African Journal of
Microbiology Research

  • Abbreviation: Afr. J. Microbiol. Res.
  • Language: English
  • ISSN: 1996-0808
  • DOI: 10.5897/AJMR
  • Start Year: 2007
  • Published Articles: 5233

Full Length Research Paper

Combination of genetic tools to discern Bacillus species isolated from hot springs in South Africa

Jocelyn Leonie Jardine
  • Jocelyn Leonie Jardine
  • Department of Biotechnology, University of Johannesburg, 37 Nind Street, Doornfontein, Gauteng, South Africa.
  • Google Scholar
Eunice Ubomba-Jaswa
  • Eunice Ubomba-Jaswa
  • Water Research Commission, Lynnwood Bridge Office Park, Bloukrans Building, 4 Daventry Street, Lynnwood Manor, Pretoria, South Africa.
  • Google Scholar


  •  Received: 02 February 2019
  •  Accepted: 02 January 2020
  •  Published: 31 August 2020

References

Aanniz T, Ouadghiri M, Melloul M, Swings J, Elfahime E, Ibijbijen J, Ismaili M, Amar, M (2015). Thermophilic bacteria in Moroccan hot springs, salt marshes and desert soils. Brazilian Journal of Microbiology 46(2):443-453.
Crossref

 

Belduz AO, Dulger S, Demirbag Z (2003). Anoxybacillus gonensis sp. nov., a moderately thermophilic, xylose-utilizing, endospore-forming bacterium. International Journal of Systematic and Evolutionary Microbiology 53(5):1315-1320.
Crossref

 
 

Branquinho R, Klein G, Kämpfer P, Peixe LV (2015). The status of the species Bacillus aerophilus and Bacillus stratosphericus. Request for an opinion. International Journal of Systematic and Evolutionary Microbiology 65(3):1101-1101.
Crossref

 
 

Cihan AC (2013). Taxonomic classification of Anoxybacillus isolates from geothermal regions in Turkey by 16S rRNA gene sequences and ARDRA, ITS-PCR, Rep-PCR analyses. Polish Journal of Microbiology 62(2):149-163.
Crossref

 
 

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. Brazilian Journal of Microbiology 43(1):309-324.
Crossref

 
 

Dashti AA, Jadaon MM, Abdulsamad AM, Dashti HM (2009). Heat treatment of bacteria: A simple method of DNA extraction for molecular techniques. Kuwait Medical Journal 41(2):117-122.

 
 

Derekova A, Mandeva R, Kambourova M (2008). Phylogenetic diversity of thermophilic carbohydrate degrading bacilli from Bulgarian hot springs. World Journal of Microbiology and Biotechnology 24(9):1697-1702.
Crossref

 
 

Derekova E, Sjøholm C, Mandeva R, Kambourova M (2007). Anoxybacillus rupiensis sp. nov., a novel thermophilic bacterium isolated from Rupi basin (Bulgaria). Extremophiles 11(4):577-583.
Crossref

 
 

Drancourt M, Raoult D (2005). Sequence-based identification of new bacteria: a proposition for creation of an orphan bacterium repository. Journal of Clinical Microbiology 43(9):4311-4315.
Crossref

 
 

Galkiewicz JP, Kellogg CA (2008). Cross-kingdom amplification using bacteria-specific primers: Complications for studies of coral microbial ecology. Applied and Environmental Microbiology 74(24):7828-7831.
Crossref

 
 

Galtier N, Lobry J (1997). Relationships between genomic GC content, RNA secondary structures, and optimal growth temperature in prokaryotes. Journal of Molecular Evolution 44(6):632-636.
Crossref

 
 

Gerday C (2002). Extremophiles: basic concepts. Series: Knowledge for sustainable development. An insight into the encyclopedia of life support systems, Vol 1. UNESCO Publishing, Paris; EOLSS Publishers, Oxford, UK 1:573-598.

 
 

Ghalib AK, Yasin M, Faisal M (2014). Characterization and metal detoxification potential of moderately thermophilic Bacillus cereus from geothermal springs of Himalaya. Brazilian Archives of Biology and Technology 57(4):554-560.
Crossref

 
 

Goh KM, Chua YS, Rahman RN, Chan R, Illias RM (2011). A comparison of conventional and miniprimer PCR to elucidate bacteria diversity in Malaysia Ulu Slim hot spring using 16S rDNA clone library. Romanian Biotechnological Letters 16:6247-6255.

 
 

Gouy M, Guindon S, Gascuel O (2010). SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27(2):221-224.
Crossref

 
 

Handelsman J (2004). Metagenomics: Application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews 68(4):669-695.
Crossref

 
 

Janda JM, Abbott SL (2007). 16SrRNA gene sequencing for Bacterial identification in the Diagnostic Laboratory: Pluses, Perils and Pitfalls. Journal of Clinical Microbiology 45(9):2761-2764.
Crossref

 
 

Jardine JL (2017). Biotechnology applications of thermophiles isolated from hot-spring water in South Africa related to wastewater bioremediation and water safety. (Dtech Biotechnology), [Unpublished]: University of Johannesburg. .

