1887

Abstract

A novel strictly anaerobic chemoorganotrophic bacterium, designated Mahy22, was isolated from sulfidic bottom water of a shallow brackish meromictic lake in Japan. Cells of the strain were Gram-stain-negative, non-motile and coccoid in shape with diameters of about 600–800 nm. The temperature range for growth was 15–37 °C, with optimum growth at 30–32 °C. The pH range for growth was pH 6.2–8.9, with optimum growth at pH 7.2–7.4. The strain grew with NaCl concentrations of 5% or below (optimum, 2–3%). Growth of the strain was enhanced by the addition of thiosulfate. The major cellular fatty acids were C and anteiso-C. Respiratory quinones were not detected. The complete genome sequence of strain Mahy22 possessed a 1 885 846 bp circular chromosome and a 12 782 bp circular genetic element. The G+C content of the genome sequence was 30.1 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family , class . The closest relative of strain Mahy22 with a validly published name was J233 with a 16S rRNA gene sequence similarity of 90.5%. Based on the results of polyphasic analysis, the name gen. nov., sp. nov. is proposed to accommodate strain Mahy22, along with reclassification of some species into gen. nov., gen. nov. and gen. nov.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005138
2021-12-07
2024-05-07
Loading full text...

Full text loading...

References

  1. Razin S. The genus Mycoplasma and related genera (class Mollicutes). The Prokaryotes 2006; 4:836–904
    [Google Scholar]
  2. Brown DR, Bradbury JM, Johansson JK. Acholeplasmatales. In Bergey’s Manual of Systematics of Archaea and Bacteria 2015 pp 1–2
    [Google Scholar]
  3. Tllly JG. Genus Acholeplasma. In Bergey’s Manual of Systematics of Archaea and Bacteria vol. 1 1984 pp 775–781
    [Google Scholar]
  4. Tully JG, Razin S. Acholeplasma axanthum, sp. n.: a new sterol-nonrequiring member of the Mycoplasmatales. J Bacteriol 1970; 103:751–754 [View Article] [PubMed]
    [Google Scholar]
  5. Volokhov DV, Neverov AA, George J, Kong H, Liu SX et al. Genetic analysis of housekeeping genes of members of the genus Acholeplasma: phylogeny and complementary molecular markers to the 16S rRNA gene. Mol Phylogenet Evol 2007; 44:699–710 [View Article] [PubMed]
    [Google Scholar]
  6. Gupta RS, Son J, Oren A. A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera. Antonie van Leeuwenhoek 2019; 112:561–588 [View Article] [PubMed]
    [Google Scholar]
  7. Kubo K, Kojima H, Fukui M. Vertical distribution of major sulfate-reducing bacteria in a shallow eutrophic meromictic lake. Syst Appl Microbiol 2014; 37:510–519 [View Article] [PubMed]
    [Google Scholar]
  8. Widdel F, Bak F. Gram-negative mesophilic sulfate-reducing bacteria. In The Prokaryotes New York, NY: Springer New York; pp 3352–3378
    [Google Scholar]
  9. Muyzer G, de Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 1993; 59:695–700 [View Article] [PubMed]
    [Google Scholar]
  10. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  11. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34:1037–1039 [View Article] [PubMed]
    [Google Scholar]
  12. Noguchi H, Taniguchi T, Itoh T. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res 2008; 15:387–396 [View Article] [PubMed]
    [Google Scholar]
  13. Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 2004; 32:11–16 [View Article] [PubMed]
    [Google Scholar]
  14. Arai W, Taniguchi T, Goto S, Moriya Y, Uehara H et al. MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes. Biosci Biotechnol Biochem 2018; 82:1515–1517 [View Article] [PubMed]
