1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 10

sp. nov., a 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing endophyte from a root of No Access

Abstract

A 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing, Gram-stain-negative, strictly aerobic, non-motile, yellow-reddish, oval-shaped bacterial strain, designated M5D2P5, was isolated from a root of , in Tumd Right Banner, Inner Mongolia, PR China. M5D2P5 grew at 10–40 °C (optimum 30–35 °C), pH 5.0–10.0 (optimum pH 8.0) and with 0–7% NaCl (optimum 3.0 %). The strain was positive for catalase and oxidase. The phylogenetic trees based on 16S rRNA gene sequences indicated that M5D2P5 clustered with JL1095, and shared 98.0, 97.3, 97.2, 96.9 and less than 96.9 % 16S rRNA gene similarities to JL1095, B2012, PTG4-2, J103, and all the other type strains, respectively. However, the phylogenomic tree showed it clustered with J103. M5D2P5 contained Q-10 as the major respiratory quinone, as well as two minor respiratory quinones, Q-7 and Q-8. Its major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified glycolipid, and four unidentified lipids. The genomic DNA G+C content was 66.5 %. The digital DNA–DNA hybridization score and the average nucleotide identity based on values of M5D2P5 to JL1095, J103, B2012, and PTG4-2, were 20.8, 23.7, 20.7, and 21.5 %, and 73.3, 79.5, 74.4, and 73.7 %, respectively. The phylogenetic and phenotypic characteristics allowed the discrimination of M5D2P5 from its phylogenetic relatives. The novel species sp. nov. is therefore proposed, and the type strain is M5D2P5 (=CGMCC 1.19149=KCTC 92132).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ACC deaminase , Acuticoccus , endophytic , halophyte , phylogenetic analysis and taxonomy
Funding
This study was supported by the:
  • Inner Mongolia University (Award 21800-5185133)
    • Principle Award Recipient: Ji-QuanSun
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005521
2022-10-17
2024-05-18
Loading full text...

Full text loading...

