1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 1

sp. nov., isolated from bean rhizosphere No Access

Abstract

A novel canavanine-degrading bacterium, strain HB002, was isolated from rhizosphere soil of a catch crop field collected from the island of Reichenau in Konstanz, Germany, and characterized by using polyphasic taxonomy. The facultative aerobe, rod-shaped, Gram-stain-negative bacterium was oxidase- and catalase-positive. The isolate was able to grow on canavanine as a sole carbon and nitrogen source. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed highest similarities to (L22-9, 99.93 %), subsp. (ATCC 49054, 99.76 %), subsp. (DBK 11, 99.63 %), (DSM 13194, 99.51 %), (DSM 13647, 99.39 %) and (ATCC29736, 99.39 %). Marker gene analysis placed the strain in the intrageneric group of , subgroup . DNA–DNA hybridization and average nucleotide identity values were both under the recommended thresholds for species delineation. The predominant fatty acids of strain HB002 were C, C cyclo ω7 and C ω7. The major respiratory quinone was Q9, followed by Q8 and minor components of Q7 and Q10. Results from the phenotypic characterization showd the strain's inability to hydrolyse gelatin and to assimilate -acetyl glucosamide and a positive enzymatic activity of acid phosphatase and naphthol-AS-BI phosphohydrolase that distinguish this strain from closely related type strains. Taken together, these results show that strain HB002 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is HB002 (=DSM 112525=LMG 32336).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bean rhizosphere , canavanine , polyphasic taxonomy and Pseudomonas canavaninivorans
Funding
This study was supported by the:
  • European Research Council (Award 681777)
    • Principle Award Recipient: JörgHartig
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005203
2022-01-24
2024-04-25
Loading full text...

Full text loading...

References

  1. Migula W. Über ein neues system der bakterien. arbeiten aus dem bakteriologischen institut der technischen hochschule zu karlsruhe; 1894; 1235–238
  2. Remold SK, Brown CK, Farris JE, Hundley TC, Perpich JA et al. Differential habitat use and niche partitioning by Pseudomonas species in human homes. Microb Ecol 2011; 62:505–517 [View Article] [PubMed]
     [Google Scholar]
  3. Sørensen J, Jensen LE, Nybroe O. Soil and rhizosphere as habitats for Pseudomonas inoculants: new knowledge on distribution, activity and physiological state derived from micro-scale and single-cell studies. Plant and Soil 2001; 232:97–108 [View Article]
     [Google Scholar]
  4. Euzéby JP. List of bacterial names with standing in nomenclature: a folder available on the internet. Int J Syst Bacteriol 1997; 47:590–592 [View Article] [PubMed]
     [Google Scholar]
  5. Weimer A, Kohlstedt M, Volke DC, Nikel PI, Wittmann C. Industrial biotechnology of Pseudomonas putida: advances and prospects. Appl Microbiol Biotechnol 2020; 104:7745–7766 [View Article] [PubMed]
     [Google Scholar]
  6. Zhang M, Gao C, Guo X, Guo S, Kang Z et al. Increased glutarate production by blocking the glutaryl-CoA dehydrogenation pathway and a catabolic pathway involving L-2-hydroxyglutarate. Nat Commun 2018; 9:2114 [View Article] [PubMed]
     [Google Scholar]
  7. Knorr S, Sinn M, Galetskiy D, Williams RM, Wang C et al. Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate. Nat Commun 2018; 9:5071 [View Article] [PubMed]
     [Google Scholar]
  8. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  9. 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]
  10. Mulet M, Lalucat J, García-Valdés E. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010; 12:1513–1530 [View Article] [PubMed]
     [Google Scholar]
  11. Hesse C, Schulz F, Bull CT, Shaffer BT, Yan Q et al. Genome-based evolutionary history of Pseudomonas spp. Environ Microbiol 2018; 20:2142–2159 [View Article] [PubMed]
     [Google Scholar]
  12. 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]
  13. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  14. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2 [View Article] [PubMed]
     [Google Scholar]
  15. Lefort V, Desper R, Gascuel O. 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]
  16. Kreft L, Botzki A, Coppens F, Vandepoele K, Van Bel M. PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. Bioinformatics 2017; 33:2946–2947 [View Article] [PubMed]
     [Google Scholar]
  17. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
     [Google Scholar]
  18. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016; 17:132 [View Article] [PubMed]
     [Google Scholar]
  19. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
     [Google Scholar]
  20. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article] [PubMed]
     [Google Scholar]
  21. Stackebrandt E, Goebel BM. Taxonomic Note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  22. Ha SM, Kim CK, Roh J, Byun JH, Yang SJ et al. Application of the whole genome-based bacterial identification system, TrueBac ID, using clinical isolates that were not identified with three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems. Ann Lab Med 2019; 39:530–536 [View Article] [PubMed]
     [Google Scholar]
  23. Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ et al. Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob Agents Chemother 2019; 63:e00483-19 [View Article] [PubMed]
     [Google Scholar]
  24. Liu B, Zheng D, Jin Q, Chen L, Yang J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res 2019; 47:D687–D692 [View Article] [PubMed]
     [Google Scholar]
  25. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  26. Garrido-Sanz D, Arrebola E, Martínez-Granero F, García-Méndez S, Muriel C et al. Classification of isolates from the Pseudomonas fluorescens complex into phylogenomic groups based in group-specific markers. Front Microbiol 2017; 8:413 [View Article] [PubMed]
     [Google Scholar]
  27. Jeffries CD, Holtman DF, Guse DG. Rapid method for determining the activity of microorganisms on nucleic acids. J Bacteriol 1957; 73:590–591 [View Article] [PubMed]
     [Google Scholar]
  28. King EO, Ward MK, Raney DE. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 1954; 44:301–307 [PubMed]
     [Google Scholar]
  29. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article] [PubMed]
     [Google Scholar]
  30. Liang J, Wang S, Yiming A, Fu L, Ahmad I et al. Pseudomonas bijieensis sp. nov., isolated from cornfield soil. Int J Syst Evol Microbiol 2019; 71:004676 [View Article] [PubMed]
     [Google Scholar]
  31. Zhao H, Ma Y, Wu X, Zhang L. Pseudomonas viciae sp. nov., isolated from rhizosphere of broad bean. Int J Syst Evol Microbiol 2020; 70:5012–5018 [View Article] [PubMed]
     [Google Scholar]
  32. Sikorski J, Stackebrandt E, Wackernagel W. Pseudomonas kilonensis sp. nov., a bacterium isolated from agricultural soil. Int J Syst Evol Microbiol 2001; 51:1549–1555 [View Article] [PubMed]
     [Google Scholar]
  33. Achouak W, Sutra L, Heulin T, Meyer JM, Fromin N et al. Pseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov., two root-associated bacteria isolated from Brassica napus and Arabidopsis thaliana. Int J Syst Evol Microbiol 2000; 50 Pt 1:9–18 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005203
Loading
Pseudomonas canavaninivorans sp. nov., isolated from bean rhizosphere
Int J Syst Evol Microbiol 72, 005203 (2022); https://doi.org/10.1099/ijsem.0.005203
/content/journal/ijsem/10.1099/ijsem.0.005203
/content/journal/ijsem/10.1099/ijsem.0.005203
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error