Annals of Microbiology

, Volume 64, Issue 3, pp 1081–1088 | Cite as

Lysinibacillus composti sp. nov., isolated from compost

  • Rifat Hayat
  • Iftikhar Ahmed
  • Jayoung Paek
  • Yeseul Sin
  • Muhammad Ehsan
  • Muhammad Iqbal
  • Akira Yokota
  • Young H. Chang
Original Article


A Gram-negative, motile, rod-shaped, endospore-forming bacterial strain, designated as NCCP-36T, was isolated from the compost of fruit and vegetable wastes. The strain NCCP-36T grew within a temperature range of 10–45 C (optimum 28 C) and a pH range of 6.5–8.5 (optimum 7.0), and its cells tolerated <50 mM boron (optimum growth without boron) and 0–5 % NaCl (w/v) in tryptic soya broth medium. Based on comparative analysis of 16S rRNA gene sequence, strain NCCP-36T showed the highest similarity to Lysinibacillus sinduriensis BLB-1T (97.52 %) and L. xylanilyticus XDB9T (96.96 %), and <97 % similarity with other closely related taxa. However, DNA–DNA relatedness between strain NCCP-36T and the closely related type strains of genus Lysinibacillus was ≤37 %. Phylogenetic and chemotaxonomic analyses [major polar lipids: diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phospholipids; predominant menaquinone: MK-7; major cellular fatty acids: iso-C15:0, antieso-C15:0, and iso-C16:0; DNA G+C contents: 37 mol %; Lys-Asp (type A4α) in cell-wall peptidoglycans as diagnostic amino acids] also support the affiliation of strain NCCP-36T to genus Lysinibacillus. Based upon DNA–DNA relatedness as well as distinctive chemotaxonomic, phylogenetic, and genotypic data, we conclude that strain NCCP-36T belongs to a novel species of genus Lysinibacillus, for which the name Lysinibacillus composti sp. nov. is proposed. The type strain is NCCP-36T (JCM 18777T = KCTC 13796T = DSMZ 24785T).


Lysinibacillus composti sp. nov. Compost Cell-wall peptidoglycans 



We gratefully acknowledge the kind help of Dr. Takuji Kudo from JCM, Tsukuba, Japan in the analysis of cell-wall peptidoglycans. This work was partially supported by PSDP Project “Research for Agricultural Development Program (RADP)” funded by Pakistan Agricultural Research Council (PARC) and by the KRIBB Research Initiative Program funded by the Ministry of Education, Science and Technology, Republic of Korea. Initial funds for these studies were provided by the Higher Education Commission of Pakistan under talent training program for young faculty members for training at National Institute for Genomics and Advanced Biotechnology, NARC, Islamabad, Pakistan and also at the Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.

Supplementary material

13213_2013_747_MOESM1_ESM.docx (1.5 mb)
Supplementary Fig. 1 (DOCX 1.52 mb)


