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Antonie van Leeuwenhoek

, Volume 112, Issue 8, pp 1161–1167 | Cite as

Lysinibacillus capsici sp. nov, isolated from the rhizosphere of a pepper plant

  • Marleny Burkett-Cadena
  • Leonardo Sastoque
  • Johanna Cadena
  • Christopher A. DunlapEmail author
Original Paper
  • 51 Downloads

Abstract

A strain of a Gram-positive, strictly aerobic, motile, rod-shaped, endospore forming bacterium was originally isolated from rhizospheric soil of a pepper plant when screening and bioprospecting for plant beneficial microorganisms. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain, PB300T, is closely related to Lysinibacillus macroides DMS 54T (99.6%) and Lysinibacillus xylanilyticus DSM 23493T (99.4%). In phenotypic characterisation, the novel strain was found to grow between 15 and 40 °C and tolerate up to 10% (w/v) NaCl. Furthermore, the strain was found to grow in media with pH 5 to 10 (optimal growth at pH 7.0). The predominant cellular fatty acids were observed to be iso-C15 : 0 (56.6 %), anteiso-C15 : 0 (14.6%), C16 :1ω7C alcohol (9.3%) and C16 : 0 (7.1%). The cell wall peptidoglycan contains lysine-aspartic acid, as in its close relatives. A draft genome was completed and the DNA G + C content was determined to be 37.5% (mol content). A phylogenomic analysis of the core genome of the new strain and 5 closely related type strains of the genus Lysinibacillus revealed that this strain formed a distinct monophyletic clade with the nearest neighbour being Lysinibacillus boronitolerans. DNA–DNA relatedness studies using in silico DNA–DNA hybridizations (DDH) showed relationships for the new strain were below the species threshold of 70%. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus capsici sp. nov. is proposed, with type strain PB300T (= NRRL B-65515T, = CCUG 72241T).

Keywords

Biostimulant PGPR Biocontrol 

Notes

Acknowledgements

The authors would like to thank Heather Walker and Miho Yoshioka for expert technical assistance. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture. The mention of firm names or trade products does not imply that they are endorsed or recommended by the USDA over other firms or similar products not mentioned. USDA is an equal opportunity provider and employer.

Funding

This work was supported by U.S. Department of Agriculture Project 5010-22000-011-00-D.

Conflict of interest

The authors declare no conflicts of interest.

Supplementary material

10482_2019_1248_MOESM1_ESM.pdf (530 kb)
Supplementary material 2 (PDF 529 kb)