 
 

Jardine JL, Abia ALK, Mavumengwana V, Ubomba-Jaswa E (2017). Phylogenetic analysis and antimicrobial profiles of cultured emerging and opportunistic pathogens (phyla Actinobacteria and Proteobacteria) identified in hot springs. International Journal of Environmental Research and Public Health 14(9):1070-1088.
Crossref

 
 

Jardine JL, Stoyan S, Mavumengwana V, Ubomba-Jaswa E, (2018). Screening of potential bioremediation enzymes from hot spring bacteria using conventional plate assays and Liquid Chromatography -tandem Mass Spectrophotometry (LC- MS/MS). Journal of Environmental Management 223:787-796.
Crossref

 
 

Khiyami MA, Serour EA, Shehata MM, Bahklia AH (2012). Thermo-aerobic bacteria from geothermal springs in Saudi Arabia. African Journal of Biotechnology 11(16):4053-4062.
Crossref

 
 

Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park S, Jeon Y, Lee J, Yi H, Won S, Chun J (2012). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. International Journal of Systematic and Evolutionary Microbiology 62(3):716-721.
Crossref

 
 

Liu Y, Kumar NR, Lai Q, Du J, Dobritsa AP, Samadpour M, Shao Z (2015). Identification of strains Bacillus aerophilus MTCC 7304T as Bacillus altitudinis and Bacillus stratosphericus MTCC 7305T as a Proteus sp. and the status of the species Bacillus aerius Shivaji et al. 2006. Request for an opinion. International Journal of Systematic and Evolutionary Microbiology 65(9):3228-3231.
Crossref

 
 

Logan NA, Forsyth G, Lebbe L, Goris J, Heyndrickx M, Balcaen A, Verhelst A, Falsen E, Ljunh A, Hansson HB, De Vos P (2002). Polyphasic identification of Bacillus and Brevibacillus strains from clinical, dairy and industrial specimens and proposal of Brevibacillus invocatus sp. nov. International Journal of Systematic and Evolutionary Microbiology 52(3):952-966.
Crossref

 
 

López-López O, Cerdán ME, González-Siso MI (2013). Hot spring metagenomics. Life 3(2):308-320.
Crossref

 
 

Ludwig W, Schleifer K, Whitman WB (2009). Revised road map to the phylum Firmicutes. In: Bergey's Manual® of Systematic Bacteriology, 2nd edn. Springer pp 1-13.
Crossref

 
 

Mandic-Mulec I, Stefanic P, Van Elsas JD (2015). Ecology of Bacillaceae. Microbiology Spectrum 3(2). 
Crossref

 
 

Maughan H, Van der Auwera G (2011). Bacillus taxonomy in the genomic era finds phenotypes to be essential though often misleading. Infection Genetics and Evolution 11(5):789-797.
Crossref

 
 

McGinnis S, Madden TL (2004). BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Research 32:20-25.
Crossref

 
 

Moyer CL, Tiedje JM, Dobbs FC, Karl DM (1996). A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Applied and Environmental Microbiology 62(7):2501-2507.
Crossref

 
 

Muto A, Osawa S (1987). The guanine and cytosine content of genomic DNA and bacterial evolution. Proceedings National Academy of Science USA 84(1):166-169.
Crossref

 
 

Narayan VV, Hatha MA, Morgan HW, Rao D (2008). Isolation and characterization of aerobic thermophilic bacteria from the Savusavu Hot Springs in Fiji. Microbes and Environment 23(4):350-352.
Crossref

 
 

Obeidat M, Khyami-Horani H, Al-Zoubi A, Otri I (2012). Isolation, characterization, and hydrolytic activities of Geobacillus species from Jordanian hot springs. African Journal of Biotechnology 11(25):6763-6768.
Crossref

 
 

Olivier J, Venter J, Jonker C (2011). Thermal and chemical characteristics of hot water springs in the northern part of the Limpopo Province, South Africa. Water South Africa 37(4):427-436.
Crossref

 
 

Oztuk M, Meterelliyoz M (2015). Practical identification of human originated Lactobacillus species by amplified ribosomal DNA restriction analysis (ARDRA) for probiotic use. Molecular Biology Reports 42(8):1323-1332.
Crossref

 
 

Pagaling E, Grant WD, Cowan DA, Jones BE, Ma Y, Ventosa A, Heaphy S (2012). Bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong, China. Extremophiles 16(4):607-618.
Crossref

 
 

Panda AK, Bisht SS, Mandal SD, Kumar MS (2016). Bacterial and archaeal community composition in hot springs from Indo-Burma region, north-east India. AMB Express 6(1):111-123.
Crossref

 
 

Panosyan H, Birkeland N (2014). Microbial diversity in an Armenian geothermal spring assessed by molecular and culture‐based methods. Journal of Basic Microbiology 54(11):1240-1250.
Crossref

 
 

Rahmani S, Forozabdah M, Mosavi M, Rezaee A (2006). Detection of bacteria by amplifying the 16S rRNA gene with universal primers and RFLP. Medical Journal of the Islamic Republic of Iran 19(4):333-338.

