1887

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Volume 72, Issue 3

sp. nov. and sp. nov.: novel sulphur-oxidizing chemolithoautotrophs isolated from the chemocline of Hospital Hole, an anchialine sinkhole in Spring Hill, Florida, USA No Access

Abstract

Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anchialine sinkhole located within the Weeki Wachee River of Florida. Gram-stain-negative cells of both strains were motile, chemotactic rods. Phylogenetic analysis of the 16S rRNA gene and predicted amino acid sequences of ribosomal proteins, average nucleotide identities, and alignment fractions suggest the strains HH1 and HH3 represent novel species belonging to the genus . The genome G+C fraction of HH1 is 47.8 mol% with a genome length of 2.61 Mb, whereas HH3 has a G+C fraction of 52.4 mol% and 2.49 Mb genome length. Major fatty acids of the two strains included C, C and C, with the addition of C 3-OH in HH1 and C in HH3. Chemolithoautotrophic growth of both strains was supported by elemental sulphur, sulphide, tetrathionate, and thiosulphate, and HH1 was also able to use molecular hydrogen. Neither strain was capable of heterotrophic growth or use of nitrate as a terminal electron acceptor. Strain HH1 grew from pH 6.5 to 8.5, with an optimum of pH 7.4, whereas strain HH3 grew from pH 6 to 8 with an optimum of pH 7.5. Growth was observed between 15–35 °C with optima of 32.8 °C for HH1 and 32 °C for HH3. HH1 grew in media with [NaCl] 80–689 mM, with an optimum of 400 mM, while HH3 grew at 80–517 mM, with an optimum of 80 mM. The name sp. nov. is proposed, and the type strain is HH1 (=DSM 111584=ATCC TSD-240). The name sp. nov is proposed, and the type strain is HH3 (=DSM 111593=ATCC TSD-241).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): cave , chemocline , chemolithoautotroph , sulphur oxidation and Thiomicrorhabdus
Funding
This study was supported by the:
  • Directorate for Biological Sciences (Award NSF-MCB-1952676)
    • Principle Award Recipient: KathleenScott
© 2022 The Authors
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2022-03-11
2024-04-18
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References

  1. Boden R, Scott KM, Williams J, Russel S, Antonen K et al. An evaluation of Thiomicrospira, Hydrogenovibrio and Thioalkalimicrobium: reclassification of four species of Thiomicrospira to each Thiomicrorhabdus gen. nov. and Hydrogenovibrio, and reclassification of all four species of Thioalkalimicrobium to Thiomicrospira . Int J Syst Evol Microbiol 2017; 67:1140–1151 [View Article] [PubMed]
     [Google Scholar]
  2. Scott KM, Williams J, Porter CMB, Russel S, Harmer TL et al. Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments. Environ Microbiol 2018; 20:2686–2708 [View Article] [PubMed]
     [Google Scholar]
  3. Mochizuki J, Kojima H, Fukui M. Thiosulfativibrio zosterae gen. nov., sp. nov., and Thiosulfatimonas sediminis gen. nov., sp. nov. Arch Microbiol 2021; 203:951–957 [View Article]
     [Google Scholar]
  4. Gonnella G, Adam N, Perner M. Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2. BMC Genomics 2019; 20:339 [View Article] [PubMed]
     [Google Scholar]
  5. Kojima H, Fukui M. Thiomicrorhabdus aquaedulcis sp. nov., a sulfur-oxidizing bacterium isolated from lake water. Int J Syst Evol Microbiol 2019; 69:2849–2853 [View Article] [PubMed]
     [Google Scholar]
  6. Liu X, Jiang L, Hu Q, Lyu J, Shao Z. Thiomicrorhabdus indica sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium isolated from a deep-sea hydrothermal vent environment. Int J Syst Evol Microbiol 2020; 70:234–239 [View Article] [PubMed]
     [Google Scholar]
  7. Liu X, Chen B, Lai Q, Shao Z, Jiang L. Thiomicrorhabdus sediminis sp. nov. and Thiomicrorhabdus xiamenensis sp. nov., novel sulfur-oxidizing bacteria isolated from coastal sediments and an emended description of the genus Thiomicrorhabdus. Int J Syst Evol Microbiol 2021; 71:004660 [View Article] [PubMed]
     [Google Scholar]
  8. Mikucki JA, Priscu JC. Bacterial diversity associated with Blood Falls, a subglacial outflow from the Taylor Glacier, Antarctica. Appl Environ Microbiol 2007; 73:4029–4039 [View Article] [PubMed]
