Publications

Publications
Leprich, D.J.*, Flood, B.E, Schroedl, P. *, Ricci, E. *, Marlow, J.J., Girguis, P., 
Bailey, J.V., 2021, Sulfur bacteria promote authigenic carbonate dissolution at marine methane seeps. ISME Journal. https://doi.org/10.1038/s41396-021-00903-3
Petryshyn, V.A., Junkins, E.N., Stamps, B.W., Bailey, J.V., Stevenson, B.S., Spear, J.R., 
Corsetti, F.A., 2021, Builders, tenants, and squatters: The origins of genetic material in modern stromatolites. Geobiology. DOI: 10.1111/gbi.12429 
Nayfach S et al. (Bailey part of IMG/M Data Consortium, 185 co-authors), 2020, A Genomic Catalog of Earth’s Microbiomes. Nature Biotechnology. 2020 Nov 9. doi: 10.1038/s41587-020-0718-6.
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. 54 (22), 14265-14274, https://doi.org/10.1021/acs.est.0c02513
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), https://doi.org/10.1111/1751-7915.13630
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. doi.org/10.1016/j.chemgeo.2019.07.034
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. https://doi.org/10.1038/s41396-019-0376-1 
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. https://doi.org/10.1111/gbi.12318
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, mBio01263-17.
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 announcements. 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. 2017;00:1–8. doi.org/10.1111/gbi.12264
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. Mumann, 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. v.13, p.588-603 Geobiology. DOI: 10.1111/gbi.12154

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. 3(3), doi: 10.1128/genomeA.00671-15.


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. *, 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. doi: 10.1099/ijs.0.000295.

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. v. 81, p.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, p. 327-334.

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, v. 12, p. 119-132. 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, p. 169-86. 


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, v. 11, p. 397-
405. 

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 – Biological Sciences, 2012, 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.

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., 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., 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, Undressing and redressing Ediacaran embryos – reply to brief communication arising. Nature, doi: 
10.1038/nature05753.

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.