1887

Abstract

A Gram-stain-negative, rod-shaped, microcystin-degrading bacterium, designated as CPCC 100929, was isolated from a fresh water reservoir in Sichuan Province, PR China. This isolate grew well at 4–37 °C and pH 6.0–8.0, with optimal growth at 28–32 °C and pH 7.0, respectively. The major cellular fatty acids were C ω7/C ω6, C, C ω7 11-methyl and C cyclo ω8. The predominant respiratory quinone was Q-10. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylcholine were detected in the polar lipids extraction. The 16S rRNA gene sequence of strain CPCC 100929 was closely related to those of members of the genus , with the highest similarity of 98.6 % to DSM 287 and 97.4–98.4 % with other identified members. In the phylogenetic trees based on 16S rRNA gene sequences and the core-genes analysis, strain CPCC 100929 was included within the clade of the genus . The values of average nucleotide identity (81.4–86.7 %) and digital DNA–DNA hybridization (25.4–44.6 %) between strain CPCC 100929 and other species were all below the thresholds for bacterial species delineation, respectively. The genomic DNA G+C content of strain CPCC 100929 was 63.6 %. The genomic sequence analysis indicated that this species contained genes encoding peroxidase, carbapenemase and the key enzyme for microcystin bio degradation, as well as rich carbohydrate-active enzyme coding genes, which might endow the micro-organism with properties to adapt to diverse environments. Based on its phenotypic and genetic properties, we propose that strain CPCC 100929 (=T1A350=KCTC 72957) is the type strain of a novel species with the name sp. nov.

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 32170021)
    • Principle Award Recipient: ZhangYuqin
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2022-11-10
2024-10-13
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References