     [Google Scholar]
  9. Galand PE, Bourrain M, De Maistre E, Catala P, Desdevises Y et al. Phylogenetic and functional diversity of Bacteria and Archaea in a unique stratified lagoon, the Clipperton atoll (N Pacific). FEMS Microbiol Ecol 2012; 79:203–217 [View Article] [PubMed]
     [Google Scholar]
  10. Nishihara H, Igarashi Y, Kodama T. Hydrogenovibrio marinus gen. nov., sp. nov., a marine obligately chemolithoautotrophic hydrogen-oxidizing bacterium. Int J Syst Bacteriol 1991; 41:130–133 [View Article]
     [Google Scholar]
  11. Watsuji T-O, Hada E, Miyazaki M, Ichimura M, Takai K. Thiomicrospira hydrogeniphila sp. nov., an aerobic, hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a seawater tank containing a block of beef tallow. Int J Syst Evol Microbiol 2016; 66:3688–3693 [View Article] [PubMed]
     [Google Scholar]
  12. Boden R, Scott KM, Rae AW, Hutt LP. Reclassification of Thiomicrospira hydrogeniphila (Watsuji et al. 2016) to Thiomicrorhabdus hydrogeniphila comb. nov., with emended description of Thiomicrorhabdus (Boden et al., 2017). Int J Syst Evol Microbiol 2017; 67:4205–4209 [View Article]
     [Google Scholar]
  13. Barco RA, Hoffman CL, Ramírez GA, Toner BM, Edwards KJ et al. In-situ incubation of iron-sulfur mineral reveals a diverse chemolithoautotrophic community and a new biogeochemical role for Thiomicrospira . Environ Microbiol 2017; 19:1322–1337 [View Article] [PubMed]
     [Google Scholar]
  14. Neely C, Bou Khalil C, Cervantes A, Diaz R, Escobar A et al. Genome sequence of Hydrogenovibrio sp. Strain SC-1, a chemolithoautotrophic sulfur and iron oxidizer. Genome Announc 2018; 6:e01581–01517 [View Article] [PubMed]
     [Google Scholar]
  15. Yoshizawa Y, Toyoda K, Arai H, Ishii M, Igarashi Y. CO2-responsive expression and gene organization of three ribulose-1,5-bisphosphate carboxylase/oxygenase enzymes and carboxysomes in Hydrogenovibrio marinus strain MH-110. J Bacteriol 2004; 186:5685–5691 [View Article] [PubMed]
     [Google Scholar]
  16. Tourova TP, Spiridonova EM, Berg IA, Kuznetsov BB, Sorokin DY. Occurrence, phylogeny and evolution of ribulose-1,5-bisphosphate carboxylase/oxygenase genes in obligately chemolithoautotrophic sulfur-oxidizing bacteria of the genera Thiomicrospira and Thioalkalimicrobium . Microbiology 2006; 152:2159–2169 [View Article] [PubMed]
     [Google Scholar]
  17. Jannasch HW, Wirsen CO, Nelson DC, Robertson LA. Thiomicrospira crunogena sp. nov., a colorless, sulfur-oxidizing bacterium from a deep-sea hydrothermal vent. Int J Syst Bacteriol 1985; 35:422–424 [View Article]
     [Google Scholar]
  18. Quasem I, Achille AN, Caddick BA, Carter TA, Daniels C et al. Peculiar citric acid cycle of hydrothermal vent chemolithoautotroph Hydrogenovibrio crunogenus, and insights into carbon metabolism by obligate autotrophs. FEMS Microbiol Lett 2017; 364: [View Article] [PubMed]
     [Google Scholar]
  19. Kuenen JG, Veldkamp H. Thiomicrospira pelophila, gen. n., sp. n., a new obligately chemolithotrophic colourless sulfur bacterium. Antonie van Leeuwenhoek 1972; 38:241–256 [View Article]
     [Google Scholar]
  20. Takai K, Hirayama H, Nakagawa T, Suzuki Y, Nealson KH et al. Thiomicrospira thermophila sp. nov., a novel microaerobic, thermotolerant, sulfur-oxidizing chemolithomixotroph isolated from a deep-sea hydrothermal fumarole in the TOTO caldera, Mariana Arc, Western Pacific. Int J Syst Evol Microbiol 2004; 54:2325–2333 [View Article] [PubMed]
     [Google Scholar]
  21. Davis M, Garey J. Microbial function and hydrochemistry within a stratified anchialine sinkhole: a window into coastal aquifer interactions. Water 2018; 10:972 [View Article]
     [Google Scholar]
  22. Dobrinski KP, Longo DL, Scott KM. A hydrothermal vent chemolithoautotroph with a carbon concentrating mechanism. J Bacteriol 2005; 187:5761–5766
     [Google Scholar]
  23. Wolfe AJ, Berg HC. Migration of bacteria in semisolid agar. Proc Natl Acad Sci USA 1989; 86:6973–6977 [View Article] [PubMed]
     [Google Scholar]