  1. Ahmed I, Yokota A, Fujiwara T (2007a) A novel highly boron tolerant bacterium, Bacillus boroniphilus sp. nov., isolated from soil, that requires boron for its growth. Extremophiles 11:217–224PubMedCrossRefGoogle Scholar
  2. Ahmed I, Yokota A, Yamazoe A, Fujiwara T (2007b) 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. doi: 10.1099/ijs.0.63867-0 PubMedCrossRefGoogle Scholar
  3. Albert RA, Archambault J, Lempa M, Hurst B, Richardson C, Gruenloh S, Duran M, Worliczek HL, Huber BE, Rossello-Mora R, Schumann P, Busse HJ (2007) Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov. Int J Syst Evol Microbiol 57(12):2729–2737. doi: 10.1099/ijs.0.65256-0 PubMedCrossRefGoogle Scholar
  4. Ash C, Farrow JAE, Wallbanks S, Collins MD (1991) Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett Appl Microbiol 13(4):202–206. doi: 10.1111/j.1472-765X.1991.tb00608.x CrossRefGoogle Scholar
  5. Ash C, Priest FG, Collins MD (1993) Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie Van Leeuwenhoek 64(3–4):253–260PubMedGoogle Scholar
  6. Chang YH, Han JI, Chun JS, Lee KC, Rhee MS, Kim YB, Bae KS (2002) Comamonas koreensis sp. nov., a non-motile species from wetland in Woopo, Korea. Int J Syst Evol Microbiol 52:377–381. doi: 10.1099/ijs.0.01734-0 PubMedGoogle Scholar
  7. Chang YH, Jung MY, Park IS, Oh HM (2008) Sporolactobacillus vineae sp nov., a spore-forming lactic acid bacterium isolated from vineyard soil. Int J Syst Evol Microbiol 58:2316–2320. doi: 10.1099/ijs.0.65608-0 PubMedCrossRefGoogle Scholar
  8. Claus D, Berkeley RCW (1986) Genus Bacillus Cohn. In: Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer K-H, Whitman WB (eds) Bergey’s manual systematic bacteriology, vol 3: The firmicutes. Williams & Wilkins, Baltimore, pp 1105–1139Google Scholar
  9. 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(5):1121–1127. doi: 10.1099/ijs.0.027995-0 PubMedCrossRefGoogle Scholar
  10. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229CrossRefGoogle Scholar
  11. Farrow JAE, Wallbanks S, Collins MD (1994) Phylogenetic interrelationships of round-spore-forming bacilli containing cell-walls based on lysine and the non-spore-forming genera Caryophanon, Exiguobacterium, Kurthia, and Planococcus. Int J Syst Bacteriol 44(1):74–82PubMedCrossRefGoogle Scholar
  12. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package). Version 3.6. distributed by the author. Department of Genome Sciences, University of Washington, SeattleGoogle Scholar
  13. Glazunova OO, Raoult D, Roux V (2006) Bacillus massiliensis sp. nov., isolated from cerebrospinal fluid. Int J Syst Evol Microbiol 56(Pt 7):1485–1488. doi: 10.1099/ijs.0.63982-0 PubMedCrossRefGoogle Scholar
  14. Hayat R, Ahmed I, Paek J, Ehsan M, Iqbal M, Chang YH (2013) A moderately boron-tolerant candidatus novel soil bacterium Lysinibacillus pakistanensis sp. nov. cand., isolated from soybean (Glycine max L.) rhizosphere. Pak J Bot 45(S1):41–50Google Scholar
  15. Heyndrickx M, Lebbe L, Kersters K, De Vos P, Forsyth C, Logan NA (1998) Virgibacillus: a new genus to accommodate Bacillus pantothenticus (Proom and Knight 1950). Emended description of Virgibacillus pantothenticus. Int J Syst Bacteriol 48:99–106CrossRefGoogle Scholar
  16. Jung MY, Kim J-S, Paek WK, Styrak I, Park I-S, Sin Y, Paek J, Park KA, Kim H, Kim HL, Chang Y-H (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(10):2347–2355. doi: 10.1099/ijs.0.033837-0 PubMedCrossRefGoogle Scholar
  17. Kämpfer P, Rossello-Mora R, Falsen E, Busse HJ, Tindall BJ (2006) Cohnella thermotolerans gen. nov., sp. nov., and classification of 'Paenibacillus hongkongensis' as Cohnella hongkongensis sp. nov. Int J Syst Evol Microbiol 56:781–786. doi: 10.1099/ijs.0.63985-0 PubMedCrossRefGoogle Scholar
  18. Kämpfer P, Martin K, Glaeser SP (2013) Lysinibacillus contaminans sp. nov., isolated from a surface water. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.049593-0 Google Scholar
  19. Kawamoto I, Oka T, Nara T (1981) Cell-wall composition of Micromonospora olivoasterospora, Micromonospora agamiensis, and related organisms. J Bacteriol 146(2):527–534PubMedCentralPubMedGoogle Scholar
  20. Krishnamurthi S, Chakrabarti T, Stackebrand E (2009) Re-examination of the taxonomic position of Bacillus silvestris Rheims et al. 1999 and proposal to transfer it to Solibacillus gen. nov as Solibacillus silvestris comb. nov. Int J Syst Evol Microbiol 59:1054–1058. doi: 10.1099/ijs.0.65742-0 PubMedCrossRefGoogle Scholar
  21. La Duc MT, Satomi M, Venkateswaran K (2004) Bacillus odysseyi sp. nov., a round-spore-forming bacillus isolated from the Mars Odyssey spacecraft. Int J Syst Evol Microbiol 54:195–201. doi: 10.1099/Ijs.0.02747 PubMedCrossRefGoogle Scholar
  22. Lee CS, Jung Y-T, Park S, Oh T-K, Yoon J-H (2010) Lysinibacillus xylanilyticus sp. nov., a xylan-degrading bacterium isolated from forest humus. Int J Syst Evol Microbiol 60(2):281–286. doi: 10.1099/ijs.0.013367-0 PubMedCrossRefGoogle Scholar
  23. Liu H, Song Y, Chen F, Zheng S, Wang G (2013) Lysinibacillus manganicus sp. nov., isolated from manganese mining soil. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.050492-0 Google Scholar
