1887

Abstract

Strain 3P27G6 was isolated from an artesian well connected to the thermal water basin of Comano Terme, Province of Trento, Italy. In phylogenetic analyses based on multilocus sequence analysis, strain 3P27G6 clustered together with WSM2073. Genome sequencing produced a 99.51 % complete genome, with a length of 7 363 057 bp and G+C content of 63.53 mol%, containing 6897 coding sequences, 55 tRNA and three rRNA. Average nucleotide identity analysis revealed that all distances calculated between strain 3P27G6 and the other genomes were below 0.9, indicating that strain 3P27G6 represents a new species. Therefore, we propose the name sp. nov. with the type strain 3P27G6 (=DSM 110654=CECT 30067). Strain 3P27G6 is a Gram-negative, rod-shaped, aerobic bacterium. Growth condition, antibiotic susceptibility, metabolic and fatty acid-methyl esters profiles of the strain were determined. Only few nodulation and nitrogen fixation genes were found in the genome, suggesting that this strain may not be specialized in nodulation or in nitrogen fixation.

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2021-12-06
2022-01-29
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References

  1. Jarvis BDW, Van Berkum P, Chen WX, Nour SM, Fernandez MP et al. Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, and Rhizobium tianshanense to Mesorhizobium gen. nov. Int J Syst Bacteriol 1997; 47:895–898 [View Article]
    [Google Scholar]
  2. Jarvis BDW, Pankhurst CE, Patel JJ. Rhizobium loti, a new species of legume root nodule bacteria. Int J Syst Bacteriol 1982; 32:378–380 [View Article]
    [Google Scholar]
  3. Mahmud K, Makaju S, Ibrahim R, Missaoui A. Current progress in nitrogen fixing plants and microbiome research. Plants 2020; 9:97 [View Article]
    [Google Scholar]
  4. Laranjo M, Alexandre A, Oliveira S. Legume growth-promoting rhizobia: An overview on the Mesorhizobium genus. Microbiological Research 2014; 169:2–17 [View Article]
    [Google Scholar]
  5. Nour SM, Fernandez MP, Normand P, Cleyet-Marel JC. Rhizobium ciceri sp. nov., consisting of strains that nodulate chickpeas (Cicer arietinum L.). Int J Syst Bacteriol 1994; 44:511–522 [View Article] [PubMed]
    [Google Scholar]
  6. Nour SM, Cleyet-Marel J-C, Normand P, Fernandez MP. Genomic heterogeneity of strains nodulating chickpeas (Cicer arietinum L.) and description of Rhizobium mediterraneum sp. nov. Int J Syst Bacteriol 1995; 45:640–648 [View Article] [PubMed]
    [Google Scholar]
  7. Chen W, Wang E, Wang S, Li Y, Chen X et al. Characteristics of Rhizobium tianshanense sp. nov., a moderately and slowly growing root nodule bacterium isolated from an arid saline environment in Xinjiang, People’s Republic of China. Int J Syst Bacteriol 1995; 45:153–159 [View Article] [PubMed]
    [Google Scholar]
  8. de Lajudie P, Willems A, Nick G, Moreira F, Molouba F et al. Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov. Int J Syst Bacteriol 1998; 48:369–382 [View Article] [PubMed]
    [Google Scholar]
  9. Ramsay JP, Sullivan JT, Stuart GS, Lamont IL, Ronson CW. Excision and transfer of the Mesorhizobium loti R7A symbiosis island requires an integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase RlxS. Mol Microbiol 2006; 62:723–734 [View Article] [PubMed]
    [Google Scholar]
  10. Ramsay JP, Hynes MF, Sullivan JT. Ronson CWBT-RM in LS Symbiosis Islands. In Brenner’s Encyclopedia of Genetics Elsevier; 2013 pp 598–600
    [Google Scholar]
  11. De Meyer SE, Tan HW, Andrews M, Heenan PB, Willems A. Mesorhizobium calcicola sp. nov., Mesorhizobium waitakense sp. nov., Mesorhizobium sophorae sp. nov., Mesorhizobium newzealandense sp. nov. and Mesorhizobium kowhaii sp. nov. isolated from sophora root nodules. Int J Syst Evol Microbiol 2016; 66:786–795 [View Article] [PubMed]
    [Google Scholar]
