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f Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater

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  • Authors: Yiran Dong1​,2​ ,  Robert A. Sanford2​ ,  Maxim I. Boyanov3​,4​ ,  Kenneth M. Kemner3​ ,  Theodore M. Flynn3​ ,  Edward J. O’Loughlin3​ ,  Randall A. Locke5​ ,  Joseph R. Weber6​ ,  Sheila M. Egan7​ , Bruce W. Fouke1​,2​,5​,6​
    • VIEW AFFILIATIONS
    • 1​ 1​Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA 2​ 2​Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL, USA 3​ 3​Biosciences Division, Argonne National Laboratory, Argonne, IL, USA 4​ 4​Institute of Chemical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria 5​ 5​Illinois State Geology Survey, University of Illinois Urbana-Champaign, Champaign, IL, USA 6​ 6​Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA 7​ 7​Department of Biochemistry, University of Illinois Urbana-Champaign, Champaign, IL, USA
  • Correspondence Yiran Dong [email protected]
  • First Published Online: 01 October 2016, International Journal of Systematic and Evolutionary Microbiology 66: 3964-3971, doi: 10.1099/ijsem.0.001295
  • Subject: New taxa - Firmicutes and related organisms
  • Received:
  • Accepted:
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Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater, Page 1 of 1

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  • A Gram-stain-negative, microaerophilic rod-shaped organism designated as strain Z9 was isolated from groundwater of 1.7 km depth from the Mt. Simon Sandstone of the Illinois Basin, Illinois, USA. Cells of strain Z9 were rod shaped with dimensions of 0.3×(1–10) µm and stained Gram-negative. Strain Z9 grew within the temperature range 20–60 °C (optimum at 30–40 °C), between pH 5 and 8 (optimum 5.2–5.8) and under salt concentrations of 1–5 % (w/v) NaCl (optimum 2.5 % NaCl). In addition to growth by fermentation and nitrate reduction, this strain was able to reduce Fe(III), Mn(IV), Co(III) and Cr(VI) when H2 or organic carbon was available as the electron donor, but did not actively reduce oxidized sulfur compounds (e.g. sulfate, thiosulfate or S). The G+C content of the DNA from strain Z9 was 36.1 mol%. Phylogenetic analysis of the 16S rRNA gene from strain Z9 showed that it belongs to the class Bacilli and shares 97 % sequence similarity with the only currently characterized member of the genus Tepidibacillus , T. fermentans. Based on the physiological distinctness and phylogenetic information, strain Z9 represents a novel species within the genus Tepidibacillus , for which the name Tepidibacillus decaturensis sp. nov. is proposed. The type strain is Z9 (=ATCC BAA-2644=DSM 103037).

  • The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA sequences of strain Z9 are KP898732 and KP898733.

  • Two supplementary figures are available with the online Supplementary Material.