    [Google Scholar]
  15. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K et al. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 2007; 8:209 [View Article] [PubMed]
    [Google Scholar]
  16. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
    [Google Scholar]
  17. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  18. Moose A. POCP calculation for two genomes. FigShare Code 2017; 10:m9
    [Google Scholar]
  19. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes [preprint]. PeerJ Preprints 2016; 4:e1900v1 [View Article]
    [Google Scholar]
  20. 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]
  21. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
    [Google Scholar]
  24. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
    [Google Scholar]
  25. Watanabe M, Kojima H, Fukui M. Labilibaculum antarcticum sp. nov., a novel facultative anaerobic, psychrotorelant bacterium isolated from marine sediment of Antarctica. Antonie van Leeuwenhoek 2019; 113:349–355 [View Article]
    [Google Scholar]
  26. Cord-Ruwisch R. A quick method for the determination of dissolved and precipitated sulfides in cultures of sulfate-reducing bacteria. J Microbiol Methods 1985; 4:33–36 [View Article]
    [Google Scholar]
  27. Imachi H, Tasumi E, Takaki Y, Hoshino T, Schubotz F et al. Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation. Sci Rep 2019; 9:1–16 [View Article]
    [Google Scholar]
  28. Imachi H, Aoi K, Tasumi E, Saito Y, Yamanaka Y et al. Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor. ISME J 2011; 5:1913–1925 [View Article] [PubMed]
    [Google Scholar]
  29. Tully JG, Whitcomb RF, Rose DL, Bove JM, Carle P et al. Acholeplasma brassicae sp. nov. and Acholeplasma palmae sp. nov., two non-sterol-requiring mollicutes from plant surfaces. Int J Syst Bacteriol 1994; 44:680–684 [View Article]
    [Google Scholar]
  30. Atobe H, Watabe J, Ogata M. Acholeplasma parvum, a new species from horses. Int J Syst Evol Microbiol 1983; 33:344–349
    [Google Scholar]
  31. Volokhov DV, Gao Y, Davidson MK, Chizhikov VE. Acholeplasma equirhinis sp. nov. isolated from respiratory tract of horse (Equus caballus) and Mycoplasma procyoni sp. nov. isolated from oral cavity of raccoon (Procyon lotor). Arch Microbiol 2020; 202:411–420 [View Article] [PubMed]
    [Google Scholar]
  32. Antunes A, Rainey FA, Wanner G, Taborda M, Pätzold J et al. A new lineage of halophilic, wall-less, contractile bacteria from a brine-filled deep of the Red Sea. J Bacteriol 2008; 190:3580–3587 [View Article] [PubMed]
    [Google Scholar]
  33. JOHANSSON K-E. Fractionation of membrane proteins from Acholeplasma laidlawii by preparative agarose-suspension electrophoresis. In Protides of the Biological Fluids Elsevier; 1974 pp 151–156
    [Google Scholar]
  34. Mayberry WR, Smith PF, Langworthy TA. Heptose-containing pentaglycosyl diglyceride among the lipids of Acholeplasma modicum. J Bacteriol 1974; 118:898–904 [View Article] [PubMed]
    [Google Scholar]
  35. Smith PF, Langworthy TA. Existence of carotenoids in Acholeplasma axanthum. J Bacteriol 1979; 137:185–188 [View Article] [PubMed]
    [Google Scholar]
  36. Aoki M, Ehara M, Saito Y, Yoshioka H, Miyazaki M et al. A long-term cultivation of an anaerobic methane-oxidizing microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor. PLoS One 2014; 9:e105356 [View Article]
    [Google Scholar]
  37. Dhillon A, Teske A, Dillon J, Stahl DA, Sogin ML. Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl Environ Microbiol 2003; 69:2765–2772 [View Article] [PubMed]