  24. Logan NA, Berge O, Bishop AH, Busse HJ, De Vos P, Fritze D, Heyndrickx M, Kampfer P, Rabinovitch L, Salkinoja-Salonen MS, Seldin L, Ventosa A (2009) Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 59(8):2114–2121. doi: 10.1099/ijs.0.013649-0 PubMedCrossRefGoogle Scholar
  25. Marmur J (1963) A procedure for the isolation of deoxyribonucleic acid from microorganisms. Method Enzymol 6:726–738. doi: 10.1016/0076-6879(63)06240-6 CrossRefGoogle Scholar
  26. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic-acid by high-performance liquid-chromatography. Int J Syst Bacteriol 39(2):159–167CrossRefGoogle Scholar
  27. Miwa H, Ahmed I, Yokota A, Fujiwara T (2009) Lysinibacillus parviboronicapiens sp nov., a low-boron-containing bacterium isolated from soil. Int J Syst Evol Microbiol 59:1427–1432. doi: 10.1099/ijs.0.65455-0 PubMedCrossRefGoogle Scholar
  28. Priest FG, Goodfellow M, Todd C (1988) A numerical classification of the genus Bacillus. J Gen Microbiol 134:1847–1882PubMedGoogle Scholar
  29. Rheims H, Fruhling A, Schumann P, Rohde M, Stackebrandt E (1999) Bacillus silvestris sp. nov., a new member of the genus Bacillus that contains lysine in its cell wall. Int J Syst Bacteriol 49:795–802PubMedCrossRefGoogle Scholar
  30. Roohi A, Ahmed I, Iqbal M, Jamil M (2012) Preliminary isolation and characterization of halotolerant and halophilic bacteria from salt mines of Karak, Pakistan. Pak J Bot 44(SI 1):365–370Google Scholar
  31. Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36(4):407–477PubMedCentralPubMedGoogle Scholar
  32. Seiler H, Scherer S, Wenning M (2013) Lysinibacillus meyeri sp. nov., isolated from a medical practice. Int J Syst Evol Microbiol 63(Pt 4):1512–1518. doi: 10.1099/ijs.0.039420-0 PubMedCrossRefGoogle Scholar
  33. Shida O, Takagi H, Kadowaki K, Komagata K (1996) Proposal for two new genera, Brevibacillus gen nov and Aneurinibacillus gen nov. Int J Syst Bacteriol 46(4):939–946PubMedCrossRefGoogle Scholar
  34. Stakebrandt E, Goebel BM (1994) 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 44:846–849Google Scholar
  35. Stackebrandt E, Swiderski J (2008) From phylogeny to systematics: the dissection of the genus Bacillus. In: Berkeley R, Heyndrickx M, Logan N, De Vos P (eds) Applications and systematics of Bacillus and relatives. Blackwell Science Ltd, Oxford, pp 8–22. doi: 10.1002/9780470696743.ch2 Google Scholar
  36. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi: 10.1093/molbev/msr121 PubMedCentralPubMedCrossRefGoogle Scholar
  37. Tindall BJ (1990) A comparative-study of the lipid-composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13(2):128–130CrossRefGoogle Scholar
  38. Wainø M, Tindall BJ, Schumann P, Ingvorsenl K (1999) Gracilibacillus gen. nov., with description of Gracilibacillus halotolerans gen. nov., sp. nov. ; transfer of Bacillus dipsosauri to Gracilibacillus dipsosauri comb. nov., and Bacillus salexigens to the genus Salibacillus gen. nov., as Salibacillus salexigens comb. nov. Int J Syst Bacteriol 49:821–831PubMedCrossRefGoogle Scholar
  39. Wisotzkey JD, Jurtshuk P Jr, Fox GE, Deinhard G, Poralla K (1992) Comparative sequence analyses on the 16S rRNA (rDNA) of Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus and proposal for creation of a new genus, Alicyclobacillus gen. nov. Int J Syst Bacteriol 42(2):263–269PubMedCrossRefGoogle Scholar
  40. Xie CH, Yokota A (2003) Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 49(6):345–349. doi: 10.2323/Jgam.49.345 PubMedCrossRefGoogle Scholar
  41. Yang LL, Huang Y, Liu J, Ma L, Mo MH, Li WJ, Yang FX (2012) Lysinibacillus mangiferihumi sp. nov., a new bacterium producing nematicidal volatiles. Antonie Van Leeuwenhoek 102(1):53–59. doi: 10.1007/s10482-012-9712-4
  42. Yoon JH, Weiss N, Lee KC, Lee IS, Kang KH, Park YH (2001) Jeotgalibacillus alimentarius gen. nov., sp nov., a novel bacterium isolated from jeotgal with L-lysine in the cell wall, and reclassification of Bacillus marinus Ruger 1983 as Marinibacillus marinus gen. nov., comb. nov. Int J Syst Evol Microbiol 51:2087–2093PubMedCrossRefGoogle Scholar
  43. Zhang L, Xu Z, Patel BK (2007) Bacillus decisifrondis sp. nov., isolated from soil underlying decaying leaf foliage. Int J Syst Evol Microbiol 57(5):974–978. doi: 10.1099/ijs.0.64440-0 PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg and the University of Milan 2013

Authors and Affiliations

  • Rifat Hayat
    • 1
    • 2
    • 4
  • Iftikhar Ahmed
    • 1
  • Jayoung Paek
    • 3
  • Yeseul Sin
    • 3
  • Muhammad Ehsan
    • 1
    • 2
  • Muhammad Iqbal
    • 1
  • Akira Yokota
    • 4
  • Young H. Chang
    • 3
  1. 1.National Culture Collection of Pakistan (NCCP), National Institute for Genomics and Advanced Biotechnology (NIGAB)National Agricultural Research Centre (NARC)IslamabadPakistan
  2. 2.Department of Soil Science & SWCPir Mehr Ali Shah Arid Agriculture UniversityRawalpindiPakistan
  3. 3.Korean Collection for Type Cultures, Biological Resources CentreKorea Research Institute of Bioscience and Biotechnology (KRIBB)Yuseong-gu, DaejeonRepublic of Korea
  4. 4.Institute of Molecular and Cellular BiosciencesUniversity of TokyoBunkyo-Ku, TokyoJapan

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