Kushneria phyllosphaerae sp. nov. and Kushneria endophytica sp. nov., plant growth promoting endophytes isolated from the halophyte plant Arthrocnemum macrostachyum Free

Abstract

Two endophytic bacteria (EAod3 and EAod7) were isolated from the aerial part of plants of Arthrocnemum macrostachyum growing in the Odiel marshes (Huelva, Spain). Phylogenetic analysis based on 16S rRNA gene sequences indicated their affiliation to the genus Kushneria . 16S rRNA gene sequences of strains EAod3 and EAod7 showed the highest similarity to Kushneria marisflavi DSM 15357T (99.0 and 97.6 %, respectively). Digital DNA–DNA hybridization studies between the draft genomes of strain EAod3 and K. marisflavi DSM 15357 corresponded to 28.5 % confirming the novel lineage of strain EAod3 in the genus Kushneria . Cells of both strains were Gram-staining-negative, aerobic and motile rods able to grow at 4–37 °C, at pH 5.0-8.0 and tolerate 0.5–25 % NaCl (w/v). They presented ubiquinone Q9 and C16 : 0, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c as the major fatty acids. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on the phenotypic and phylogenetic results, strains EAod3 (=CEC 9073=LMG 29856) and EAod7 (=CECT 9075=LMG 29858) are proposed as new representatives of the genus Kushneria, and the proposed names are Kushneria phyllosphaerae sp. nov. and Kushneria endophytica sp. nov., respectively. The whole genome sequence of strain EAod3 has a total length of 3.8 Mbp and a G+C content of 59.3 mol%.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002897
2018-07-16
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/9/2800.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002897&mimeType=html&fmt=ahah

