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Caenimonas sedimenti sp. nov., Isolated from Sediment of the Wastewater Outlet of an Agricultural Chemical Plant

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Abstract

A novel bacterial strain, designated HX-9-20T, was isolated from the sediment collected from the wastewater outlet of an agricultural chemical plant in Maanshan city, Anhui province, PR China. Cells of strain HX-9-20T were Gram-staining-negative, rod-shaped, translucent, non-motile, and strictly aerobic. Growth was observed between 15 and 35 °C (optimum 30 °C), at pH 6.0–8.0 (optimum pH 7.0), and in the presence of 0–0.4% (w/v) NaCl (optimum 0.2%). The predominant cellular fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The major quinone was ubiquinone Q-8. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and an aminophospholipid. Strain HX-9-20T contains 2-hydroxyputrescine and putrescine as the major polyamine. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HX-9-20T was affiliated with the genus Caenimonas, exhibiting the highest sequence similarities with Caenimonas koreensis EMB320T (97.3% similarity) and Ramlibacter humi 18×22-1T (97.0%), and less than 97.0% similarity with other type strains. The average nucleotide identity (ANI) and digital DNA–DNA hybridization values (dDDH) between HX-9-20T and C. koreensis EMB320T were 76.9% and 23.5% respectively. The ANI and dDDH between HX-9-20T and R. humi 18×22-1T were 80.3% and 23.6%, respectively. The G + C content of the genomic DNA was 67.5 mol%. On the basis of the polyphasic taxonomic data, strain HX-9-20T represents a novel species of the genus Caenimonas, for which the name Caenimonas sedimenti sp. nov. is proposed. The type strain is HX-9-20T (=KCTC 72473T=CCTCC AB 2019266T).

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References

  1. Willems W, Deley A, Gillis J (1991) Comamonadaceae, a new family encompassing the acidovorans. Int J Syst Bacteriol 41:445–450

    Article  Google Scholar 

  2. Ryu SH, Lee DS, Park M (2008) Caenimonas koreensis gen. nov., sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 58:1064–1068

    Article  CAS  PubMed  Google Scholar 

  3. Kim SJ, Weon HY, Kim YS (2012) Caenimonas terrae sp. nov., isolated from a soil sample in Korea, and emended description of the genus Caenimonas. J Microbiol 50:864–868

    Article  PubMed  Google Scholar 

  4. Parte AC (2014) LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:613–616

    Article  Google Scholar 

  5. Frank JA, Reich CI, Sharma S (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461–2470

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Kim OS, Cho YJ, Lee K (2012) Introducing EzTaxon-e: a prokaryotic 16s rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    Article  CAS  PubMed  Google Scholar 

  7. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  8. Felsenstein J (1981) Evolutionary trees from DNA sequences : a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

  9. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  11. Felsensten J (1985) Confidence limits on phylogenies : an approach using the bootstrap. Evolution 39(4):783–791

    Article  Google Scholar 

  12. Powers EM (1995) Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61:3756–3758

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Bernadet J, Nakagawa Y (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52(3):1049–1070

    Google Scholar 

  14. Zhang J, Chen SA, Zheng JW (2012) Catellibacterium nanjingense sp. nov., a propanil-degrading bacterium isolated from activated sludge, and emended description of the genus Catellibacterium. Int J Syst Evol Microbiol 62:495–499

    Article  CAS  PubMed  Google Scholar 

  15. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Methods for general and molecular bacteriology, pp 607–654

  16. Hiroyuki O, Tsutomu H (1983) Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium. Antonie Van Leeuwenhoek 49:429–446

    Google Scholar 

  17. Sasser M (2006) Bacterial identification by gas chromatographic analysis of fatty acid methyl esters. Microbial ID, Newark, NY

    Google Scholar 

  18. Minnikin DE, O'Donnell AG (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  19. Collins M, Pirouz T, Goodfellow M (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    Article  CAS  PubMed  Google Scholar 

  20. Hiraishi A, Ueda Y, Ishihara J (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457

    Article  CAS  Google Scholar 

  21. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

  22. Busse J, Auling G (1988) Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11:1–8

    Article  CAS  Google Scholar 

  23. Yoon SH, Ha SM, Lim J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek. Int J Gen Mol Microbiol 110:1281–1286

    CAS  Google Scholar 

  24. Chun J, Oren A, Ventosa A (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

    Article  CAS  PubMed  Google Scholar 

  25. Aziz RK, Bartels D, Best AA (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75

    Article  PubMed  PubMed Central  Google Scholar 

  26. Whitman W, Coleman D, Wiebe W (2009) Shifting the genomic gold standard for the prokaryotic species definition. PNAS 95:6578–6583

    Article  Google Scholar 

  27. Meier-Kolthoff JP, Auch AF, Klenk HP (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60

    Article  PubMed  PubMed Central  Google Scholar 

  28. Zhang XJ, Feng GD, Yao Q (2019) Ramlibacter humi sp. nov., isolated from tropical forest soil. Int J Syst Evol Microbiol 69:3460–3464

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Key R&D Program of China (2016YFD0801102), the National Natural Science Foundation of China (Nos. 31770117 and 31970096).

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Authors and Affiliations

  1. Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

    Jianyi Xu, Mengyao Sheng, Zhou Yang, Jiguo Qiu & Jian He

  2. The College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

    Jun Zhang

  3. Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637099, Sichuan, China

    Lei Zhang

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  1. Jianyi Xu
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  2. Mengyao Sheng
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  5. Jun Zhang
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Contributions

JH and JYX carried out the concepts. JYX, MYS, and ZY participated in the research and analyzed the data. LZ and JGQ provided assistances for literature search and data acquisition. JYX drafted the manuscript. JH and JZ performed manuscript review. All authors read and approved the final manuscript.

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Correspondence to Jun Zhang or Jian He.

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The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences and the whole genome of strains HX-9-20T are MN317366 and VOBQ00000000, respectively.

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Xu, J., Sheng, M., Yang, Z. et al. Caenimonas sedimenti sp. nov., Isolated from Sediment of the Wastewater Outlet of an Agricultural Chemical Plant. Curr Microbiol 77, 3767–3772 (2020). https://doi.org/10.1007/s00284-020-02145-6

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  • DOI: https://doi.org/10.1007/s00284-020-02145-6

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