References

  1. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold L-M et al. Analysis of 1,000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Front Microbiol 2020; 11:468 [View Article] [PubMed]
     [Google Scholar]
  2. Hou L, Zhang Y, Sun J, Xie X. Acuticoccus yangtzensis gen. nov., sp. nov., a novel member in the family Rhodobacteraceae, isolated from the surface water of the Yangtze Estuary. Curr Microbiol 2015; 70:176–182 [View Article] [PubMed]
     [Google Scholar]
  3. Lai Q, Liu X, Sun F, Shao Z. Acuticoccus sediminis sp. nov., isolated from deep-sea sediment of the Indian Ocean and proposal of Acuticoccaceae fam. nov. Int J Syst Evol Microbiol 2019; 69:1173–1178 [View Article] [PubMed]
     [Google Scholar]
  4. Yin Q, Liang J, Zhang L, Ma K, Hu Z-L et al. Acuticoccus kandeliae sp. nov., isolated from rhizosphere soil of the mangrove plant Kandelia, and emended description of Acuticoccus yangtzensis. Int J Syst Evol Microbiol 2018; 68:3316–3321 [View Article]
     [Google Scholar]
  5. Li Z, Hu W, Huang S, Huang Y, Li F et al. Acuticoccus mangrovi sp. nov., with an antibacterial property, isolated from mangrove sediment. Int J Syst Evol Microbiol 2021; 71:005137 [View Article] [PubMed]
     [Google Scholar]
  6. Hou L, Sun J, Xie X, Jiao N, Zhang Y. Genome sequence of Acuticoccus yangtzensis JL1095T (DSM 28604T) isolated from the Yangtze Estuary. Stand Genomic Sci 2017; 12:91 [View Article] [PubMed]
     [Google Scholar]
  7. Lodewyckx C, Vangronsveld J, Porteous F, Moore ERB, Taghavi S et al. Endophytic bacteria and their potential applications. CRC Crit Rev Plant Sci 2002; 21:583–606 [View Article]
     [Google Scholar]
  8. Suryanarayanan TS. The need to study the holobiome for gainful uses of endophytes. Fungal Biol Rev 2002; 34:144–150 [View Article]
     [Google Scholar]
  9. Naing AH, Maung T-T, Kim CK. The ACC deaminase-producing plant growth-promoting bacteria: Influences of bacterial strains and ACC deaminase activities in plant tolerance to abiotic stress. Physiol Plant 2021; 173:1992–2012 [View Article] [PubMed]
     [Google Scholar]
  10. Penrose DM, Glick BR. Enzymes that regulate ethylene levels--1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, ACC synthase and ACC oxidase. Indian J Exp Biol 1997; 35:1–17
     [Google Scholar]
  11. Huang X-X, Xu L, Shang J, Sun J-Q. Marinilactibacillus kalidii sp. nov., an indole acetic acid-producing endophyte isolated from a shoot of halophyte Kalidium cuspidatum. Curr Microbiol 2022; 79:198 [View Article] [PubMed]
     [Google Scholar]
  12. Huang X-X, Xu L, Sun J-Q. Gracilibacillus suaedae sp. nov., an indole acetic acid-producing endophyte isolated from a root of Suaeda salsa. Int J Syst Evol Microbiol 2021; 71:005140 [View Article] [PubMed]
     [Google Scholar]
  13. Wang HT, Xu L, Sun JQ. Aquibacillus kalidii sp. nov., an indole acetic acid-producing endophyte from a shoot of Kalidium cuspidatum, and reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011. Int J Syst Evol Microbiol 2021; 71:005030 [View Article]
     [Google Scholar]
  14. Kumari A, Das P, Parida AK, Agarwal PK. Proteomics, metabolomics, and ionomics perspectives of salinity tolerance in halophytes. Front Plant Sci 2015; 6:537 [View Article] [PubMed]
     [Google Scholar]
  15. Sun JQ, Xu LA, Liu M, Wang XY, Wu XL. Flavobacterium suaedae sp. nov., an endophyte isolated from the root of Suaeda corniculata. Int J Syst Evol Microbiol 2016; 66:1943–1949 [View Article] [PubMed]
     [Google Scholar]
  16. Cherif-Silini H, Silini A, Yahiaoui B, Ouzari I, Boudabous A. Phylogenetic and plant-growth-promoting characteristics of Bacillus isolated from the wheat rhizosphere. Ann Microbiol 2016; 66:1087–1097 [View Article]
     [Google Scholar]
  17. Sun J-Q, Xu L, Guo Y, Li W-L, Shao Z-Q et al. Kribbella deserti sp. nov., isolated from rhizosphere soil of Ammopiptanthus mongolicus. Int J Syst Evol Microbiol 2017; 67:692–696 [View Article] [PubMed]
     [Google Scholar]
  18. 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]
  19. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin 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]
  20. 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]
  21. Felsenstein J. Confidence limits on phylogenies an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  22. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  23. Xu L, Zhang H, Xing Y-T, 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]
     [Google Scholar]
  24. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  25. 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]
  26. 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]
     [Google Scholar]
  27. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238 [View Article] [PubMed]
     [Google Scholar]
  28. Mahmud SA, Nagahisa K, Hirasawa T, Yoshikawa K, Ashitani K et al. Effect of trehalose accumulation on response to saline stress in Saccharomyces cerevisiae. Yeast 2009; 26:17–30 [View Article] [PubMed]
     [Google Scholar]
  29. Boniolo FS, Rodrigues RC, Delatorre EO, da Silveira MM, Flores VMQ et al. Glycine betaine enhances growth of nitrogen-fixing bacteria Gluconacetobacter diazotrophicus PAL5 under saline stress conditions. Curr Microbiol 2009; 59:593–599 [View Article]
     [Google Scholar]
  30. Smibert RM, Krieg NR. Phenotypic characterization. In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  31. Dong X-Z, Cai M-Y. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  32. 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]
  33. Fraser SL, Jorgensen JH. Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 1997; 41:2738–2741 [View Article] [PubMed]
     [Google Scholar]
  34. Komagata K, Suzuki K-I. Lipid and cell wall analysis in bacterial systematics. Method Microbiol 1987; 19:161–207
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005521
Loading
Acuticoccus kalidii sp. nov., a 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing endophyte from a root of Kalidium cuspidatum
Int J Syst Evol Microbiol 72, 005521 (2022); https://doi.org/10.1099/ijsem.0.005521
/content/journal/ijsem/10.1099/ijsem.0.005521
/content/journal/ijsem/10.1099/ijsem.0.005521
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