. Nealson, D. Emerson, R. Barco, B. Tully, and J. Amend. 2019. Genome sequence of Mariprofundus sp. strain EBB-1: a novel marine autotroph isolated from an iron-sulfur mineral. Genome Announcements
  • Emerson, D. 2019. Biogenic iron dust: a novel approach to ocean iron fertilization as a means of large scale removal of carbon dioxide from the atmosphere. Frontiers in Marine Science 6:22. Doi: 10.3.389/fmars.2019.00022
  • McAllister, S.M., R.M. Moore, A. Gartman, G.W. Luther III, D. Emerson, and C. Chan. 2019. Marine Fe-oxidizing Zetaproteobacteria: Historical, ecological, and genomic perspectives. FEMS Microbiology Ecology. Advance Access Pub/ 95, doi: 10.1093/femsec/fiz015.
  • Emerson, D. 2019. The role of iron-oxidizing bacteria in biocorrosion: a review. Biofouling. Doi: 10.1080/08927014.1526281.
  • Smith, H., K. Abuyen, J. Tremblay, P. Savalia, I. Perez-Rodrigues, D. Emerson, B. Tully, and J. Amend. 2018. Genome sequence of Geothermobacter sp. HR-1 an iron-reducer from the Loihi Seamount. Genome Announcements 6:e00339-18. https://doi.org/10.1128/genomeA.00339-18.
  • Neely, C., C. B. Khalil, A. Cervantes, R. Diaz, A. Escobar, K. Ho, S. Hoefler, H. Smith, K. Abuyen, P. Savalia, K. Nealson, D. Emerson, B. Tully, R. Barco, and J. Amend. 2018. Genome sequence of Hydrogenovibrio sp. SC-1, a Chemolithoautotrophic, Sulfur and Iron Oxidizer. Genome Announcements. 6:e01581-17. https://doi.org/10.1128/genomeA.01581-17.
  • Floyd, M., A.J. Williams, A. Grubisic, and D. Emerson. 2018. Metabolic processes preserved as biosignatures in neutrophilic Fe-oxidizing organisms: Implications for biosignature detection on Mars. Astrobiology J. 19: published online ahead of print, Doi: 10.1089/ast.2017.1745
  • Fleming E.J., T. Woyke, R. Donatello, M.M. Kuypers, A. Sczyrba, S. Littmann, and D. Emerson. 2018. Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea. Applied and Environmental Microbiology. 84:e02239-17. https://doi.org/10.1128/AEM.02239-17. (received an AEM Spotlight journal highlight)
  • Lueder, U., G. Druschel, D. Emerson, A. Kappler, and C. Schmidt. 2018. Quantitative analysis of O2 and Fe2+ profiles in gradient tubes for cultivation of microaerophilic iron(II)-oxidizing bacteria. FEMS Microbiology Ecology. Advance Access Pub. 94: doi: 10.1093/femsec/fix177
  • Beam, J.P., J.J. Scott, S.M. McAllister, C.S. Chan, J. McManus, F.J.R. Meysman, and D. Emerson. 2018. Potential for biological rejuvenation of iron oxides in bioturbated marine sediments. ISME J. Online: https://doi.org/10.1038/s41396-017-0032-6.
  • Vesenka, J. J. Havu, and D. Emerson. 2017. A model for sheath formation coupled to motility in Leptothrix ochracea. Geomicrobiology J. 35:366-374.
  • Smith, H., K. Abuyen, J. Tremblay, P. Savalia, I. Perez-Rodrigues, D. Emerson, B. Tully, and J. Amend. 2018. Genome sequence of Geothermobacter sp. HR-1 an iron-reducer from the Loihi Seamount. Genome Announcements 6:e00339-18. https://doi.org/10.1128/genomeA.00339-18
  • Girguis, P, D. Fornari, N. Hayman, and D. Emerson. 2018. Developing Submergence Science in the Next Decade (DESCEND-2016). Proceedings of a Workshop. www.unols.org
  • Neely, C., C. B. Khalil, A. Cervantes, R. Diaz, A. Escobar, K. Ho, S. Hoefler, H. Smith, K. Abuyen, P. Savalia, K. Nealson, D. Emerson, B. Tully, R. Barco, and J. Amend. 2018. Genome sequence of Hydrogenovibrio sp. SC-1, a Chemolithoautotrophic, Sulfur and Iron Oxidizer. Genome Announcements. 6:e01581-17. https://doi.org/10.1128/genomeA.01581-17.
  • 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