  1. Zegura B, Straser A, Filipič M. Genotoxicity and potential carcinogenicity of cyanobacterial toxins – a review. Mutat Res 2011; 727:16–41 [View Article]
    [Google Scholar]
  2. An DS, Im WT, Yang HC, Lee ST. Shinella granuli gen. nov., sp. nov., and proposal of the reclassification of Zoogloea ramigera ATCC 19623 as Shinella zoogloeoides sp. nov. Int J Syst Evol Microbiol 2006; 56:443–448
    [Google Scholar]
  3. Matsui T, Shinzato N, Tamaki H, Muramatsu M, Hanada S. Shinella yambaruensis sp. nov., a 3-methyl-sulfolane-assimilating bacterium isolated from soil. Int J Syst Evol Microbiol 2009; 59:536–539 [View Article] [PubMed]
    [Google Scholar]
  4. Subhash Y, Lee SS. Shinella curvata sp. nov., isolated from hydrocarbon-contaminated desert sands. Int J Syst Evol Microbiol 2016; 66:3929–3934 [View Article] [PubMed]
    [Google Scholar]
  5. Lee M, Woo SG, Ten LN. Shinella daejeonensis sp. nov., a nitrate-reducing bacterium isolated from sludge of a leachate treatment plant. Int J Syst Evol Microbiol 2011; 61:2123–2128 [View Article] [PubMed]
    [Google Scholar]
  6. Vaz-Moreira I, Faria C, Lopes AR, Svensson LA, Moore ER et al. Shinella fusca sp. nov., isolated from domestic waste compost. Int J Syst Evol Microbiol 2010; 60:144–148
    [Google Scholar]
  7. Lin DX, Wang ET, Tang H, Han TX, He YR et al. Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea. Int J Syst Evol Microbiol 2008; 58:1409–1413
    [Google Scholar]
  8. Mu Y, Jia WB, Ke Z, Zhuang W, Wang HM et al. Shinella pollutisoli sp. nov., isolated from tetrabromobisphenol A-contaminated soil. Int J Syst Evol Microbiol 2018; 68:2602–2606
    [Google Scholar]
  9. Wu H, Shen J, Wu R, Sun X, Li J et al. Biodegradation mechanism of 1H-1,2,4-triazole by a newly isolated strain Shinella sp. NJUST26. Sci Rep 2016; 6:29675
    [Google Scholar]
  10. Qiu J, Li N, Lu Z, Yang Y, Ma Y et al. Conversion of nornicotine to 6-hydroxy-nornicotine and 6-hydroxy-myosmine by Shinella sp. strain HZN7. Appl Microbiol Biotechnol 2016; 100:10019–10029
    [Google Scholar]
  11. Jiang HJ, Ma Y, Qiu GJ, Wu FL, Chen SL. Biodegradation of nicotine by a novel strain Shinella sp. HZN1 isolated from activated sludge. J Environ Sci Health B 2011; 46:703–708 [View Article]
    [Google Scholar]
  12. Jain A, Jain R, Jain S. Motility testing – hanging drop method and stab. Basic Tech Biochem Microbiol Mol Biol 2020:121–122
    [Google Scholar]
  13. Magee CM, Rodeheaver G, Edgerton MT, Edlich RF. A more reliable gram staining technic for diagnosis of surgical infections. Am J Surg 1975; 130:341–346 [View Article] [PubMed]
    [Google Scholar]
  14. Yuan L-J, Zhang Y-Q, Guan Y, Wei Y-Z, Li Q-P et al. Saccharopolyspora antimicrobica sp. nov., an actinomycete from soil. Int J Syst Evol Microbiol 2008; 58:1180–1185 [View Article] [PubMed]
    [Google Scholar]
  15. Manage PM, Edwards C, Singh BK, Lawton LA. Isolation and identification of novel microcystin-degrading bacteria. Appl Environ Microbiol 2009; 75:6924–6928 [View Article] [PubMed]
    [Google Scholar]
  16. 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]
  17. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
    [Google Scholar]
  18. Kroppenstedt R. Fatty acid and menaquinone analysis of actinomycetes and related organisms. Soc Appl Bacteriol Tech Ser 1985; 20:173–199
    [Google Scholar]
  19. Li W-J, Xu P, Schumann P, Zhang Y-Q, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article] [PubMed]
    [Google Scholar]
  20. 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]
  21. 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]
  22. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  23. 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] [PubMed]
    [Google Scholar]
  24. Kimura M. The Neutral Theory of Molecular Evolution Cambridge University Press; 1983 [View Article]
    [Google Scholar]
  25. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Systematic Biology 1969; 18:1–32 [View Article]
    [Google Scholar]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  28. Yoon SH, Ha SM, 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]
  29. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  30. Zhang D-F, Cui X-W, Zhao Z, Zhang A-H, Huang J-K et al. Sphingomonas hominis sp. nov., isolated from hair of a 21-year-old girl. Antonie van Leeuwenhoek 2020; 113:1523–1530 [View Article] [PubMed]
    [Google Scholar]
  31. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  32. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article] [PubMed]
    [Google Scholar]
  33. Yang S, Song S, Yan Q, Fu X, Jiang Z et al. Biochemical characterization of the first fungal glycoside hydrolyase family 3 β-N-acetylglucosaminidase from Rhizomucor miehei. J Agric Food Chem 2014; 62:5181–5190 [View Article] [PubMed]
    [Google Scholar]
  34. Zhou J, Song Z, Zhang R, Chen C, Wu Q et al. A Shinella β-N-acetylglucosaminidase of glycoside hydrolase family 20 displays novel biochemical and molecular characteristics. Extremophiles 2017; 21:699–709 [View Article] [PubMed]
    [Google Scholar]
  35. Schauer J, Gatermann SG, Hoffmann D, Hupfeld L, Pfennigwerth N. GPC-1, a novel class A carbapenemase detected in a clinical Pseudomonas aeruginosa isolate. J Antimicrob Chemother 2020; 75:911–916 [View Article]
    [Google Scholar]
  36. Li J, Li R, Li J. Current research scenario for microcystins biodegradation – a review on fundamental knowledge, application prospects and challenges. Sci Total Environ 2017; 595:615–632 [View Article]
    [Google Scholar]
  37. Ho L, Sawade E, Newcombe G. Biological treatment options for cyanobacteria metabolite removal–a review. Water Res 2012; 46:1536–1548 [View Article]
    [Google Scholar]
  38. Bourne DG, Riddles P, Jones GJ, Smith W, Blakeley RL. Characterisation of a gene cluster involved in bacterial degradation of the cyanobacterial toxin microcystin LR. Environ Toxicol 2001; 16:523–534 [View Article] [PubMed]
    [Google Scholar]
  39. Shimizu K, Maseda H, Okano K, Kurashima T, Kawauchi Y et al. Enzymatic pathway for biodegrading microcystin LR in Sphingopyxis sp. C-1. J Biosci Bioeng 2012; 114:630–634 [View Article] [PubMed]
    [Google Scholar]
  40. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
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