Department of Earth and Environmental Sciences
Newton Horace Winchell School of Earth and Environmental Sciences

Jake Bailey


435 Tate Hall


Associate Professor
PhD, 2008, University of Southern California

Geobiology Research Group Website:

Research Interests

The Earth's lithosphere, hydrosphere, and atmosphere are profoundly influenced by the activities of microorganisms. Geobiological processes that underpin modern biogeochemical cycles also shaped ancient environments, from the formation of authigenic mineral deposits, to the oxygenation of Earth's early atmosphere. My primary scientific interest is to better understand interactions between the biosphere and geosphere in both modern and ancient settings. 

In order to accomplish these goals, our lab takes the following approaches:

  • We study microbes and their metabolisms with the goals of better understanding their biology, evolution and biogeochemical significance. In some cases, we work with organisms that we have isolated. In other cases, we employ culture-independent approaches such as FISH, metagenomics, metatranscriptomics, and itag/amplicon-enabled community characterization.  
  • We study sulfide-oxidizing lithotrophs, especially the world's largest bacteria - Thiomargarita spp.
  • We study polyphosphate metabolism and its role in diverse environments, from ocean sediments to dental plaque
  • We actively seek to establish new methods, such as immunodetection, for detecting and studying modern and ancient microbial activity.


Active Research and Interests

  • Investigating the ecophysiology and genomics of sulfide-oxidizing bacteria such as Thiomargarita

  • Exploring the role of sulfur-oxidizing bacteria in the precipitation and dissolution of authigenic minerals

  • Understanding the role of polyphosphate metabolism(s) in sediment geochemistry and human dental caries

  • Exploring the metabolic and ecological diversity of chemolithoautotrophic microbes

  • Developing antibodies as in-situ organic biomarker detection tools


Professional Society Membership

  • Geological Society of America
  • International Society for Microbial Ecology
  • American Geophysical Union
  • Geochemical Society
  • Society for the Advancement of Chicanos and Native Americans in Science


Honors and Awards

  • Simons Foundation Early Career Investigator in Marine Microbial Ecology and Evolution, 2015 
  • Kavli Frontiers of Science Fellow, 2014
  • Alfred P. Sloan Foundation Research Fellow, 2014
  • UMN Graduate and Professional Student Assembly Outstanding Advisor Award, 2013
  • UMN McKnight Land Grant Professorship, 2013
  • National Science Foundation CAREER Grant, 2011-2016
  • Agouron Institute Geobiology Postdoctoral Fellowship, 2008
  • National Science Foundation Graduate Research Fellowship, 2005


Selected Publications

  • Jones, D., Johnson, N.W., Mitchell, C., Walker, G., Bailey, J.V., Pastor, J., Swain, E., 2020, Diverse communities of hgcAB+ microorganisms methylate mercury in freshwater sediments subjected to experimental sulfate loading. Environmental Science & Technology.

  • Medina-Ferrer, F.*, Hobart, K.H., Bailey, J.V., 2020, Field detection of urease and carbonic anhydrase activity using rapid and economical tests to assess microbially-induced carbonate precipitation, Microbial Biotechnology. 13(6),

  • Larina, E., Bottjer, D.J., Corsetti, F.A., Zonneveld, J-P. Celestian, A., Bailey, J.V., 2019,  Uppermost Triassic phosphorites from Willison Lake, Canada: link to fluctuating euxinic-anoxic conditions in northeastern Panthalassa before the end-Triassic mass extinction. Scientific Reports, v.9, Article number: 18790. 

  • Lumiste, K., Mänd, K., Bailey, J.V., Paiste, P., Lang, L., Lepland, A., Kirsimäe, K., 2019, REE+Y uptake and diagenesis in Recent sedimentary apatites. Chemical Geology.

  •  Jones, D.S.*, Walker, G.M., Johnson, N.W., Mitchell, C.P.J., Coleman Wasik, J.K., Bailey, J.V., 2019, Molecular evidence for novel mercury methylating microorganisms in sulfate-impacted lakes. ISME Journal. 

  • Zoss, R.*, Medina-Ferrer*, F., Flood, B.E.*, Jones, D.S.*, Louw, D.C., Bailey, J.V., 2019, Microbial communities associated with phosphogenic sediments and phosphoclast-associated DNA of the Benguela Upwelling System. Geobiology, 17:76–90.

  • Flood, B.E.*, Leprich, D.*, Bailey, J.V., 2018, The complete genome of Celeribacter baekdonensis strain LH4, a thiosulfate-oxidizing alphaproteobacterial isolate from Gulf of Mexico continental slope sediments. ASM Genome Announcements.

