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Abstract

A novel Gram-negative, spore forming, obligately anaerobic, thermophilic, chitin-degrading bacterium, designated UUS1-1, was isolated from compost on Ishigaki Island, Japan by enrichment culturing using chitin powder as the carbon source. The strain has unique, long, hair-like rod morphological features and exhibits strong degradation activity toward crystalline chitin under thermophilic conditions. Growth of the novel strain was observed at 45–65 °C (optimum, 55 °C) and pH 6.5–7.5 (optimum, pH 7.0). In addition to chitin, the strain utilized several other carbon sources, including -acetylglucosamine, glucose, galactose, mannose, maltose, cellobiose, fructose and sucrose. The end products of chitin degradation were acetate, lactate, H and CO. Phylogenetic tree analysis based on 16S rRNA gene sequences revealed a clear affiliation of the proposed bacterium to the phylum ; the most closely related species were LX-B and DSM6193 with similarities of 90.4 and 87.8 %, respectively. The G+C content of the genomic DNA was 52.1 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of UUS1-1 and LX-B were 65.5 and 21.0 %, respectively. The cellular fatty acid composition of the strain was C, anteiso-C, C, C 3-OH and dimethyl acetal-C. Based on phenotypic, chemotaxonomic and genotypic analysis, strain UUS1-1 represents a novel genus and species, for which the name gen. nov., sp. nov. is proposed. The type strain is UUS1-1 (=JCM 33882=DSM 111537).

Funding
This study was supported by the:
  • JPMJSA1801
    • Principle Award Recipient: AkihikoKosugi
  • JPMJER1502
    • Principle Award Recipient: AkihikoKosugi
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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2021-03-16
2022-01-19
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References

  1. Gooday GW. The ecology of chitin degradation. In Marshall KC. editor Adv Microb Ecol Boston, MA: Springer US; 1990 pp 387–430
    [Google Scholar]
  2. Hamed I, Özogul F, Regenstein JM. Industrial applications of crustacean by-products (chitin, chitosan, and chitooligosaccharides): a review. Trends Food Sci Tech 2016; 48:40–50 [View Article]
    [Google Scholar]
  3. Le B, Yang SH. Microbial chitinases: properties, current state and biotechnological applications. World J Microbiol Biotechnol 2019; 35:144 [View Article][PubMed]
    [Google Scholar]
  4. Widyasti E, Shikata A, Hashim R, Sulaiman O, Sudesh K et al. Biodegradation of fibrillated oil palm trunk fiber by a novel thermophilic, anaerobic, xylanolytic bacterium Caldicoprobacter sp. CL-2 isolated from compost. Enzyme Microb Technol 2018; 111:21–28 [View Article][PubMed]
    [Google Scholar]
  5. Shikata A, Sermsathanaswadi J, Thianheng P, Baramee S, Tachaapaikoon C et al. Characterization of an anaerobic, thermophilic, alkaliphilic, high lignocellulosic biomass-degrading bacterial community, ISHI-3, isolated from biocompost. Enzyme Microb Technol 2018; 118:66–75 [View Article]
    [Google Scholar]
  6. Hungate RE. Chapter IV a roll tube method for cultivation of strict anaerobes. Method Microbiol Academic Press; 1969 pp 117–132
    [Google Scholar]
  7. Hsu SC, Lockwood JL. Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. Appl Microbiol 1975; 29:422–426 [View Article][PubMed]
    [Google Scholar]
  8. Shikata A, Sermsathanaswadi J, Thianheng P, Baramee S, Tachaapaikoon C et al. Characterization of an anaerobic, thermophilic, alkaliphilic, high lignocellulosic biomass-degrading bacterial community, ISHI-3, isolated from biocompost. Enzyme Microb Technol 2018; 118:66–75 [View Article][PubMed]
    [Google Scholar]
  9. Heuer H, Krsek M, Baker P, Smalla K, Wellington EM. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 1997; 63:3233–3241 [View Article][PubMed]
    [Google Scholar]
  10. Dos Santos HRM, Argolo CS, Argôlo-Filho RC, Loguercio LL. A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information. BMC Microbiol 2019; 19:74 [View Article][PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol 1992; 9:678–687 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  16. Liu Y, Qiao J-T, Yuan X-Z, Guo R-B, Qiu Y-L. Hydrogenispora ethanolica gen. nov., sp. nov., an anaerobic carbohydrate-fermenting bacterium from anaerobic sludge. Int J Syst Evol Microbiol 2014; 64:1756–1762 [View Article][PubMed]
    [Google Scholar]
  17. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013; 41:D590–D596 [View Article][PubMed]
    [Google Scholar]
  18. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 1998; 180:366–376 [View Article][PubMed]
    [Google Scholar]
  19. Haouari O, Fardeau M-L, Cayol J-L, Casiot C, Elbaz-Poulichet F et al. Desulfotomaculum hydrothermale sp. nov., a thermophilic sulfate-reducing bacterium isolated from a terrestrial Tunisian hot spring. Int J Syst Evol Microbiol 2008; 58:2529–2535 [View Article][PubMed]
    [Google Scholar]
  20. Tasaki M, Kamagata Y, Nakamura K, Mikami E. Isolation and characterization of a thermophilic benzoate-degrading, sulfate-reducing bacterium, Desulfotomaculum thermobenzoicum sp. nov. Arch Microbiol 1991; 155:348–352 [View Article]
    [Google Scholar]
  21. Imachi H, Sekiguchi Y, Kamagata Y, Hanada S, Ohashi A et al. Pelotomaculum thermopropionicum gen. nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium. Int J Syst Evol Microbiol 2002; 52:1729–1735 [View Article][PubMed]
    [Google Scholar]
  22. Nepomnyashchaya YN, Slobodkina GB, Baslerov RV, Chernyh NA, Bonch-Osmolovskaya EA et al. Moorella humiferrea sp. nov., a thermophilic, anaerobic bacterium capable of growth via electron shuttling between humic acid and Fe(III). Int J Syst Evol Microbiol 2012; 62:613–617 [View Article][PubMed]
    [Google Scholar]
  23. Ungkulpasvich U, Uke A, Baramee S, Kosugi A. Draft genome sequence data of the anaerobic, thermophilic, chitinolytic bacterium strain UUS1-1 belonging to genus Hydrogenispora of the uncultured taxonomic OPB54 cluster. Data Brief 2020; 33:106528 [View Article][PubMed]
    [Google Scholar]
  24. Yoon S-H, Ha S-min, 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]
    [Google Scholar]
  25. 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]
  26. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  29. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article][PubMed]
    [Google Scholar]
  30. Markowitz VM, Mavromatis K, Ivanova NN, Chen I-MA, Chu K et al. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278 [View Article][PubMed]
    [Google Scholar]
  31. Xu T, Qi M, Liu H, Cao D, Xu C et al. Chitin degradation potential and whole-genome sequence of Streptomyces diastaticus strain CS1801. AMB Express 2020; 10:29 [View Article][PubMed]
    [Google Scholar]
  32. Schneider CA, Rasband WS, Eliceiri KW. NIH image to ImageJ: 25 years of image analysis. Nat Methods 2012; 9:671–675 [View Article][PubMed]
    [Google Scholar]
  33. Beveridge TJ. Structures of gram-negative cell walls and their derived membrane vesicles. J Bacteriol 1999; 181:4725–4733 [View Article][PubMed]
    [Google Scholar]
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