 
 

Rai P, Sharma A, Saxena P, Soni A, Chakdar H, Kashyap P, Srivastava A, Sharma A (2015). Comparison of molecular and phenetic typing methods to assess diversity of selected members of the genus Bacillus. Microbiology 84(2):236-246.
Crossref

 
 

Rajendhran J, Gunasekaran P (2011). Microbial phylogeny and diversity: small subunit ribosomal RNA sequence analysis and beyond. Microbiological Research 166(2):99-110.
Crossref

 
 

Rössler D, Ludwig W, Schleifer KH, Lin C, McGill TJ, Wisotzkey JD, Jurtshuk P, Fox G (1991). Phylogenetic diversity in the genus Bacillus as seen by 16S rRNA sequencing studies. Systemic and Applied Microbiology 14(3):266-269.
Crossref

 
 

Sharma A, Jani K, Shouche YS, Pandey A (2014). Microbial diversity of the Soldhar hot spring, India, assessed by analyzing 16S rRNA and protein-coding genes. Annuals of Microbiology 65(3):1323-1332.
Crossref

 
 

Shivaji S, Chaturvedi P, Suresh K, Reddy G, Dutt C, Wainwright M, Narlika J, Bhargava P (2006). Bacillus aerius sp. nov., Bacillus aerophilus sp. nov., Bacillus stratosphericus sp. nov. and Bacillus altitudinis sp. nov., isolated from cryogenic tubes used for collecting air samples from high altitudes. International Journal of Systematic and Evolutionary Microbiology 56:1465-1473.
Crossref

 
 

Sklarz MY, Angel R, Gillor O, Ines M, Soraes M (2009), Evaluating amplified rDNA restriction analysis assay for identification of bacterial communities. Antoinie van Leeuwenhoek 96(4):659-664.
Crossref

 
 

Tekere M, Lötter A, Olivier J, Jonker N, Venter S (2011). Metagenomic analysis of bacterial diversity of Siloam hot water spring, Limpopo, South Africa. African Journal of Biotechnology 10(78):18005-18012.
Crossref

 
 

Tekere M, Prinsloo A, Olivier J, Jonker N, Venter SN (2012). An evaluation of the bacterial diversity at Tshipise, Mphephu and Sagole hot water springs, Limpopo Province, South Africa. African Journal of Microbiology Research 6(23):4993-5004.
Crossref

 
 

Ten LN, Baek SH, Im WT, Liu QM, Aslam Z, Lee ST (2006). Bacillus panaciterrae sp. nov., isolated from soil of a ginseng field. International Journal of Systematic and Evolutionary Microbiology 56(8):2861-2866.
Crossref

 
 

Wahyudi AT, Prasojo BJ, Mubarik RM (2010). Diversity of antifungal compounds-producing Bacillus spp. isolated from rhizosphere of soybean plant based on ARDRA and 16S rRNA. Hayati Journal of Biosciences 17(3):145-150.
Crossref

 
 

Wang H, Xia X, Hickey D (2006). Thermal adaptation of the small subunit ribosomal RNA gene: a comparative study. Journal of Molecular Evolution 63(1):120-126.
Crossref

 
 

Wei W, Davis RE, Lee M, Zhao Z (2007). Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups. International Journal of Systematic and Evolutionary Microbiology 57(8):1855-1867.
Crossref

 
 

Wu X, Walker MJ, Hornitzkey M, Chin J (2006). Development of a group-specific PCR combined with ARDRA for the identification of Bacillus species of environmental significance. Journal of Microbiological Methods 64(1):107-119.
Crossref

 
 

Xu D, Cote JC (2003) Phylogenetic relationships between Bacillus species and related genera inferred from comparison of 3' end 16S rDNA and 5' end 16S-23S ITS nucleotide sequences. International Journal of Systematic and Evolutionary Microbiology 53(3):695-704.
Crossref

 
 

Yamane K, Hattori Y, Ohtagaki H, Fujiwara K (2011). Microbial diversity with dominance of 16S rRNA gene sequences with high GC contents at 74 and 98°C subsurface crude oil deposits in Japan. FEMS Microbiology Ecology 76(2):220-235.
Crossref

 
 

Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer K, Whitman W, Euzeby J, Amann R, Rosello-Mora R (2014). Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Reviews Microbiology 12(9):635-645.
Crossref

 
 

Yıldırım Ä° H, Yıldırım SC, Koçak N (2011). Molecular methods for bacterial genotyping and analyzed gene regions. Journal of Microbiology and Infectious Diseases 1(1):42-46.
Crossref

 
 

Zhang CM, Huang XW, Pan WZ, Zhang J, Wei KB, Klenk HP, Tang S, Li W, Zhang K (2011). Anoxybacillus tengchongensis sp. nov. and Anoxybacillus eryuanensis sp. nov., facultatively anaerobic, alkalitolerant bacteria from hot springs. International Journal of Systematic and Evolutionary Microbiology 61(1):118-122.
Crossref