  12. Vidal C, Chantreuil C, Berge O, Mauré L, Escarré J et al. Mesorhizobium metallidurans sp. nov., a metal-resistant symbiont of Anthyllis vulneraria growing on metallicolous soil in Languedoc, France. Int J Syst Evol Microbiol 2009; 59:850–855 [View Article] [PubMed]
    [Google Scholar]
  13. Han TX, Han LL, Wu LJ, Chen WF, Sui XH et al. Mesorhizobium gobiense sp. nov. and Mesorhizobium tarimense sp. nov., isolated from wild legumes growing in desert soils of Xinjiang, China. Int J Syst Evol Microbiol 2008; 58:2610–2618 [View Article] [PubMed]
    [Google Scholar]
  14. Zhu YJ, Lu JK, Chen YL, Wang SK, Sui XH et al. Mesorhizobium acaciae sp. nov., isolated from root nodules of Acacia melanoxylon R. Br. Int J Syst Evol Microbiol 2015; 65:3558–3563 [View Article] [PubMed]
    [Google Scholar]
  15. Nandasena KG, O’Hara GW, Tiwari RP, Willems A, Howieson JG. Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov., isolated from Biserrula pelecinus L. in Australia. Int J Syst Evol Microbiol 2009; 59:2140–2147 [View Article] [PubMed]
    [Google Scholar]
  16. Li J, Xin W, Xu Z-Z, Xiang F-Q, Zhang J-J et al. Mesorhizobium carbonis sp. nov., isolated from coal bed water. Antonie van Leeuwenhoek 2019; 112:1221–1229 [View Article]
    [Google Scholar]
  17. Yuan C-G, Jiang Z, Xiao M, Zhou E-M, Kim C-J et al. Mesorhizobium sediminum sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2016; 66:4797–4802 [View Article] [PubMed]
    [Google Scholar]
  18. Fu G-Y, Yu X-Y, Zhang C-Y, Zhao Z, Wu D et al. Mesorhizobium oceanicum sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2017; 67:2739–2745 [View Article] [PubMed]
    [Google Scholar]
  19. Pedron R, Esposito A, Bianconi I, Pasolli E, Tett A et al. Genomic and metagenomic insights into the microbial community of a thermal spring. Microbiome 2019; 7:8 [View Article] [PubMed]
    [Google Scholar]
  20. Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE et al. Community-led, integrated, reproducible multi-omics with anvi’o. Nat Microbiol 2021; 6:3–6 [View Article] [PubMed]
    [Google Scholar]
  21. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7 [View Article] [PubMed]
    [Google Scholar]
  22. Schaeffer P, Millet J, Aubert JP. Catabolic repression of bacterial sporulation. Proc Natl Acad Sci USA 1965; 54:704–711 [View Article] [PubMed]
    [Google Scholar]
  23. Fujisawa T, Okamoto S, Katayama T, Nakao M, Yoshimura H et al. CyanoBase and RhizoBase: Databases of manually curated annotations for cyanobacterial and rhizobial genomes. Nucleic Acids Res 2014; 42:D666–70 [View Article] [PubMed]
    [Google Scholar]
  24. Marcos-García M, Menéndez E, Ramírez-Bahena MH, Mateos PF, Peix Á et al. Mesorhizobium helmanticense sp. nov., isolated from Lotus corniculatus nodules. Int J Syst Evol Microbiol 2017; 67:2301–2305 [View Article] [PubMed]
    [Google Scholar]
  25. Zhang J, Guo C, Chen W, de Lajudie P, Zhang Z et al. Mesorhizobium wenxiniae sp. nov., isolated from chickpea (Cicer arietinum L.) in China. Int J Syst Evol Microbiol 2018; 68:1930–1936 [View Article] [PubMed]
    [Google Scholar]
  26. Edgar RC. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  27. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  28. 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]
  29. Lafay B, Burdon JJ. Molecular diversity of rhizobia occurring on native shrubby legumes in Southeastern Australia. Appl Environ Microbiol 1998; 64:3989–3997 [View Article] [PubMed]
    [Google Scholar]
  30. Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genus Stenotrophomonas. Front Microbiol 2018; 9:1–22 [View Article] [PubMed]
    [Google Scholar]
  31. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:1–8 [View Article]
    [Google Scholar]
  32. Stamatakis A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
    [Google Scholar]
  33. 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]
  34. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 2017; 35:725–731 [View Article] [PubMed]
    [Google Scholar]
