Diversity and phylogenetic profiling of niche-specific Bacilli from extreme environments of India
- 860 Downloads
The diversity of culturable, aerobic and heterotrophic Bacillus and Bacillus-derived genera (BBDG) was investigated in various extreme environments (including thermal springs, cold deserts, mangroves, salt lakes, arid regions, salt pans and acidic soils) of India. Heat treatment followed by enrichment in different media led to a total of 893 bacterial isolates. Amplified ribosomal DNA restriction analysis (ARDRA) using three restriction enzymes AluI, MspI and HaeIII led to the clustering of these isolates into 12–74 groups for the different sites at 75 % similarity index, adding up to 559 groups. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 392 bacilli, grouped in two families, Bacillaceae (89.03 %) and Paenibacillaceae (10.97 %), and included 13 different genera with 75 distinct species. It was found that among the thirteen genera, nine (Bacillus, Halobacillus, Lysinibacillus, Oceanobacillus, Pontibacillus, Salinibacillus, Sediminibacillus, Thalassobacillus and Virgibacillus) belonged to Bacillaceae and four (Ammoniphilus, Aneurinibacillus, Brevibacillus and Paenibacillus) belonged to Paenibacillaceae. Novel isolates tolerant to low and high pH and temperature, salt and low moisture were identified. The major outcome of the present investigation was the identification of niche-specific species and also the ubiquitous presence of selected species of BBDG, which illustrate the diversity and pervasive nature of BBDG in extreme environments.
KeywordsARDRA Bacillus Bacillus derived genera 16S rRNA gene Extreme habitats
The authors are grateful to the Division of Microbiology, Indian Agricultural Research Institute (IARI), New Delhi and the National Agricultural Innovation Project (NAIP), Indian Council of Agricultural Research for providing the facilities and financial support to undertake these investigations. There are no conflicts of interest.
The experiments undertaken comply with the current laws of India, the country where the investigation was undertaken.
- Cihan AC, Tekin N, Ozcan B, Cokmus C (2012) The genetic diversity of genus Bacillus and the related genera revealed by 16S rRNA Gene sequences and ARDRA analyses isolated from geothermal regions of turkey. Braz J Microbiol 309–324Google Scholar
- Claus D, Berkeley RCW (1986) Genus Bacillus. In: Sneath PHA, Mair NS, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 2. The Williams and Wilkins, Baltimore, pp 1105–1140Google Scholar
- Fortina MG, Pukall R, Schumann P, Mora D, Parini C, Manachini PL, Stackebrandt E (2001) Ureibacillus gen. nov., a new genus to accommodate Bacillus thermosphaericus (Anderson et al. 1995), amendation of Ureibacillus thermosphaericus and description of Ureibacillus terrenus sp. nov. Int J Syst Evol Microbiol 51:447–455CrossRefPubMedGoogle Scholar
- Hengstmann U, Chin K, Janssen PH, Liesack W (1999) Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from anoxic rice paddy soil. Appl Environ Microbiol 511:5050–5058Google Scholar
- Khan M, Patel CB (2007) Plant growth promoting effect of Bacillus firmus strain NARS1 isolated from central Himalayan region of India on Cicer arientnum at low temperature. Egypt Afr Crop Sci Soc 8:1179–1181Google Scholar
- Kumar M, Yadav AN, Tiwari R, Prasanna R, Saxena AK (2013) Deciphering the diversity of culturable thermotolerant bacteria from Manikaran hot springs. Ann Microbiol. doi: 10.1007/s13213-013-0709-7.