    [Google Scholar]
  38. Gleeson DF, Williamson C, Grasby SE, Pappalardo RT, Spear JR et al. Low temperature S(0) biomineralization at a supraglacial spring system in the Canadian High Arctic. Geobiology 2011; 9:360–375 [View Article] [PubMed]
    [Google Scholar]
  39. Masui N, Morono Y, Inagaki F. Microbiological assessment of circulation mud fluids during the first operation of riser drilling by the deep-earth research vessel Chikyu. Geomicrobiol J 2008; 25:274–282 [View Article]
    [Google Scholar]
  40. Duncan KE, Gieg LM, Parisi VA, Tanner RS, Tringe SG et al. Biocorrosive thermophilic microbial communities in Alaskan North Slope oil facilities. Environ Sci Technol 2009; 43:7977–7984 [View Article] [PubMed]
    [Google Scholar]
  41. Ghosh A, Bhadury P. Investigating monsoon and post-monsoon variabilities of bacterioplankton communities in a mangrove ecosystem. Environ Sci Pollut Res 2017; 25:5722–5739 [View Article]
    [Google Scholar]
  42. Qiao J-T, Qiu Y-L, Yuan X-Z, Shi X-S, Xu X-H et al. Molecular characterization of bacterial and archaeal communities in a full-scale anaerobic reactor treating corn straw. Bioresour Technol 2013; 143:512–518 [View Article] [PubMed]
    [Google Scholar]
  43. Skennerton CT, Haroon MF, Briegel A, Shi J, Jensen GJ et al. Phylogenomic analysis of Candidatus “Izimaplasma” species: free-living representatives from a Tenericutes clade found in methane seeps. ISME J 2016; 10:2679–2692 [View Article] [PubMed]
    [Google Scholar]
  44. Wang Y, Huang J-. M, Zhou Y-. L, Almeida A, Finn RD et al. Phylogenomics of expanding uncultured environmental tenericutes provides insights into their pathogenicity and evolutionary relationship with bacilli. BMC Genomics 2020; 21:408
    [Google Scholar]
  45. Rose DL, Tully JG, Del Giudice RA. Acholeplasma morum, a new non-sterol-requiring species. Int J Syst Evol Microbiol 1980; 30:647–654
    [Google Scholar]
  46. Angulo AF, Reijgers R, Brugman J, Kroesen I, Hekkens FE et al. Acholeplasma vituli sp. nov., from bovine serum and cell cultures. Int J Syst Evol Microbiol 2000; 50:1125–1131 [View Article] [PubMed]
    [Google Scholar]
  47. Sneath PHA, McGowan V, Skerman VBD. Approved lists of bacterial names. Int J Syst Evol Microbiol 1980; 30:225–420 [View Article]
    [Google Scholar]
  48. Hill AC. Acholeplasma cavigenitalium sp. nov., isolated from the vagina of guinea pigs. Int J Syst Evol Microbiol 1992; 42:589–592
    [Google Scholar]
  49. Leach RH. Further studies on classification of bovine strains of Mycoplasmatales, with proposals for new species, Acholeplasma modicum and Mycoplasma alkalescens. Microbiology 1973; 75:135–153
    [Google Scholar]
  50. Kirchhoff H. Acholeplasma equifetale and Acholeplasma hippikon, two new species from aborted horse fetuses. Int J Syst Evol Microbiol 1978; 28:76–81
    [Google Scholar]
  51. Edward DGF, Freundt EA. Amended nomenclature for strains related to Mycoplasma laidlawii. Microbiology 1970; 62:1–2
    [Google Scholar]
  52. al-Aubaidi JM, Dardiri AH, Muscoplatt CC, McCauley EH. Identification and characterization of Acholeplasma oculusi spec. nov. from the eyes of goats with keratoconjunctivitis. Cornell Vet 1973; 63:117–129 [PubMed]
    [Google Scholar]
  53. Knight TF. Reclassification of Mesoplasma pleciae as Acholeplasma pleciae comb. nov. on the basis of 16S rRNA and gyrB gene sequence data. Int J Syst Evol Microbiol 2004; 54:1951–1952 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005138
Loading
/content/journal/ijsem/10.1099/ijsem.0.005138
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error