  • Mänd, K., Kirsimäe, K., Lepland, A., Crosby C.H.*, Bailey, J.V., Konhauser, K., Wirth, R., Schreiber, A., and Lumiste, K., 2018, Authigenesis of biomorphic apatite particles from modern upwelling zone sediments off Namibia. 640–658 Geobiology. 10.1111/gbi.12309

  • Medina-Ferrer, F.* §, Bailey, J.V. §, Corsetti, F., Moldowan, J.M, Barbanti, S.M., Caron, D., Bryant-Huppert, J.*, 2018, Assessing biomarker syngeneity: An in situ approach using monoclonal antibodies.  Organic Geochemistry, v.124, 112-122.

  • Breiland, A., Flood, B.E., Nikrad, J., Bakarich, J., Husman, M., TaekHyun, R. , Jones, R. Bailey, J.V., 2018, Polyphosphate-accumulating bacteria: Potential contributors to mineral dissolution in the oral cavity. Applied and Environmental Microbiology. Volume 84, Issue 7.

  • Harrison, B.K., Myrbo, A., Flood, B.E., Bailey, J.V., 2018, Abrupt burial imparts persistent changes to the bacterial diversity of turbidite-associated sediment profiles. Geobiology. DOI: 10.1111/gbi.12271 

  •  Bailey, J.V., Flood, B.E., Ricci, E., Delherbe, N., (2017) Imaging of cellular oxidoreductase activity suggests mixotrophic
      metabolisms in Thiomargarita spp. mBio. v. 8, No. 5, mBio 01263-17.

  • Jones, D.S., Roepke, E.W., Hua, A., Flood, B.E., and Bailey, J.V., (2017) Complete genome sequence of Sulfuriferula sp. str. AH1, a
      sulfur-oxidizing autotroph isolated from weathered sulfide-bearing mine tailings from the Duluth Complex in Minnesota. ASM genome
    . v. 5, no. 32.

  • Jones, D.S., Lapakko, K.A., Wenz, Z.J., Olson, M.C., Roepke, E.W., Sadowsky, M.J., Novak, P.J., Bailey, J.V., (2017) Novel microbial
      assemblages dominate weathered sulfide-bearing rock from copper-nickel deposits in the Duluth Complex, Minnesota, USA. Applied and  
      Environmental Microbiology
    . v.83, no.16.

  • Crosby, C.H., Bailey, J.V., (2017) Experimental precipitation of apatite pseudofossils resembling fossil embryos, Geobiology.

  • Crosby, C.H., Bailey, J.V., (2017), An economical apparatus for the observation and harvesting of mineral precipitation experiments 
      with light microscopy. Biogeosciences 14, 2151–2154.

  • Sharrar, AM, Flood, B.E., Bailey, J.V., Jones, D.S., Biddanda, B.A., Ruberg, S.A., Marcus, D.N., and Dick, G.J., (2017) Novel large sulfur bacteria in the metagenomes of groundwater-fed chemosynthetic microbial mats in the Lake Huron basin, Frontiers in Extreme Microbiology. doi: 10.3389/fmicb.2017.00791

  • Winkel, M., Salman, V., Woyke, T., Richter, M., Schulz-Vogt, H., Flood, B.E., Bailey, J.V., Mußmann, M., (2016) Single-cell sequencing of Thiomargarita reveals genomic flexibility for adaptation to dynamic redox conditions. Frontiers in Extreme Microbiology.

  • Flood, B.E., Fliss, P., Jones, D.S.,  Dick, G., Jain, S. Kaster, A.K., Winkel, M. Muβmann, M. Bailey, J.V. (2016) Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity. Frontiers in Extreme Microbiology. 7:603. doi: 10.3389/fmicb.2016.00603

  • Harrison, B.K., Myrbo, A., Flood, B.E., Bailey, J.V. (2016) Recovery of subannual microbial community information from individual sedimentary laminae using a freeze-coring approach. Limnology and Oceanography, DOI: 10.1002/lno.10250

  • Jones, D.S., Flood, B.E. , Bailey, J.V. (2015) Metatranscriptomic insights into polyphosphate metabolism in marine sediments. ISME Journal, DOI:10.1038/ismej.2015.169

  • Stevens, E.N., Bailey, J.V., Flood, B.E.*, Jones, D.S., Gilhooly III, W.P., Joye, S.B., Teske, A., Mason, O.U., (2015) Barite encrustation of benthic sulfur-oxidizing bacteria at a marine cold seep. Geobiology. DOI: 10.1111/gbi.12154

  • Mason, O.U. §, Case, D.H.§, Naehr, T.H., Lee, R.W., Thomas, R.B., Bailey, J.V., Orphan, V.J., (2015) Comparison of archaeal and bacterial diversity in methane seep carbonate nodules and host sediments, Eel River Basin and Hydrate Ridge, USA. Microbial Ecology; DOI 10.1007/s00248-015-0615-6.

