1887

Abstract

p-Hydroxybenzoate is an allelopathic compound commonly found in soil from long-term monoculture cropping systems. During the bacterial diversity analysis of saline soil, a Gram-negative, non-spore forming, non-motile, aerobic p-hydroxybenzoate-degrading bacterial strain, designated LN3S51, was isolated from saline soil which was sampled from Tumd Right Banner, Inner Mongolia, northern China. Strain LN3S51 grew at 4–40 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–15 % NaCl (optimum 3.0 %). Though strain LN3S51 has the highest 16S rRNA gene similarities to GJSW-31 (96.0 %), the phylogenetic tree based on the 16S rRNA gene sequences showed that it clustered with SM1902 (95.8 %), TG-679 (93.9 %), and LMIT002 (93.9 %). Strain LN3S51 contained Q-10 as the major ubiquinone. Phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), diphosphatidylglycerol (DPG), an unidentified aminolipid (AL), and two unidentified lipids (L) were the major polar lipids. The major fatty acids were sum feature 8 (C c and/or C c), C, C, and C c 11-methyl. The genome of strain LN3S51 consisted of a 2 257 066 bp chromosome and four plasmids with a 59.1 mol% of genomic DNA G+C content. The average nucleotide identity (ANI) and digital DNA–DNA hybridization score (dDDH) values of strain LN3S51 to SM1902, TG-679, LMIT002, and GJSW-31 were 69.6, 70.9, 70.6, and 69.5 %, and 20.0, 19.5, 19.0, and 20.0 %, respectively. Based on the results of phylogenetic, chemtaxonomic and phenotypic characterization, strain LN3S51 is considered to represent a novel species in a new genus within the family , for which gen. nov. sp. nov. is proposed. The type strain is LN3S51 (=CGMCC 1.17099=KCTC 72457).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31960020)
    • Principle Award Recipient: Ji-QuanSun
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004719
2021-02-25
2022-05-27
Loading full text...

Full text loading...

References

  1. Garrity G, Brenner DJ, Kreig N. Staley JT Bergey’s Manual of Systematic Bacteriology, Vol. 2, Part C (The Alpha-, Beta-, Delta-,and Epsilonproteobacteria) New York: Springer; 2005 pp 161–229
    [Google Scholar]
  2. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM. Analysis of 1,000+ Type-Strain genomes substantially improves taxonomic ification of Alphaproteobacteria . Front Microbiol 2020; 11:468 [View Article][PubMed]
    [Google Scholar]
  3. Parte AC. LPSN--list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article][PubMed]
    [Google Scholar]
  4. Ren Y, Chen C, Ye Y, Wang R, Han S et al. Meridianimarinicoccus roseus gen. nov., sp. nov., a novel genus of the family Rhodobacteraceae isolated from seawater. Int J Syst Evol Microbiol 2019; 69:504–510 [View Article][PubMed]
    [Google Scholar]
  5. Zhu J, Hong P, Wang S, Hu Z, Wang H. Phycocomes zhengii gen. nov., sp. nov., a marine bacterium of the family Rhodobacteraceae isolated from the phycosphere of Chlorella vulgaris. Int J Syst Evol Microbiol 2019; 69:535–541 [View Article][PubMed]
    [Google Scholar]
  6. Sun Y-Y, Dang Y-R, He X-Y, Wang J-M, Liu N-H et al. Fluviibacterium aquatile gen. nov., sp. nov., isolated from estuary sediment. Int J Syst Evol Microbiol 2020; 70:105–111 [View Article][PubMed]
    [Google Scholar]
  7. Sun JQ, Xu L, Tang YQ, Chen FM, Wu X-L. Simultaneous degradation of phenol and n-hexadecane by Acinetobacter strains. Bioresour Technol 2012; 123:664–668 [View Article][PubMed]
    [Google Scholar]
  8. Ma J-P WZ, Lu P, Wang H-J, Ali SW et al. Biodegradation of the sulfonylurea herbicide chlorimuron-ethyl by the strain Pseudomonas sp. LW3. FEMS Microbiol Lett 2010; 296:203–209
    [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. Thompson JD, Gibson TJ, Plewniak F, Jeanpougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  11. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  12. 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]
  13. Rzhetsky A. Nei M A simple method for estimating and testing Minimum-Evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  14. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [View Article][PubMed]
    [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  16. Xu L, Zhang H, Xing YT, Li N, Wang S et al. Complete genome sequence of Sphingobacterium psychroaquaticum strain SJ-25, an aerobic bacterium capable of suppressing fungal pathogens. Curr Microbiol 2020; 77:115-122 [View Article][PubMed]
    [Google Scholar]
  17. 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]
  18. Rodriguez-R LM, KK T. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PEER J 2016; 4:e1900
    [Google Scholar]
  19. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article][PubMed]
    [Google Scholar]
  20. 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]
  21. Smibert RM, Krieg NR. Phenotypic characterization. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  22. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  23. Kim B-C, Jeong W-J, Kim DY, Oh H-W, Kim H et al. Paenibacillus pueri sp. nov., isolated from Pu'er tea. Int J Syst Evol Microbiol 2009; 59:1002–1006 [View Article][PubMed]
    [Google Scholar]
  24. Fraser SL, Jorgensen JH. Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chem 1997; 41:2738–2741 [View Article][PubMed]
    [Google Scholar]
  25. Kates M. Techniques of Lipidology, 2nd ed. Amsterdam: Elsevier; 1986
    [Google Scholar]
  26. Komagata K, Suzuki K. Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  27. Subhash Y, Lee S-S. Rhodobacter sediminis sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2016; 66:2965–2970 [View Article][PubMed]
    [Google Scholar]
  28. Suresh G, Sailaja B, Ashif A, Dave BP, Sasikala C et al. Description of Rhodobacter azollae sp. nov. and Rhodobacter lacus sp. nov. Int J Syst Evol Microbiol 2017; 67:3289–3295 [View Article][PubMed]
    [Google Scholar]
  29. Park S, Park J-M, Lee K-C, Bae KS, Yoon J-H. Boseongicola aestuarii gen. nov., sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:2618–2624 [View Article][PubMed]
    [Google Scholar]
  30. Park S, Park J-M, Park D-S, Yoon J-H. Litoreibacter ponti sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2014; 64:3810–3815 [View Article][PubMed]
    [Google Scholar]
  31. Romanenko LA, Tanaka N, Frolova GM, Svetashev VI, Mikhailov VV. Litoreibacter albidus gen. nov., sp. nov. and Litoreibacter janthinus sp. nov., members of the class Alphaproteobacteria isolated from the seashore. Int J Syst Evol Microbiol 2011; 61:148–154 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004719
Loading
/content/journal/ijsem/10.1099/ijsem.0.004719
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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