© 2016 IUMS | Published by the Microbiology Society

  • Boone D. R., Liu Y., Zhao Z. J., Balkwill D. L., Drake G. R., Stevens T. O., Aldrich H. C..( 1995;). Bacillus infernus sp. nov. an Fe(III)- and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface. . Int J Sys Bacteriol 45: 441––448.[CrossRef]
    [Google Scholar]
  • Boucher Y., Douady C. J., Sharma A. K., Kamekura M., Doolittle W. F..( 2004;). Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. . J Bacteriol 186: 3980––3990. [CrossRef] [PubMed]
    [Google Scholar]
  • Bowen B. B., Ochoa R. I., Wilkens N. D., Brophy J., Lovell T. R., Fischietto N., Medina C. R., Rupp J. A..( 2011;). Depositional and diagenetic variability within the cambrian mount simon sandstone: implications for carbon dioxide sequestration. . Environ Geosci 18: 69––89. [CrossRef]
    [Google Scholar]
  • Caccavo F., Lonergan D. J., Lovley D. R., Davis M., Stolz J. F., McInerney M. J..( 1994;). Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. . Appl Environ Microbiol 60: 3752––3759.[PubMed]
    [Google Scholar]
  • Canfield D. E., Jorgensen B. B., Fossing H., Glud R., Gundersen J., Ramsing N. B., Thamdrup B., Hansen J. W., Nielsen L. P., Hall P. O. J..( 1993;). Pathways of organic-carbon oxidation in 3 continental-margin sediments. . Mar Geol 113: 27––40.[CrossRef]
    [Google Scholar]
  • Dong Y., Kumar C. G., Chia N., Kim P. J., Miller P. A., Price N. D., Cann I. K., Flynn T. M., Sanford R. A. et al.( 2014a;). Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir. . Environ Microbiol 16: 1695––1708. [CrossRef] [PubMed]
    [Google Scholar]
  • Dong Y., Sanford R. A., Locke R. A., Cann I. K., Mackie R. I., Fouke B. W..( 2014b;). Fe-oxide grain coatings support bacterial Fe-reducing metabolisms in 1.7-2.0 km-deep subsurface quartz arenite sandstone reservoirs of the Illinois Basin (USA). . Front Microbiol 5: 511. [CrossRef] [PubMed]
    [Google Scholar]
  • Dong Y., Chang Y.-J., Sanford R. A., Fouke B. W..( 2016;). Draft genome sequence of Tepidibacillus decaturensis strain Z9, an anaerobic, moderately thermophilic, and heterotrophic bacterium from the deep subsurface of the Illinois Basin, USA. . Genome Announc 4: e00190–e00216. [CrossRef] [PubMed]
    [Google Scholar]
  • Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackebrandt E..( 2006;). Bacteria: firmicutes, syanobacteria. . In The Prokaryotes: A Handbook on the Biology of Bacteria. New York, NY:: Springer Science & Business Media, LLC;.
     [Google Scholar]
  • Edwards K. J., Becker K., Colwell F..( 2012;). The deep, dark energy biosphere: intraterrestrial life on earth. . Ann Rev Earth Planet Sci 40: 551––568. [CrossRef]
    [Google Scholar]
  • Fredrickson J. K., McKinley J. P., Bjornstad B. N., Long P. E., Ringelberg D. B., White D. C., Krumholz L. R., Suflita J. M., Colwell F. S. et al.( 1997;). Pore‐size constraints on the activity and survival of subsurface bacteria in a late cretaceous shale‐sandstone sequence, northwestern New Mexico. . Geomicrobiol J 14: 183––202. [CrossRef]
    [Google Scholar]
  • Gibbs C. R..( 1976;). Characterization and application of FerroZine iron reagent as a ferrous iron indicator. . Anal Chem 48: 1197––1201. [CrossRef]
    [Google Scholar]
  • Halebian S., Harris B., Finegold S. M., Rolfe R. D..( 1981;). Rapid method that aids in distinguishing Gram-positive from Gram-negative anaerobic bacteria. . J Clin Microbiol 13: 444––448.[PubMed]
    [Google Scholar]