References

  1. Ahmed I, Yokota A, Yamazoe A, Fujiwara T (2007) Proposal of Lysinibacillus boronitolerans gen. nov. sp. nov., and transfer of Bacillus fusiformis to Lysinibacillus fusiformis comb. nov. and Bacillus sphaericus to Lysinibacillus sphaericus comb. nov. Int J Syst Evol Microbiol 57:1117–1125.  https://doi.org/10.1099/ijs.0.63867-0 CrossRefGoogle Scholar
  2. Andrade LF, de Souza GL, Nietsche S, Xavier AA, Costa MR, Cardoso AM, Pereira MC, Pereira DF (2014) Analysis of the abilities of endophytic bacteria associated with banana tree roots to promote plant growth. J Microbiol 52:27–34.  https://doi.org/10.1007/s12275-014-3019-2 CrossRefGoogle Scholar
  3. Auch AF, von Jan M, Klenk HP, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134.  https://doi.org/10.4056/sigs.531120.CrossRefGoogle Scholar
  4. Breznak JA, Costilow RN (1994) Physicochemical factors in growth. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 137–154Google Scholar
  5. Coorevits A, Dinsdale AE, Heyrman J, Schumann P, Van Landschoot A, Logan NA, De Vos P (2012) Lysinibacillus macroides sp. nov., nom. rev. Int J Syst Evol Microbiol 62:1121–1127.  https://doi.org/10.1099/ijs.0.027995-0 CrossRefGoogle Scholar
  6. He M, Li X, Liu H, Miller SJ, Wang G, Rensing C (2011) Characterization and genomic analysis of a highly chromate resistant and reducing bacterial strain Lysinibacillus fusiformis ZC1. J Hazard Mater 185:682–688.  https://doi.org/10.1016/j.jhazmat.2010.09.072 CrossRefGoogle Scholar
  7. Jolley KA, Maiden MC (2010) BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinform 11:595.  https://doi.org/10.1186/1471-2105-11-595 CrossRefGoogle Scholar
  8. Jung MY, Kim JS, Paek WK, Styrak I, Park IS, Sin Y, Paek J, Park KA, Kim H, Kim HL, Chang YH (2012) Description of Lysinibacillus sinduriensis sp. nov., and transfer of Bacillus massiliensis and Bacillus odysseyi to the genus Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi comb. nov. with emended description of the genus Lysinibacillus. Int J Syst Evol Microbiol 62:2347–2355.  https://doi.org/10.1099/ijs.0.033837-0 CrossRefGoogle Scholar
  9. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874.  https://doi.org/10.1093/molbev/msw054 CrossRefGoogle Scholar
  10. Lee CS, Jung YT, Park S, Oh TK, Yoon JH (2010) Lysinibacillus xylanilyticus sp. nov., a xylan-degrading bacterium isolated from forest humus. Int J Syst Evol Microbiol 60:281–286.  https://doi.org/10.1099/ijs.0.013367-0 CrossRefGoogle Scholar
  11. Lee I, Kim YO, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103.  https://doi.org/10.1099/ijsem.0.000760 CrossRefGoogle Scholar
  12. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform.  https://doi.org/10.1186/1471-2105-14-60 Google Scholar
  13. Rahi P, Kurli R, Khairnar M, Jagtap S, Pansare AN, Dastager SG, Shouche YS (2017) Description of Lysinibacillus telephonicus sp. nov., isolated from the screen of a cellular phone. Int J Syst Evol Microbiol 67:2289–2295.  https://doi.org/10.1099/ijsem.0.001943 CrossRefGoogle Scholar
  14. Rahman A, Nahar N, Nawani NN, Jass J, Ghosh S, Olsson B, Mandal A (2015) Comparative genome analysis of Lysinibacillus B1-CDA, a bacterium that accumulates arsenics. Genomics.  https://doi.org/10.1016/j.ygeno.2015.09.006 Google Scholar
  15. Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131.  https://doi.org/10.1073/pnas.0906412106 CrossRefGoogle Scholar
  16. Schleifer KH (1985) Chapter 5. Analysis of the chemical composition and primary structure of murein. In: Bergan T (ed) Methods in microbiology. Academic Press, London, pp 123–156Google Scholar
  17. Singh RK, Kumar DP, Solanki MK, Singh P, Srivastva AK, Kumar S, Kashyap PL, Saxena AK, Singhal PK, Arora DK (2013) Optimization of media components for chitinase production by chickpea rhizosphere associated Lysinibacillus fusiformis B-CM18. J Basic Microbiol 53:451–460.  https://doi.org/10.1002/jobm.201100590 CrossRefGoogle Scholar
  18. Sun JQ, Xu L, Wu XL (2017) Lysinibacillus alkalisoli sp. nov., isolated from saline-alkaline soil. Int J Syst Evol Microbiol 67:67–71.  https://doi.org/10.1099/ijsem.0.001571 CrossRefGoogle Scholar
  19. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526Google Scholar
  20. Vendan RT, Yu YJ, Lee SH, Rhee YH (2010) Diversity of endophytic bacteria in ginseng and their potential for plant growth promotion. J Microbiol 48:559–565.  https://doi.org/10.1007/s12275-010-0082-1 CrossRefGoogle Scholar
  21. Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (2009) The Firmicutes. Bergey’s manual of systematic bacteriology, 2nd edn. vol 3. Springer, New YorkGoogle Scholar
  22. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464.  https://doi.org/10.1099/00207713-37-4-463 CrossRefGoogle Scholar
  23. Xu K, Yuan Z, Rayner S, Hu X (2015) Genome comparison provides molecular insights into the phylogeny of the reassigned new genus Lysinibacillus. BMC Genom 16:140.  https://doi.org/10.1186/s12864-015-1359-x CrossRefGoogle Scholar
  24. Zhang S, White TL, Martinez MC, McInroy JA, Kloepper JW, Klassen W (2010) Evaluation of plant growth-promoting rhizobacteria for control of phytophthora blight on squash under greenhouse conditions. Biol Control 53:129–135.  https://doi.org/10.1016/j.biocontrol.2009.10.015 CrossRefGoogle Scholar

Copyright information

© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2019

Authors and Affiliations

  1. 1.Pathways Biologic LLCPlant CityUSA
  2. 2.Crop Bioprotection Research Unit, Agricultural Research Service, United States Department of AgricultureNational Center for Agricultural Utilization ResearchPeoriaUSA

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