- Larkin JM, Stokes JL (1966) Isolation of psychrophilic species of Bacillus. J Bacteriol 915:1667–1671Google Scholar
- Mohamed EAH, Abe M, Ghanem KM, Abdel-Fattah YR, Nakagawa Y, El-Helow ER (2006) Diversity of Bacillus genotypes in soil samples from El-Omayed biosphere reserve in Egypt. J Cult Collect 5:78–84Google Scholar
- Nazina TN, Tourova TP, Poltaraus AB, Novikova EV, Grigoryan AA, Ivanova AE, Lysenko AM, Petrunyaka VV, Osipov GA, Belyaev SS (2001) Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. thermocatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans. Int J Syst Evol Microbiol 51:433–446PubMedGoogle Scholar
- Priest FG (1993) Systematics and ecology of Bacillus. In: Sonenshein AL, Hoch JA, Losick R (eds) Bacillus subtilis and other gram-positive bacteria: biochemistry, physiology, and molecular genetics. American Society of Microbiology, Washington, pp 3–16Google Scholar
- Sahay H, Mahfooz S, Singh AK, Singh S, Kaushik R, Saxena AK, Arora DK (2012) Exploration and characterization of agriculturally and industrially important haloalkaliphilic bacteria from environmental samples of hyper saline Sambhar lake, India. World J Microbiol Biotechnol 28:3207–3217CrossRefPubMedGoogle Scholar
- Singh AK, Tripathi BM, Sahay H, Singh RN, Kaushik R, Saxena AK, Arora DK (2010) Biochemical and molecular characterization of thermo-alkali tolerant xylanase producing bacteria from thermal springs of Manikaran. Indian J Microbiol 50:2–9. doi: 10.1007/s12088-010-0071-4 CrossRefPubMedCentralPubMedGoogle Scholar
- Spring S, Ludwig W, Marquez MC, Ventosa A, Schleifer KH (1996) Halobacillus gen. nov., with descriptions of Halobacillus litoralis sp. nov. and Halobacillus trueperi sp. nov., and transfer of Sporosarcina halophila to Halobacillus halophilus comb. nov. Int J Syst Bacteriol 46:492–496CrossRefGoogle Scholar
- Srinivas TNR, Rao SN, Reddy PVV, Pratibha MS, Sailaja B, Kavya B, Kishore KH, Begum Z, Singh SM, Shivaji S (2009) Bacterial diversity and bio prospecting for cold-active lipases, amylases and proteases, from culturable bacteria of Kongsfjorden and Ny-Ålesund, Svalbard, Arctic. Curr Microbiol 59:537–54CrossRefPubMedGoogle Scholar
- Tambekar DH, Dhundale VR (2012) Studies on the physiological and cultural diversity of bacilli characterized from Lonar lake (MS) India. Biosci Discov 3:34–39Google Scholar
- Verma P, Yadav AN, Kazy SK, Saxena AK, Suman A (2013) Elucidating the diversity and plant growth promoting attributes of wheat (Triticum aestivum) associated acidotolerant bacteria from southern hills zone of India. Natl J Life Sci 10:219–226Google Scholar
- Waino M, Tindall BJ, Schumann P, Ingvorsen 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 49:821–831CrossRefPubMedGoogle Scholar
- Wisotzkey JD, Jurtshuk JRP, 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 42:263–269CrossRefPubMedGoogle Scholar
- Yoon J-H, Kang S-J, Schumann P, Oh T-K (2010) Jeotgalibacillus salarius sp. nov., isolated from a marine saltern, and reclassification of Marinibacillus marinus and Marinibacillus campisalis as Jeotgalibacillus marinus comb. nov. and Jeotgalibacillus campisalis comb. nov., respectively. Int J Syst Evol Microbiol 60:15–20CrossRefPubMedGoogle Scholar
- Zaitsev GM, Tsitko IV, Rainey FA, Trotsenko YA, Uotila JS, Stackebrandt E, Salkinoja-Salonen MS (1998) New aerobic ammonium-dependent obligately oxalotrophic bacteria: description of Ammoniphilus oxalaticus gen. nov., sp. nov. and Ammoniphilus oxalivorans gen. nov., sp. nov. Int J Syst Bacteriol 48:151–163CrossRefPubMedGoogle Scholar