  24. Mitchell JH, Leonard JM, Delaney J, Girguis PR, Scott KM. Hydrogen does not appear to be a major electron donor for symbiosis with the deep-sea hydrothermal vent tubeworm Riftia pachyptila . Appl Environ Microbiol 2019; 86:e01522–01519 [View Article] [PubMed]
     [Google Scholar]
  25. Pirt SJ. Principles of Microbe and Cell Cultivation New York: Halsted Press; 1975
     [Google Scholar]
  26. Karagouni AD, Slater JH. Growth of the blue-green alga Anacystis nidulans during washout from light- and carbon dioxide-limited chemostats. FEMS Microbiol Lett 1978; 4:295–299 [View Article]
     [Google Scholar]
  27. Boden R, Hutt LP. Determination of kinetic parameters and metabolic modes using the chemostat. In Steffan RJ. eds Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation Handbook of Hydrocarbon and Lipid Microbiology Cham: Springer Nature; 2019 pp 363–404
     [Google Scholar]
  28. Pitcher RS, Watmough NJ. The bacterial cytochrome cbb3 oxidases. Biochim Biophys Acta 2004; 1655:388–399 [View Article] [PubMed]
     [Google Scholar]
  29. Nelson DC, Jannasch HW. Chemoautotrophic growth of a marine Beggiatoa in sulfide-gradient cultures. Arch Microbiol 1983; 136:262–269 [View Article]
     [Google Scholar]
  30. Hansen M, Perner M. Reasons for Thiomicrospira crunogena’s recalcitrance towards previous attempts to detect its hydrogen consumption ability. Environ Microbiol Rep 2016; 8:53–57 [View Article] [PubMed]
     [Google Scholar]
  31. German Collection of Microorganisms and Cell Cultures GmbH Analysis of cellular fatty acids. DSMZ; 2021 https://www.dsmz.de/services/microorganisms/biochemical-analysis/cellular-fatty-acids
  32. German Collection of Microorganisms and Cell Cultures GmbH Respiratory quinones. DSMZ; 2021 https://www.dsmz.de/services/microorganisms/biochemical-analysis/respiratory-quinones
  33. Joint Genome Institute Bacterial genomic DNA isolation using CTAB. JGI; 2012 https://jgi.doe.gov/wp-content/uploads/2014/02/JGI-Bacterial-DNA-isolation-CTAB-Protocol-2012.pdf
  34. Chen I-MA, Chu K, Palaniappan K, Pillay M, Ratner A et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res 2019; 47:D666–D677 [View Article] [PubMed]
     [Google Scholar]
  35. Søndergaard D, Pedersen CNS, Greening C. HydDB: A web tool for hydrogenase classification and analysis. Sci Rep 2016; 6:34212 [View Article] [PubMed]
     [Google Scholar]
  36. Boden R, Hutt LP, Huntemann M, Clum A, Pillay M et al. Permanent draft genome of Thermithiobacillus tepidarius DSM 3134T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia . Stand Genomic Sci 2016; 11:74 [View Article]
     [Google Scholar]
  37. Hutt LP, Huntemann M, Clum A, Pillay M, Palaniappan K et al. Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria . Stand Genomic Sci 2017; 12: [View Article]
     [Google Scholar]
  38. Frolov EN, Kublanov IV, Toshchakov SV, Lunev EA, Pimenov NV et al. Form III RubisCO-mediated transaldolase variant of the Calvin cycle in a chemolithoautotrophic bacterium. Proc Natl Acad Sci USA 2019; 116:18638–18646 [View Article] [PubMed]
     [Google Scholar]
  39. Mangiapia M. USF MCB4404L Brown T-RW, Chaput D, Haller E et al. Proteomic and mutant analysis of the CO2 concentrating mechanism of hydrothermal vent chemolithoautotroph Thiomicrospira crunogena . J Bacteriol 2017; 199:e00871–00816 [View Article] [PubMed]
     [Google Scholar]
  40. Scott KM, Leonard J, Boden R, Chaput D, Dennison C et al. Diversity in CO2 concentrating mechanisms among chemolithoautotrophs from the genera Hydrogenovibrio, Thiomicrorhabdus, and Thiomicrospira, ubiquitous in sulfidic habitats worldwide. Appl Environ Microbiol 2019; 85:e02096–02018 [View Article]
     [Google Scholar]
  41. Scott KM, Harmer TL, Gemmell BJ, Kramer AM, Sutter M et al. Ubiquity and functional uniformity in CO2 concentrating mechanisms in multiple phyla of Bacteria is suggested by a diversity and prevalence of genes encoding candidate dissolved inorganic carbon transporters. FEMS Microbiol Lett 2020; 367:13 [View Article] [PubMed]
     [Google Scholar]
