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Arthrobacter sedimenti sp. nov., isolated from river sediment in Yuantouzhu park, China

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Abstract

A Gram-stain positive, motile, aerobic and rod-shaped strain (MIC A30T) was isolated from river sediment in Yuantouzhu park, Wuxi City, China. Growth occurred at 20–40 °C, at pH 6.0–9.0 and at 0–5.0% NaCl. Strain MIC A30T was moderately related to Arthrobacter liuii CGMCC 1.12778T (97.9%), Arthrobacter pokkaliiT (97.9%) and Arthrobacter globiformis NBRC 12137T (96.7%) by 16S rRNA analysis. The DNA–DNA relatedness values between strain MIC A30T and these reference strains were below 30%. The DNA G+C content was 63.1 mol%. Average nucleotide identity (ANI) and genome-to-genome distance (GGD) values between strain MIC A30T and A. liuii CGMCC 1.12778T were 60.34% and 29.39%, respectively. Quinone was identified as MK-9(H2). Major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Major fatty acids were iso-C15:0, anteiso-C15:0 and anteiso-C17:0. Whole-cell sugars were galactose, mannose and rhamnose. The cell wall peptidoglycan contained A4α peptidoglycan type with lysine as the diagnostic diamino acid. Based on several taxonomic results, strain MIC A30T is identified as a novel species in genus Arthrobacter, whose name is proposed as Arthrobacter sedimenti sp. nov. The type strain is MIC A30T (= KACC 19599T = CGMCC 1.13474T).

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References

  • Buck JD (1982) Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993

    CAS  PubMed  PubMed Central  Google Scholar 

  • Busse HJ (2016) Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus. Int J Syst Evol Microbiol 66:9–37

    Article  CAS  PubMed  Google Scholar 

  • Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 48:459–470

    CAS  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Conn HJ, Dimmick I (1947) Soil bacteria similar in morphology to mycobacterium and corynebacterium. J Bacteriol 54:291–303

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Hasegawa T, Takizawa M, Tanida S (1983) A rapid analysis for chemical grouping of aerobic Actinomycetes. J Gen Appl Microbiol 29:319–322

    CAS  Google Scholar 

  • Hu HY, Lim BR, Goto N, Fujie K (2001) Analytical precision and repeatability of respiratory quinones for quantitative study of microbial community structure in environmental samples. J Microbiol Methods 47:17–24

    CAS  PubMed  Google Scholar 

  • Kluge AG, Farris JS (1969) Quantitative phyletics and the evolution of anurans. Syst Biol 18:1–32

    Google Scholar 

  • Koch C, Schumann P, Stackebrandt E (1995) Reclassification of Micrococcus agilis (Ali-Cohen 1889) to the genus Arthrobacter as Arthrobacter agilis comb. nov. and emendation of the genus Arthrobacter. Int J Syst Bacteriol 45:837–839

    CAS  PubMed  Google Scholar 

  • Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703

    CAS  PubMed  Google Scholar 

  • Krishnan R, Menon RR, Tanaka N, Busse HJ, Krishnamurthi S, Rameshkumar N (2016) Arthrobacter pokkalii sp nov, a novel plant associated Actinobacterium with plant beneficial properties, isolated from Saline Tolerant Pokkali Rice, Kerala, India. PloS one 11:e0150322

    PubMed  Google Scholar 

  • Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367

    CAS  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 70 for bigger datasets. Mol Biol Evol 33:1870–1874

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ludwig W, Euzéby JP, Whitman WB (2012) Taxonomic outline of the phylum Actinobacteria. Bergey’s Manual of Systematic Bacteriology. Springer, New York, pp 29–31

    Google Scholar 

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

    Google Scholar 

  • 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

    CAS  Google Scholar 

  • Minnikin DE (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    CAS  Google Scholar 

  • 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 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Inc, Newark

    Google Scholar 

  • Schleifer KH, Kandler O (1973) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 37:258

    Google Scholar 

  • Simpson J, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I (2009) a parallel assembler for short read sequence. Data Genome Res 19:1117–1123

    CAS  PubMed  Google Scholar 

  • Skerman VBD (1960) A guide to the identification of the genera of bacteria. Acad Med 35:92

    Google Scholar 

  • Stabili L, Gravili C, Tredici SM, Piraino S, Talà A, Boero F, Alifano P (2008) Epibiotic Vibrio luminous bacteria isolated from some Hydrozoa and Bryozoa species. Microb Ecol 56:625–636

    CAS  PubMed  Google Scholar 

  • Stackebrandt E, Fowler VJ, Fiedler F, Seiler H (1983) Taxonomic studies on Arthrobacter nicotianae and related taxa: description of Arthrobacter uratoxydans sp. nov. and Arthrobacter sulfureus sp. nov. and reclassification of Brevibacterium protophormiae as Arthrobacter protophormiae comb. nov. Syst Appl Microbiol 4:470–486

    CAS  PubMed  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Google Scholar 

  • Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yan ZF, Trinh H, Moya G, Lin P, Li CT, Kook MC, Yi TH (2015) Lysobacter rhizophilus sp. nov., isolated from rhizosphere soil of mugunghwa, the nationalflower of South Korea. Int J Syst Evol Microbiol 66:4754–4759

    Google Scholar 

  • Yan ZF, Lin P, Chu X, Kook MC, Li CT, Yi TH (2016) Aeromicrobium halotolerans sp. Nov., isolated from desert soil sample. Arch Microbiol 198:423–427

    CAS  PubMed  Google Scholar 

  • Yan ZF, Lin P, Li CT, Kook M, Yi TH (2018) Actinotalea solisilvae sp. nov., isolated from forest soil and emended description of the genus Actinotalea. Int J Syst Evol Microbiol 68:788–794

    CAS  PubMed  Google Scholar 

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yu XY, Zhang L, Ren B, Yang N, Liu M, Liu XT, Zhang LX, Ding LX (2015) Arthrobacter liuii sp. nov., resuscitated from Xinjiang desert soil. Int J Syst Evol Microbiol 65:896–901

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by Fundamental Research Funds for the Central Universities (JUSRP11961).

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Authors and Affiliations

  1. School of Pharmaceutical Sciences, Jiangnan University, 1800 Lihu Ave, Wuxi, 21422, China

    Pei Lin

  2. State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Ave, Wuxi, 21422, China

    Zheng-Fei Yan

  3. Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China

    Chang-Tian Li

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  1. Pei Lin
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  2. Zheng-Fei Yan
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  3. Chang-Tian Li
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Contributions

PL was the main author and led conception, design, data analysis and drafting. ZFY contributed to the design and drafting of this manuscript. CTL contributed to data acquisition and analysis, drafting and critical review. All authors gave final approval of the manuscript and agreement to accountability.

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Correspondence to Zheng-Fei Yan or Chang-Tian Li.

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Communicated by Erko Stackebrandt.

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Lin, P., Yan, ZF. & Li, CT. Arthrobacter sedimenti sp. nov., isolated from river sediment in Yuantouzhu park, China. Arch Microbiol 202, 2551–2556 (2020). https://doi.org/10.1007/s00203-020-01968-y

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  • DOI: https://doi.org/10.1007/s00203-020-01968-y

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