  35. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: Soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8:12–24 [View Article]
    [Google Scholar]
  36. Seemann T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  37. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol 2017; 34:2115–2122 [View Article] [PubMed]
    [Google Scholar]
  38. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic Local Alignment Search Tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  39. Gaby JC, Buckley DH. A comprehensive aligned nifH gene database: A multipurpose tool for studies of nitrogen-fixing bacteria. Database 2014; 2014:1–8 [View Article]
    [Google Scholar]
  40. Aserse AA, Woyke T, Kyrpides NC, Whitman WB, Lindström K. Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T. Stand in Genomic Sci 2017; 12:74 [View Article]
    [Google Scholar]
  41. Demont N, Debellé F, Aurelle H, Dénarié J, Promé JC. Role of the Rhizobium meliloti nodF and nodE genes in the biosynthesis of lipo-oligosaccharidic nodulation factors. J Biol Chem 1993; 268:20134–20142 [PubMed]
    [Google Scholar]
  42. Baev N, Schultze M, Barlier I, Ha DC, Virelizier H et al. Rhizobium nodM and nodN genes are common nod genes: nodM encodes functions for efficiency of nod signal production and bacteroid maturation. J Bacteriol 1992; 174:7555–7565 [View Article] [PubMed]
    [Google Scholar]
  43. Rivilla R, Sutton JM, Downie JA. Rhizobium leguminosarum NodT is related to a family of outer-membrane transport proteins that includes TolC, PrtF, CyaE and AprF. Gene 1995; 161:27–31 [View Article]
    [Google Scholar]
  44. Sullivan JT, Trzebiatowski JR, Cruickshank RW, Gouzy J, Brown SD et al. Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. J Bacteriol 2002; 184:3086–3095 [View Article] [PubMed]
    [Google Scholar]
  45. States DJ, Gish W. Combined use of sequence similarity and codon bias for coding region identification. J Comput Biol 1994; 1:39–50 [View Article] [PubMed]
    [Google Scholar]
  46. Bianconi I, Milani A, Cigana C, Paroni M, Levesque RC et al. Positive signature-tagged mutagenesis in Pseudomonas aeruginosa: Tracking patho-adaptive mutations promoting airways chronic infection. PLoS Pathog 2011; 7:e1001270 [View Article] [PubMed]
    [Google Scholar]
  47. R Core TeamR: A language and environment for statistical computing Vienna, Austria: R Project; 2018 https://www.r-project.org/
  48. Acin-Albiac M, Filannino P, Gobbetti M, Di Cagno R. Microbial high throughput phenomics: The potential of an irreplaceable omics. Computational and Structural Biotechnology Journal 2020; 18:2290–2299 [View Article]
    [Google Scholar]
  49. Vaas LAI, Sikorski J, Hofner B, Fiebig A, Buddruhs N et al. opm: an R package for analysing OmniLog(R) phenotype microarray data. Bioinformatics 2013; 29:1823–1824 [View Article] [PubMed]
    [Google Scholar]
  50. Vehkala M, Shubin M, Connor TR, Thomson NR, Corander J et al. Novel R pipeline for analyzing biolog phenotypic microarray data. PLoS One 2015; 10:e0118392 [View Article]
    [Google Scholar]
  51. Kahm M, Hasenbrink G, Lichtenberg-Fraté H, Ludwig J, Kschischo M. grofit : fitting biological growth curves with R. J Stat Soft 2010; 33:1–21 [View Article]
    [Google Scholar]
  52. Galardini M, Mengoni A, Biondi EG, Semeraro R, Florio A et al. DuctApe: a suite for the analysis and correlation of genomic and OmniLogTM phenotype microarray data. Genomics 2014; 103:1–10 [View Article]
    [Google Scholar]
  53. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCCNewsl 1990; 20:1–6
    [Google Scholar]
  54. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
    [Google Scholar]
  55. Tighe SW, de Lajudie P, Dipietro K, Lindström K, Nick G et al. Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System. Int J Syst Evol Microbiol 2000; 50 Pt 2:787–801 [View Article] [PubMed]
    [Google Scholar]
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