  • Heimann A., Johnson C. M., Beard B. L., Valley J. W., Roden E. E., Spicuzza M. J., Beukes N. J..( 2010;). Fe, C, and O isotope compositions of banded iron formation carbonates demonstrate a major role for dissimilatory iron reduction in ~2.5Ga marine environments. . Earth Planet Sci Lett 294: 8––18. [CrossRef]
    [Google Scholar]
  • Jorgensen B. B..( 2012;). Shrinking majority of the deep biosphere. . P Natl USA 109: 15976––15977. [CrossRef]
    [Google Scholar]
  • Kim M., Oh H.-S., Park S.-C., Chun J..( 2014;). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. . Int J Syst Evol Microbiol 64: 346––351. [CrossRef]
    [Google Scholar]
  • L'Haridon S., Miroshnichenko M. L., Kostrikina N. A., Tindall B. J., Spring S., Schumann P., Stackebrandt E., Bonch-Osmolovskaya E. A., Jeanthon C..( 2006;). Vulcanibacillus modesticaldus gen. nov. sp. nov., a strictly anaerobic, nitrate-reducing bacterium from deep-sea hydrothermal vents. . Int J Syst Evol Micr 56: 1047––1053.[CrossRef]
    [Google Scholar]
  • Lalonde K., Mucci A., Ouellet A., Gélinas Y..( 2012;). Preservation of organic matter in sediments promoted by iron. . Nature 483: 198––200. [CrossRef] [PubMed]
    [Google Scholar]
  • Lehours A.-C., Rabiet M., Morel-Desrosiers N., Morel J.-P., Jouve L., Arbeille B., Mailhot G., Fonty G..( 2010;). Ferric iron reduction by fermentative strain BS2 isolated from an iron-rich anoxic environment (Lake Pavin, France). . Geomicrobiol J 27: 714––722. [CrossRef]
    [Google Scholar]
  • Liu S. V., Zhou J., Zhang C., Cole D. R., Gajdarziska-Josifovska M., Phelps T. J..( 1997;). Thermophilic Fe(III)-reducing bacteria from the deep subsurface: the evolutionary implications. . Science 277: 1106––1109. [CrossRef]
    [Google Scholar]
  • Lovley D. R..( 1991;). Dissimilatory Fe(III) and Mn(IV) reduction. . Microbiol Rev 55: 259––287.[PubMed]
    [Google Scholar]
  • Lovley D. R., Phillips E. J..( 1986;). Organic matter mineralization with reduction of ferric iron in anaerobic sediments. . Appl Environ Microbiol 51: 683––689.[PubMed]
    [Google Scholar]
  • Lovley D. R., Chapelle F. H..( 1995;). Deep subsurface microbial processes. . Rev Geophy 33: 365––381. [CrossRef]
    [Google Scholar]
  • Lovley D. R., Holmes D. E., Nevin K. P..( 2004;). Dissimilatory Fe(III) and Mn(IV) reduction. . Adv Microb Physiol 49: 219––286. [CrossRef] [PubMed]
    [Google Scholar]
  • Melton E. D., Swanner E. D., Behrens S., Schmidt C., Kappler A..( 2014;). The interplay of microbially mediated and abiotic reactions in the biogeochemical Fe cycle. . Nat Rev Microbiol 12: 797––808. [CrossRef] [PubMed]
    [Google Scholar]
  • Mirarab S., Nguyen N., Guo S., Wang L. S., Kim J., Warnow T..( 2015;). PASTA: ultra-large multiple sequence alignment for nucleotide and amino-acid sequences. . J Comput Biol 22: 377––386. [CrossRef] [PubMed]
    [Google Scholar]
  • Mouné S., Eatock C., Matheron R., Willison J. C., Hirschler A., Herbert R., Caumette P..( 2000;). Orenia salinaria sp. nov., a fermentative bacterium isolated from anaerobic sediments of Mediterranean salterns. . Int J Syst Evol Microbiol 50: 721––729. [CrossRef] [PubMed]
    [Google Scholar]
  • Nealson K. H..( 1997;). Sediment bacteria: who's there, what are they doing, and what's new?. Annu Rev Earth Planet Sci 25: 403––434. [CrossRef] [PubMed]
    [Google Scholar]
  • Nealson K. H., Belz A., McKee B..( 2002;). Breathing metals as a way of life: geobiology in action. . Antonie Van Leeuwenhoek 81: 215––222.[PubMed] [CrossRef]
    [Google Scholar]
  • Pollock J., Weber K. A., Lack J., Achenbach L. A., Mormile M. R., Coates J. D..( 2007;). Alkaline iron(III) reduction by a novel alkaliphilic, halotolerant, Bacillus sp. isolated from salt flat sediments of Soap Lake. . Appl Microbiol Biotechnol 77: 927––934. [CrossRef] [PubMed]
