1887

Abstract

A bacterial strain, arapr2, was isolated from agricultural soil sampled in Reims, France. Based on its 16S rRNA gene sequence, the strain was affiliated to the family and more specifically to the genus . The strain had 98.31 % 16S rRNA gene sequence similarity to its closest relative CR11 and 98.25 % to NCCP-246. Genome relatedness indexes revealed that the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between arapr2 and its closest relative ( CR11) were 92.97 % and 52.00 %, respectively; for NCCP-246, the ANI and dDDH values were 82.46 and 27.6%, respectively. The genomic DNA of strain arapr2 was 6.02 Mbp long, had a DNA G+C content of 40.4 mol% and had 5504 protein-coding genes. The results obtained in this study suggests that strain arapr2 (CIP 111872=LMG 31848) represents a new species for which the name sp. nov. is proposed. Due to the fact that this strain has been isolated using wheat straw as carbon source, this novel bacterial strain represents a promising biotechnological tool for the fractionation of lignocellulosic biomass in the context of biorefinery development.

Funding
This study was supported by the:
  • French Region Grand Est, Grand Reims and the European Regional Development Fund (ERDF)
    • Principle Award Recipient: ludovicBesaury
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2021-08-18
2024-12-07
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References

  1. Kim MK, Na J-R, Cho DH, Soung N-K, Yang D-C. Parapedobacter koreensis gen. nov., sp. nov. Int J Syst Evol Microbiol 2007; 57:1336–1341 [View Article] [PubMed]
    [Google Scholar]
  2. Steyn P, Segers P, Vancanneyt M, Sandra P, Kersters K et al. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Evol Microbiol 1998; 48:165–177
    [Google Scholar]
  3. Xia X, Wu S, Han Y, Liao S, Wang G. Pelobium manganitolerans gen. nov., sp. nov., isolated from sludge of a manganese mine. Int J Syst Evol Microbiol 2016; 66:4954–4959 [View Article] [PubMed]
    [Google Scholar]
  4. Yabuuchi E, Kaneko T, Yano I, Moss CW, Miyoshi N. Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucose-nonfermenting gram-negative rods in CDC groups IIK-2 and IIb. Int J Syst Evol Microbiol 1983; 33:580–598
    [Google Scholar]
  5. Jagannadham MV, Chattopadhyay MK, Subbalakshmi C, Vairamani M, Narayanan K et al. Carotenoids of an Antarctic psychrotolerant bacterium, Sphingobacterium antarcticus, and a mesophilic bacterium, Sphingobacterium multivorum. Arch Microbiol 2000; 173:418–424 [View Article] [PubMed]
    [Google Scholar]
  6. Kim K-H, Ten LN, Liu Q-M, Im W-T, Lee S-T. Sphingobacterium daejeonense sp. nov., isolated from a compost sample. Int J Syst Evol Microbiol 2006; 56:2031–2036 [View Article] [PubMed]
    [Google Scholar]
  7. Mehnaz S, Weselowski B, Lazarovits G. Sphingobacterium canadense sp. nov., an isolate from corn roots. Syst Appl Microbiol 2007; 30:519–524 [View Article] [PubMed]
    [Google Scholar]
  8. Lambiase A, Rossano F, Del Pezzo M, Raia V, Sepe A et al. Sphingobacterium respiratory tract infection in patients with cystic fibrosis. BMC Res Notes 2009; 2:262 [View Article] [PubMed]
    [Google Scholar]
  9. He W, Guo J, Guo H, An M, Huang W et al. Sphingobacterium puteale sp. nov., isolated from a deep subsurface aquifer. Int J Syst Evol Microbiol 2019; 69:3356–3361 [View Article] [PubMed]
    [Google Scholar]
  10. Vieira F, Nahas E. Comparison of microbial numbers in soils by using various culture media and temperatures. Microbiol Res 2005; 160:197–202 [View Article] [PubMed]
    [Google Scholar]
  11. 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]
  12. Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using clustalW and clustalX. Curr Protoc Bioinformatics 2002; Chapter 2:Unit 2.3:
    [Google Scholar]
  13. Lai W-A, Hameed A, Liu Y-C, Hsu Y-H, Lin S-Y et al. Sphingobacterium cibi sp. nov., isolated from the food-waste compost and emended descriptions of Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 and Sphingobacteriumthermophilum Yabe et al. 2013. Int J Syst Evol Microbiol 2016; 66:5336–5344 [View Article] [PubMed]
    [Google Scholar]
  14. Kumar S, Stecher G, Tamura K. mega7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  15. Cheng JF, Guo JX, Bian YN, Chen ZL, Li CL et al. Sphingobacterium athyrii sp. nov., a cellulose- and xylan-degrading bacterium isolated from a decaying fern (Athyrium wallichianum Ching. Int J Syst Evol Microbiol 2019; 69:752–760 [View Article] [PubMed]
    [Google Scholar]
  16. 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]
  17. Marqués AM, Burgos-Díaz C, Aranda FJ, Teruel JA, Manresa À et al. Sphingobacterium detergens sp. nov., a surfactant-producing bacterium isolated from soil. Int J Syst Evol Microbiol 2012; 62:3036–3041 [View Article] [PubMed]
    [Google Scholar]
  18. Liu R, Liu H, Zhang C-X, Yang S-Y, Liu X-H et al. Sphingobacterium siyangense sp. nov., isolated from farm soil. Int J Syst Evol Microbiol 2008; 58:1458–1462 [View Article] [PubMed]
    [Google Scholar]
  19. Ahmed I, Ehsan M, Sin Y, Paek J, Khalid N et al. Sphingobacterium pakistanensis sp. nov., a novel plant growth promoting rhizobacteria isolated from rhizosphere of Vigna mungo. Antonie van Leeuwenhoek 2014; 105:325–333 [View Article] [PubMed]
    [Google Scholar]
  20. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  21. Bystrykh LV, Fernández-Moreno MA, Herrema JK, Malpartida F, Hopwood DA et al. Production of actinorhodin-related “blue pigments” by Streptomyces coelicolor A3(2). J Bacteriol 1996; 178:2238–2244 [View Article] [PubMed]
    [Google Scholar]
  22. Giuffrè A, Borisov VB, Arese M, Sarti P, Forte E. Cytochrome bd oxidase and bacterial tolerance to oxidative and nitrosative stress. Biochimica et Biophysica Acta (BBA)-Bioenergetics 2014; 1837:1178–1187 [View Article]
    [Google Scholar]
  23. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article] [PubMed]
    [Google Scholar]
  24. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 2009; 37:D233–D238 [View Article]
    [Google Scholar]
  25. 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]
    [Google Scholar]
  26. Tolonen AC, Haas W, Chilaka AC, Aach J, Gygi SP et al. Proteome‐wide systems analysis of a cellulosic biofuel‐producing microbe. Mol Syst Biol 2011; 7:461 [View Article] [PubMed]
    [Google Scholar]
  27. Bauer A. Antibiotic susceptibility testing by a standardized single disc method. Am J clin pathol 1966; 45:149–158
    [Google Scholar]
  28. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
    [Google Scholar]
  29. Kuykendall L, Roy M, O’Neill J, Devine T. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 1988; 38:358–361
    [Google Scholar]
  30. Tindall B. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202
    [Google Scholar]
  31. Tindall B. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  32. Kumar S, Stecher G, Tamura K. mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  33. 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]
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