sp. nov., a N-fixing bacterium isolated from forest soil and emendation of the genus and the species and Free

Abstract

A motile, Gram-stain-negative, rod-shaped bacterium, designated G-4-1-14, was obtained from forest soil sampled at Gwanggyo mountain, Gyeonggi-do, Republic of Korea. Cells were colourless, aerobic, grew optimally at 28–35 °C and hydrolysed DNA and casein. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain G-4-1-14 formed a lineage within the genus . The closest members were ATCC 70068 (98.6 % sequence similarity), EMB43 (98.2 %), A-7 (97.7 %), IAM 12136 (96.9 %) and Buc (96.2 %). The major respiratory quinone was ubiquinone-8 and the principal polar lipids were phosphatidylethanolamine, phosphatidyl--methylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The predominant cellular fatty acids were summed feature 3 (iso-C 2-OH/C 7) and C. The DNA G+C content was 65.9 mol%. The average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain G-4-1-14 and other type strains were ≤81.6 and ≤24.9 %, respectively, which are below the species demarcation thresholds. Based on the results of phenotypic, phylogenetic and genomic analyses, strain G-4-1-14 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is G-4-1-14 (=KACC 21618=NBRC 114358). In addition, we propose emendation of the genus and the species and .

Funding
This study was supported by the:
  • National Research Foundation (KR) (Award 2019R1F1A1058501)
    • Principle Award Recipient: Jaisoo Kim
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004416
2020-08-25
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/10/5312.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004416&mimeType=html&fmt=ahah

References

  1. Itzigsohn H. Entwicklungsvorgänge von Zoogloea, Oscillaria, Synedra, Staurastrum, Spirotaenia und chroolepus. Sitzungs-Berichte der Gesellschaft naturforschender Freunde zu Berlin, 19 November 1867 Berlin: Akademische Buchdruckerei in der Nicolai’schen Buchhandlung; 1868
    [Google Scholar]
  2. Shin YK, Hiraishi A, Sugiyama J. Molecular systematics of the genus Zoogloea and emendation of the genus. Int J Syst Bacteriol 1993; 43:826–831 [View Article][PubMed]
    [Google Scholar]
  3. Dugan PR, Stoner DL, Pickrum HM. The genus Zoogloea . In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer K-H. (editors) The Prokaryotes New York: Springer; 1992 pp 3952–3964
    [Google Scholar]
  4. Mohn WW, Wilson AE, Bicho P, Moore ER. Physiological and phylogenetic diversity of bacteria growing on resin acids. Syst Appl Microbiol 1999; 22:68–78 [View Article][PubMed]
    [Google Scholar]
  5. Shao Y, Chung BS, Lee SS, Park W, Lee S-S et al. Zoogloea caeni sp. nov., a floc-forming bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2009; 59:526–530 [View Article][PubMed]
    [Google Scholar]
  6. Xie C-H, Yokota A. Zoogloea oryzae sp. nov., a nitrogen-fixing bacterium isolated from rice paddy soil, and reclassification of the strain ATCC 19623 as Crabtreella saccharophila gen. nov., sp. nov. Int J Syst Evol Microbiol 2006; 56:619–624 [View Article][PubMed]
    [Google Scholar]
  7. Farkas M, Táncsics A, Kriszt B, Benedek T, Tóth EM et al. Zoogloea oleivorans sp. nov., a floc-forming, petroleum hydrocarbon-degrading bacterium isolated from biofilm. Int J Syst Evol Microbiol 2015; 65:274–279 [View Article][PubMed]
    [Google Scholar]
  8. Dahal RH, Kim J. Fluviicola kyonggii sp. nov., a bacterium isolated from forest soil and emended description of the genus Fluviicola . Int J Syst Evol Microbiol 2018; 68:1885–1889 [View Article][PubMed]
    [Google Scholar]
  9. Dahal RH, Chaudhary DK, Kim J. Pinisolibacter ravus gen. nov., sp. nov., isolated from pine forest soil and allocation of the genera Ancalomicrobium and Pinisolibacter to the family Ancalomicrobiaceae fam. nov., and emendation of the genus Ancalomicrobium Staley 1968. Int J Syst Evol Microbiol 2018; 68:1955–1962 [View Article][PubMed]
    [Google Scholar]
  10. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article][PubMed]
    [Google Scholar]
  11. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  12. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed]
    [Google Scholar]
  13. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  14. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  15. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000; 7:203–214 [View Article][PubMed]
    [Google Scholar]
  16. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article][PubMed]
    [Google Scholar]
  17. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
    [Google Scholar]
  18. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
    [Google Scholar]
  19. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I, SI N, min HS et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:281–285 [View Article][PubMed]
    [Google Scholar]
  20. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
    [Google Scholar]
  23. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article][PubMed]
    [Google Scholar]
  24. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article][PubMed]
    [Google Scholar]
  25. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  26. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  27. Doetsch RN. Determinative methods of light microscopy. In Gerdhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA. (editors) Manual of Methods for General Bacteriology Washington, DC, USA: American Society for Microbiology; 1981 pp 21–33
    [Google Scholar]
  28. Breznak JA, Costilow RN et al. Physicochemical factors in growth. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Bacteriology Washinton, DC, USA: American Society of Microbiology; 2007 pp 309–329
    [Google Scholar]
  29. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC USA: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  30. Dahal RH, Kim J. Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov., two novel members of the family Cytophagaceae isolated from forest soil. Arch Microbiol 2018; 200:1067–1074 [View Article][PubMed]
    [Google Scholar]
  31. Mormak DA, Casida LE. Study of Bacillus subtilis endospores in soil by use of a modified endospore stain. Appl Environ Microbiol 1985; 49:1356–1360 [View Article][PubMed]
    [Google Scholar]
  32. Chaudhary DK, Kim J. Noviherbaspirillum agri sp. nov., isolated from reclaimed grassland soil, and reclassification of Herbaspirillum massiliense (Lagier et al., 2014) as Noviherbaspirillum massiliense comb. nov. Int J Syst Evol Microbiol 2017; 67:1508–1515 [View Article][PubMed]
    [Google Scholar]
  33. Sasser M. Bacterial Identification by Gas Chromatographic Analysis of Fatty Acid Methyl Esters (GC-FAME), MIDI Tech Note 101 Newark. MIDI Inc; 1990
    [Google Scholar]
  34. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  35. Komagata K, Suzuki K. 4 lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
    [Google Scholar]
  36. Unz RF. Genus IV. Zoogloea Itzigsohn 1868, 30AL . In Krieg NR, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology Baltimore: Williams & Wilkins; 1984 pp 214–219
    [Google Scholar]
  37. Montero-Calasanz MDC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium . Int J Syst Evol Microbiol 2013; 63:4386–4395 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004416
Loading
/content/journal/ijsem/10.1099/ijsem.0.004416
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed