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Abstract

A novel, Gram-stain-positive, aerobic, non-spore-forming, non-motile and irregular rod-shaped bacterium designated Q22 was isolated from the rhizosphere soil of mangrove plant, collected in Zhangzhou, Fujian province, China. Strain Q22 was able to grow at 10–40 °C (optimum 30 °C), pH 5.5–9.0 (optimum 7.0–8.0) and with 0–5.0% (w/v) NaCl (optimum 1.0 %). The genomic DNA G+C content was 71.9%. The average nucleotide identity, and DNA–DNA hybridization values between strain Q22 and the reference strains were 79.7–88.9% and 22.6–37.4%, respectively. The predominant isoprenoid quinone was MK-12 and the major fatty acids were o-C, -C and -C. The major polar lipids of strain Q22 were diphosphatidylglycerol, phosphatidylglycerol, one glycolipid and three unidentified lipids. The strain Q22 contained 2,4-diaminobutyric acid, alanine acid, glutamic acid and glycine in the peptidoglycans. The phylogenetic analysis and genotypic features, along with the phenotypic and chemotaxonomic characteristics, indicate that strain Q22 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Q22 (=MCCC 1K03340= KCTC 39961).

Funding
This study was supported by the:
  • National Key R&D Program Foundation of China (Award 2018YFD0600201-02)
    • Principle Award Recipient: Liqin Zhang
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2020-10-12
2021-08-02
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References

  1. Gledhill WE, Casida LE. Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to actinomyces and Nocardia. Appl Microbiol 1969; 18:340–349 [View Article][PubMed]
    [Google Scholar]
  2. Zgurskaya HI, Evtushenko LI, Akimov VN, Voyevoda HV, Dobrovolskaya TG et al. Emended description of the genus Agromyces and description of Agromyces cerinus subsp. cerinus sp. nov., subsp. nov., Agromyces cerinus subsp. nitratus sp. nov., subsp. nov., Agromyces fucosus subsp. fucosus sp. nov., subsp. nov., and Agromyces fucosus subsp. hippuratus sp. nov., subsp. nov. Int J Syst Bacteriol 1992; 42:635–641 [View Article]
    [Google Scholar]
  3. Takeuchi M, Hatano K. Agromyces luteolus sp. nov., Agromyces rhizospherae sp. nov. and Agromyces bracchium sp. nov., from the mangrove rhizosphere. Int J Syst Evol Microbiol 2001; 51:1529–1537 [View Article][PubMed]
    [Google Scholar]
  4. Jurado V, Groth I, Gonzalez JM, Laiz L, Saiz-Jimenez C et al. Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov. Int J Syst Evol Microbiol 2005; 55:153–157 [View Article][PubMed]
    [Google Scholar]
  5. Yoon JH, Schumann P, Kang SJ, Park S, Oh TK et al. Agromyces terreus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2008; 58:1308–1312 [View Article][PubMed]
    [Google Scholar]
  6. Zhang D-C, Schumann P, Liu H-C, Xin Y-H, Zhou Y-G et al. Agromyces bauzanensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2010; 60:2341–2345 [View Article][PubMed]
    [Google Scholar]
  7. Thawai C, Tanasupawat S, Suwanborirux K, Kudo T. Agromyces tropicus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61:605–609 [View Article][PubMed]
    [Google Scholar]
  8. Lee M, Ten LN, Woo SG, Park J. Agromyces soli sp. nov., isolated from farm soil. Int J Syst Evol Microbiol 2011; 61:1286–1292 [View Article][PubMed]
    [Google Scholar]
  9. Chen J, Chen H-M, Zhang Y-Q, Wei Y-Z, Li Q-P et al. Agromyces flavus sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 2011; 61:1705–1709 [View Article][PubMed]
    [Google Scholar]
  10. Hamada M, Shibata C, Ishida Y, Tamura T, Yamamura H et al. Agromyces iriomotensis sp. nov. and Agromyces subtropicus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:833–838 [View Article][PubMed]
    [Google Scholar]
  11. Huang JR, Ming H, Li S, Meng XL, Zhang JX et al. Agromyces insulae sp. nov., an actinobacterium isolated from a soil sample. Int J Syst Evol Microbiol 2016; 66:2002–2007 [View Article][PubMed]
    [Google Scholar]
  12. Corretto E, Antonielli L, Sessitsch A, Compant S, Gorfer M et al. Agromyces aureus sp. nov., isolated from the rhizosphere of Salix caprea L. grown in a heavy-metal-contaminated soil. Int J Syst Evol Microbiol 2016; 66:3749–3754 [View Article][PubMed]
    [Google Scholar]
  13. Embley TM. The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett Appl Microbiol 1991; 13:171–174 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. 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]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  18. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  19. Kim M, Oh H-S, Park S-C, 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]
  20. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM et al. ABySS: a parallel assembler for short read sequence data. Genome Res 2009; 19:1117–1123 [View Article][PubMed]
    [Google Scholar]
  21. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article][PubMed]
    [Google Scholar]
  22. 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]
  23. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  24. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  25. 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]
  26. 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]
  27. Lefort V, Desper R, Gascuel O, Vincent L, Richard D. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article][PubMed]
    [Google Scholar]
  28. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article][PubMed]
    [Google Scholar]
  29. Pan J, Sun C, Zhang XQ, Huo YY, Zhu XF et al. A novel species from marine sediment of Pacific Ocean as Paracoccus sediminis sp. nov. Int J Syst Evol Microbiol 2014; 64:2512–2516
    [Google Scholar]
  30. Smibert R. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, D.C., USA: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  31. Zhu XF, Jia XM, Zhang XQ, YH W, Chen ZY. Modern Experimental Technique of Microbiology Hangzhou: Zhejiang University Press (English translation); 2011
    [Google Scholar]
  32. Zhang WY, Huo YY, Zhang XQ, Zhu XF, Wu M. Halolamina salifodinae sp. nov. and Halolamina salina sp. nov., two extremely halophilic archaea isolated from a salt mine. Int J Syst Evol Microbiol 2013; 63:4380–4385 [View Article][PubMed]
    [Google Scholar]
  33. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1988; 19:1–67
    [Google Scholar]
  34. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  35. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial Systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  36. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic Characterization and the Principles of Comparative Systematics Washington, DC: American Society of Microbiology; 2007
    [Google Scholar]
  37. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article]
    [Google Scholar]
  38. Uchida K, Kudo T, Suzuki K-I, Nakase T. A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 1999; 45:49–56 [View Article][PubMed]
    [Google Scholar]
  39. Saddler GS, Tavecchia P, Lociuro S, Zanol M, Colombo L et al. Analysis of madurose and other actinomycete whole cell sugars by gas chromatography. J Microbiol Methods 1991; 14:185–191 [View Article]
    [Google Scholar]
  40. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
    [Google Scholar]
  41. Jia Y-Y, Sun C, Pan J, Zhang W-Y, Zhang X-Q et al. Devosia pacifica sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2014; 64:2637–2641 [View Article][PubMed]
    [Google Scholar]
  42. Wang R, Chen C, Su Y, Yu X, Zhang C et al. Agromyces mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil. Curr Microbiol 2018; 75:1055–1061 [View Article][PubMed]
    [Google Scholar]
  43. Chen Z, Guan Y, Wang J, Li J. Agromyces binzhouensis sp. nov., an actinobacterium isolated from a coastal wetland of the Yellow River Delta. Int J Syst Evol Microbiol 2016; 66:833–838 [View Article][PubMed]
    [Google Scholar]
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