  • Flood, B.E. , Jones, D.S., Bailey, J.V., (2015) The complete genome of Sedimenticola thiotaurini strain SIP-G1, a polyphosphate and polyhydroxyalkanoate-accumulating sulfur-oxidizing gammaproteobacterium isolated from salt marsh sediments. ASM Genome Announcements.

  • Flood, B.E. , Bailey, J.V., Jones, D.S., (2015) Sedimenticola thiotaurini sp. nov., a sulfide-oxidizing bacterium isolated from saltmarsh sediments, emended description of  the genus Sedimenticola and holotype strain Sedimenticola selenatireducens. International Journal of Systematic and Evolutionary Microbiology.

  • Jones, D.S., Flood, B.E., Bailey, J.V. (2015) Metatranscriptomic analysis of diminutive Thiomargarita-like bacteria (“Candidatus Thiopilula spp.”) from abyssal cold seeps of the Barbados Accretionary Prism. Applied and Environmental Microbiology. 81:3142–3156.

  • Vietti, L.A., Bailey, J.V., Fox, D.L., and Rogers, R.R., (2015) Rapid formation of framboidal sulfides on bone surfaces from a simulated marine carcass fall. Palaios. v. 30.

  • Crosby, C.H., Bailey, J.V., and Sharma, M., (2014), Fossil evidence of iron-oxidizing chemolithotrophy linked to phosphogenesis in the wake of the Great Oxidation Event. Geology, v. 42, p. 1015-1018.

  • Flood, B.E, Bailey, J.V., Biddle, J.F. (2014), Horizontal gene transfer and the rock record: comparative genomics of phylogenetically distant bacteria that induce wrinkle structure formation in modern sediments.  Geobiology. doi: 10.1111/gbi.12072.

  • Salman, V., Bailey, J.V., Teske, A. (2013) Phylogenetic and morphologic complexity of giant sulphur bacteria. Antonie Van Leeuwenhoek v.104(2):169-86. doi: 10.1007/s10482-013-9952

  • Bailey, J.V., Corsetti, F.A., Greene, S.E., Crosby, C.H.*, Liu, P., Orphan, V.J., (2013) Filamentous sulfur bacteria preserved in modern and ancient phosphatic sediments: implications for the role of oxygen and bacteria in phosphogenesis.Geobiology doi: 10.1111/gbi.12046

  • Crosby, C.H.*, Bailey, J.V., (2012) The role of microbes in the formation of modern and ancient phosphatic mineral deposits. Frontiers in Aquatic Microbiology. v. 3, p. 3-9:241. doi: 10.3389/fmicb.2012.00241

  • Cunningham, J. A., Thomas, C.-W., Bengtson, S., Marone, F., Stampanoni, M., Turner, F. R., Bailey, J. V., Raff, R. A., Raff, E. C., Donoghue, P. C. J., (2012) Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils. Proceedings of the Royal Society B, v. 279, 1857-1864.

  • Bailey, J.V., Salman, V., Rouse, G.W., Schulz-Vogt, H.N., Levin, L.A., Orphan, V.J., (2011) Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria. ISME Journal, v. 5, p. 1926-1935.

  • Bailey, J.V., (2011) Breathing room for early animals. Nature Geoscience., v. 4, p. 354-355.

  • Salman, V., Amann, R., Girnth, A-C., Polerecky, L., Bailey, J.V., Høgslund, S., Jessen, G., Pantoja, S., and Schulz-Vogt, H., (2011) A single-cell sequencing approach to the classification of large, vacuolated sulfide-oxidizing bacteria. Systematic and Applied Microbiology, v. 34, p.243-259.

  • Bailey, J.V., Raub, T.D., Meckler, A.N., Harrison, B.K., Raub, T.M.D., Green, A.M., and Orphan, V.J., (2010) Pseudofossils in relict methane seep carbonates resemble endemic microbial consortia. Palaeogeography, Palaeoclimatology, Palaeoecology, v. 285, p. 131-142.

  • Bailey, J.V., Orphan, V.J., Joye, S.B., and Corsetti, F.A., (2009) Chemotrophic microbial mats and their potential for preservation in the rock record. Astrobiology, v. 9, p. 843-859.

  • Bailey, J.V., Joye, S.B., Kalanetra, K.M., Flood, B.E., and Corsetti, F.A., (2007) Evidence of giant sulphur bacteria in Neoproterozoic phosphorites. Nature, v. 445, p. 198-201.

  • Bailey, J.V., Corsetti, F.A., Bottjer, D.J., and Marenco, K.N., (2006) Microbially-mediated environmental influences on metazoan colonization of matground ecosystems: evidence from the Lower Cambrian Harkless Formation. Palaios, v. 21, p. 215-226.

  • Bailey, J.V., Cohen, A.S., and Kring, D.A., (2005) Lacustrine fossil preservation in acidic environments: Implications of experimental and field studies for the Cretaceous-Paleogene Boundary acid rain trauma. Palaios, v. 20, p. 376-389.