    [Google Scholar]
  • Ritalahti K. M., Amos B. K., Sung Y., Wu Q., Koenigsberg S. S., Löffler F. E..( 2006;). Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. . Appl Environ Microbiol 72: 2765––2774. [CrossRef] [PubMed]
    [Google Scholar]
  • Roden E. E., McBeth J. M., Blöthe M., Percak-Dennett E. M., Fleming E. J., Holyoke R. R., Luther G. W., Emerson D., Schieber J..( 2012;). The Microbial ferrous wheel in a neutral pH groundwater Seep. . Front Microbiol 3: 172. [CrossRef] [PubMed]
    [Google Scholar]
  • Roh Y., Liu S. V., Li G., Huang H., Phelps T. J., Zhou J..( 2002;). Isolation and characterization of metal-reducing Thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado. . Appl Environ Microbiol 68: 6013––6020. [CrossRef] [PubMed]
    [Google Scholar]
  • Schloss P. D., Westcott S. L., Ryabin T., Hall J. R., Hartmann M., Hollister E. B., Lesniewski R. A., Oakley B. B., Parks D. H. et al.( 2009;). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. . Appl Environ Microbiol 75: 7537––7541. [CrossRef] [PubMed]
    [Google Scholar]
  • Singh A. K., Ulanov A. V., Li Z., Jayaswal R. K., Wilkinson B. J..( 2011;). Metabolomes of the psychrotolerant bacterium Listeria monocytogenes 10403S grown at 37 °C and 8 °C. . Int J Food Microbiol 148: 107––114. [CrossRef] [PubMed]
    [Google Scholar]
  • Slobodkina G. B., Panteleeva A. N., Kostrikina N. A., Kopitsyn D. S., Bonch-Osmolovskaya E. A., Slobodkin A. I..( 2013;). Tepidibacillus fermentans gen. nov., sp. nov.: a moderately thermophilic anaerobic and microaerophilic bacterium from an underground gas storage. . Extremophiles 17: 833––839. [CrossRef] [PubMed]
    [Google Scholar]
  • Stackebrandt E..( 2006;). Defining taxonomic ranks. . In Prokaryotes: A Handbook on the Biology of Bacteria, , 3rd edn.,vol. 1 , pp. 29––57.
     [Google Scholar]
  • Stackebrandt E., Goebel B. M..( 1994;). A place for DNA-DNA reassociation and 16s ribosomal-RNA sequence-analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44: 846––849.[CrossRef]
    [Google Scholar]
  • Stamatakis A..( 2006;). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. . Bioinformatics 22: 2688––2690. [CrossRef] [PubMed]
    [Google Scholar]
  • Sun D. L., Jiang X., Wu Q. L., Zhou N. Y..( 2013;). Intragenomic heterogeneity of 16S rRNA genes causes overestimation of prokaryotic diversity. . Appl Environ Microbiol 79: 5962––5969. [CrossRef] [PubMed]
    [Google Scholar]
  • Thamdrup B..( 2000;). Bacterial manganese and iron reduction in aquatic sediments. . Adv Microb Ecol 16: 41––84.[CrossRef]
    [Google Scholar]
  • Tindall B. J., Sikorski J., Smibert R. A., Krieg N. R..( 2007;). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology , pp. 330––393. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Martzluf G. A., Schmidt T. M., Snyder L. R.. Washington, DC:: ASM Press;.
     [Google Scholar]
  • Vargas M., Kashefi K., Blunt-Harris E. L., Lovley D. R..( 1998;). Microbiological evidence for Fe(III) reduction on early Earth. . Nature 395: 65––67. [CrossRef] [PubMed]
    [Google Scholar]
  • Williams K. H., Long P. E., Davis J. A., Wilkins M. J., N'Guessan A. L., Steefel C. I., Yang L., Newcomer D., Spane F. A. et al.( 2011;). Acetate availability and its influence on sustainable bioremediation of uranium-contaminated groundwater. . Geomicrobiol J 28: 519––539. [CrossRef]
    [Google Scholar]
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