  42. Smith AJ, Hoare DS. Specialist phototrophs, lithotrophs, and methylotrophs: a unity among a diversity of procaryotes?. Bacteriol Rev 1977; 41:419–448 [View Article]
     [Google Scholar]
  43. Wood AP, Aurikko JP, Kelly DP. A challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy?. FEMS Microbiol Rev 2004; 28:335–352 [View Article] [PubMed]
     [Google Scholar]
  44. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article]
     [Google Scholar]
  45. Stackebrandt E. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  46. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
     [Google Scholar]
  47. Boden R, Hutt LP, Rae AW. Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the “Proteobacteria”, and four new families within the orders Nitrosomonadales and Rhodocyclales . Int J Syst Evol Microbiol 2017; 67:1191–1205 [View Article]
     [Google Scholar]
  48. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  49. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C et al. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 2012; 158:1005–1015 [View Article] [PubMed]
     [Google Scholar]
  50. Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH et al. A genus definition for bacteria and archaea based on a standard genome relatedness index. mBio 2020; 11:e02475–02419 [View Article]
     [Google Scholar]
  51. Brinkhoff T, Muyzer G, Wirsen CO, Kuever J. Thiomicrospira chilensis sp. nov., a mesophilic obligately chemolithoautotrophic sulfuroxidizing bacterium isolated from a Thioploca mat. Int J Syst Bacteriol 1999; 49:875–879 [View Article] [PubMed]
     [Google Scholar]
  52. Brinkhoff T, Muyzer G, Wirsen CO, Kuever J. Thiomicrospira kuenenii sp. nov. and Thiomicrospira frisia sp. nov., two mesophilic obligately chemolithoautotrophic sulfur-oxidizing bacteria isolated from an intertidal mud flat. Int J Syst Bacteriol 1999; 49:385–392 [View Article]
     [Google Scholar]
  53. Brinkhoff T, Sievert SM, Kuever J, Muyzer G. Distribution and diversity of sulfur-oxidizing Thiomicrospira spp. at a shallow-water hydrothermal vent in the Aegean Sea (Milos, Greece). Appl Environ Microbiol 1999; 65:3843–3849 [View Article]
     [Google Scholar]
  54. Knittel K, Kuever J, Meyerdierks A, Meinke R, Amann R et al. Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov., psychrophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacteria isolated from marine Arctic sediments. Int J Syst Evol Microbiol 2005; 55:781–786 [View Article] [PubMed]
     [Google Scholar]
  55. Giovannelli D, Grosche A, Starovoytov V, Yakimov M, Manini E et al. Galenea microaerophila gen. nov., sp. nov., a mesophilic, microaerophilic, chemosynthetic, thiosulfate-oxidizing bacterium isolated from a shallow-water hydrothermal vent. Int J Syst Evol Microbiol 2012; 62:3060–3066 [View Article]
     [Google Scholar]
  56. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  57. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  58. Hurvich CM, Tsai CL. Regression and time series model selection in small samples. Biometrika 1989; 76:297–307 [View Article]
     [Google Scholar]
  59. Akaike H. Information theory and an extension of the maximum likelihood principle. In Parzen E, Tanabe K, Kitagawa G. eds Selected Papers of Hirotugu Akaike New York, NY: Springer New York; 1998 pp 199–213
     [Google Scholar]
  60. Brewer MJ, Butler A, Cooksley SL, Freckleton R. The relative performance of AIC, AICC and BIC in the presence of unobserved heterogeneity. Methods Ecol Evol 2016; 7:679–692 [View Article]
     [Google Scholar]
  61. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article]
     [Google Scholar]
  62. Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008; 25:1307–1320 [View Article] [PubMed]
     [Google Scholar]
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Thiomicrorhabdus heinhorstiae sp. nov. and Thiomicrorhabdus cannonii sp. nov.: novel sulphur-oxidizing chemolithoautotrophs isolated from the chemocline of Hospital Hole, an anchialine sinkhole in Spring Hill, Florida, USA
Int J Syst Evol Microbiol 72, 005233 (2022); https://doi.org/10.1099/ijsem.0.005233
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