References

  1. Franzmann PD, Wehmeyer U, Stackebrandt E. Halomonadaceae fam. nov., a new family of the class Proteobacteria to accommodate the genera Halomonas and Deleya. Syst Appl Microbiol 1988; 11:16–19 [View Article]
    [Google Scholar]
  2. Sánchez-Porro C, de La Haba RR, Soto-Ramírez N, Márquez MC, Montalvo-Rodríguez R et al. Description of Kushneria aurantia gen. nov., sp. nov., a novel member of the family Halomonadaceae, and a proposal for reclassification of Halomonas marisflavi as Kushneria marisflavi comb. nov., of Halomonas indalinina as Kushneria indalinina comb. nov. and of Halomonas avicenniae as Kushneria avicenniae comb. nov. Int J Syst Evol Microbiol 2009; 59:397–405 [View Article][PubMed]
    [Google Scholar]
  3. Soto-Ramírez N, Sánchez-Porro C, Rosas S, González W, Quiñones M et al. Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico. Int J Syst Evol Microbiol 2007; 57:900–905 [View Article][PubMed]
    [Google Scholar]
  4. Cabrera A, Aguilera M, Fuentes S, Incerti C, Russell NJ et al. Halomonas indalinina sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almeria, southern Spain. Int J Syst Evol Microbiol 2007; 57:376–380 [View Article][PubMed]
    [Google Scholar]
  5. Yoon JH, Choi SH, Lee KC, Kho YH, Kang KH et al. Halomonas marisflavae sp. nov., a halophilic bacterium isolated from the Yellow Sea in Korea. Int J Syst Evol Microbiol 2001; 51:1171–1177 [View Article][PubMed]
    [Google Scholar]
  6. LPSN 2018; List of prokaryotes standing in nomenclature: genus, Kushneria. www.bacterio.net/kushneria.html [accessed 5 February 2018]
  7. Yun JH, Park SK, Lee JY, Jung MJ, Bae JW. Kushneria konosiri sp. nov., isolated from the Korean salt-fermented seafood Daemi-jeot. Int J Syst Evol Microbiol 2017; 67:3576–3582 [View Article][PubMed]
    [Google Scholar]
  8. List editor IJSEM Notification that new names and new combinations have appeared in volume 51, part 3, of the IJSEM. Int J Syst Evol Microbiol 2001; 51:1231–1233 [View Article][PubMed]
    [Google Scholar]
  9. Bangash A, Ahmed I, Abbas S, Kudo T, Shahzad A et al. Kushneria pakistanensis sp. nov., a novel moderately halophilic bacterium isolated from rhizosphere of a plant (Saccharum spontaneum) growing in salt mines of the Karak area in Pakistan. Antonie van Leeuwenhoek 2015; 107:991–1000 [View Article][PubMed]
    [Google Scholar]
  10. Zou Z, Wang G. Kushneria sinocarnis sp. nov., a moderately halophilic bacterium isolated from a Chinese traditional cured meat. Int J Syst Evol Microbiol 2010; 60:1881–1886 [View Article][PubMed]
    [Google Scholar]
  11. Navarro-Torre S, Mateos-Naranjo E, Caviedes MA, Pajuelo E, Rodríguez-Llorente ID. Isolation of plant-growth-promoting and metal-resistant cultivable bacteria from Arthrocnemum macrostachyum in the Odiel marshes with potential use in phytoremediation. Mar Pollut Bull 2016; 110:133–142 [View Article][PubMed]
    [Google Scholar]
  12. Navarro-Torre S, Barcia-Piedras JM, Caviedes MA, Pajuelo E, Redondo-Gómez S et al. Bioaugmentation with bacteria selected from the microbiome enhances Arthrocnemum macrostachyum metal accumulation and tolerance. Mar Pollut Bull 2017; 117:340–347 [View Article][PubMed]
    [Google Scholar]
  13. Arahal DR, Vreeland RH, Litchfield CD, Mormile MR, Tindall BJ et al. Recommended minimal standards for describing new taxa of the family Halomonadaceae. Int J Syst Evol Microbiol 2007; 57:2436–2446 [View Article][PubMed]
    [Google Scholar]
  14. Yoon SH, Ha SM, 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]
  15. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014; 15:R46 [View Article][PubMed]
    [Google Scholar]
  16. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM; 2013arXiv:1303.3997v2
  17. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  18. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
    [Google Scholar]
  19. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article][PubMed]
    [Google Scholar]
  20. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  21. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011; 8:785–786 [View Article][PubMed]
    [Google Scholar]
  22. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567–580 [View Article][PubMed]
    [Google Scholar]
  23. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007; 35:W52–W57 [View Article][PubMed]
    [Google Scholar]
  24. Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP et al. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat Biotechnol 2017; 35:676–683 [View Article][PubMed]
    [Google Scholar]
  25. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  26. Montero-Calasanz MC, Göker M, Pötter G, Rohde M, Spröer C et al. Geodermatophilus arenarius sp. nov., a xerophilic actinomycete isolated from Saharan desert sand in Chad. Extremophiles 2012; 16:903–909 [View Article][PubMed]
    [Google Scholar]
  27. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
    [Google Scholar]
  28. Halebian S, Harris B, Finegold SM, Rolfe RD. Rapid method that aids in distinguishing Gram-positive from Gram-negative anaerobic bacteria. J Clin Microbiol 1981; 13:444–448[PubMed]
    [Google Scholar]
  29. Vaas LA, Sikorski J, Michael V, Göker M, Klenk HP. Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS One 2012; 7:e34846 [View Article][PubMed]
    [Google Scholar]
  30. Vaas LA, 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]
  31. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
    [Google Scholar]
  32. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  33. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  34. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  35. Kroppenstedt RM, Goodfellow M. The family Thermonosporaceae: Actinocorallia, Actinomadura, Spirillisporay Thermomonospora. In Dworkin M, Falkow S, Schleifer KH, Stackebrandt E. (editors) Archaea y Bacteria: Firmicutes, Actinomycetes: The Prokariotes, 3rd ed. vol. 3 New York: Springer; 2006 pp. 682–724
    [Google Scholar]
  36. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  37. Ventosa A, Nieto JJ, Oren A. Biology of moderately halophilic aerobic bacteria. Microbiol Mol Biol Rev 1998; 62:504–544[PubMed]
    [Google Scholar]
  38. Montero-Calasanz MC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium. Int J Syst Evol Microbiol 2013; 63:4386–4395 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002897
Loading
/content/journal/ijsem/10.1099/ijsem.0.002897
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed