Study of bioinformatics and phylogenetic relationship of Iranian Bacillus thuringiensis strains by using 16S rDNA gene sequence
Subject Areas :
Bacteriology
Maryam Rashki
1
,
Mojtaba Mortazavi
2
1 - Department of Biodiversity, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
2 - Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
Received: 2021-12-22
Accepted : 2022-05-10
Published : 2022-06-05
Keywords:
polymerase chain reaction,
Bioinformatics,
blast,
Software,
16S rDNA,
Abstract :
Background & Objectives: Gram-positive bacterium, Bacillus thuringiensis, produces protein crystals with insecticidal properties. Partial rDNA sequence analysis is used to study the evolution and classification of living organisms. The study was conducted on 16S rDNA sequence of five native isolates of Bacillus thuringiensis using the polymerase chain reaction technique.
Materials & Methods: Characteristics and phylogenetic relationships between five sequences of native isolates along with other isolates in the gene bank and other species of the genus Bacillus were performed with Mesquite software and leBIBIQBPP database.
Results: The five native isolates were 92.06 to 99.93% similar to each other and 99.73% to 100% similar to other isolates of Bacillus thuringiensis. Phylogenetic trees showed Bt 1019, Bt 1020 and Bt 1039 in the first group and Bt 1001 and Bt 1091 in the second group. Based on Bt 1001 sequence analysis using leBIBIQBPP, the minimum distance with Bacillus frigoritolerans was obtained. The sequence of Bacillus anthracis was close to Bt 1019. The Bt 1020 sequence was closest to Bacillus cereus. In the case of Bt 1039, in addition to Bacillus cereus, the lowest distance was observed with Bacillus marcorinectum. The Bt 1091 sequence showed the most similarity with Bacillus frigoritolerans.
Conclusion: Protein crystals were observed in the native bacteria. Toxic crystals are produced only by Bacillus thuringiensis. BLAST program for 16S rDNA gene sequence in the native isolates also showed the most similarity to Bacillus thuringiensis isolates in the gene bank. Moreover, the results predicted that the three native isolates Bt 1019, Bt 1020 and Bt 1039 could be toxic against lepidopteran pests and two isolates Bt 1001 and Bt 1091 could be toxic against coleopteran pests.
References:
References
Ibarra JE, Del Rincon MC, Orduz S, Noriega D, Benintende G, Monnerat R, Regis L, De Oliveira CM, Lanz H, Rodriguez MH, Sanchez J, Pena G, Bravo A. Diversity of Bacillus thuringiensis strains from Latin America with insecticidal activity against different mosquito species. Appl Environ Microbiol. 2003; 69: 5269-5274.
Crickmore N, Zeigler DR, Schnepf E, Van Rie J, Lereclus D, Baum J, Bravo A, Dean DH. Revision of the nomenclature for the Bacillus thuringiensis pesticidal crystal proteins. Microbiol Mol Biol Rev. 2004; 62 (3): 807–813.
Nazarian A, Jahangiri R, Salehi Jouzani Gh, Seifinejad A, Soheilivand S, Bagheri O, Keshavarzi M, Alamisaeid Kh. Coleopteran-specific and putative novel cry genes in Iranian native Bacillus thuringiensis collection. J invertebr pathol. 2009; 102: 101-109.
Beron CM, Curatti L, Salerno GL. New strategy for identification of novel cry-type genes from Bacillus thuringiensis strains. Appl Environ Microbiol. 2005; 71 (2): 761–765.
Tamez-Guerra P, Damas G, Iracheta MM, Oppert B, Gomez-Flores R, Rodriguez-Padilla C. Differences in susceptibility and physiological fitness of Mexican field Trichoplusia ni strains exposed to Bacillus thuringiensis. J Econ Entomol. 2006; 99: 937–945.
Woo PCY, Lau SKP, Teng JLL, Tse H, Yuen KY. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect. 2008; 14: 908-934.
Goto K, Jiang W, Zheng Q, Oku Y, Kamiya H, Itoh T, Ito M. Epidemiology of Helicobacter infection in wild rodents in the Xinjiang-Uygur autonomous region of China. Curr Microbiol. 2004; 49: 221-223.
Ticknor LO, Kolstø AB, Hill KK, Keim P, Laker MT, Tonks M, Jackson PJ. Fluorescent amplified fragment length polymorphism analysis of Norwegian Bacillus cereus and Bacillus thuringiensis soil isolates. Appl Environ Microbiol. 2001; 67:4863-73.
Devulder G, Perrie`re G, Baty F, Flandrois JP. BIBI, a bioinformatics bacterial identification tool. J Clin Microbiol. 2003; 41: 1785–1787.
Travers RS, Martin PAW, Reichelderfer CF. Selective process for efficient isolation of soil Bacillus spp. Appl Environ Microbiol. 1987; 53(6): 1263-1266.
Yılmaz S, Ayvaz A, Akbulut M, Azizoglu U, Karabörklü S. A novel Bacillus thuringiensis strain and its pathogenicity against three important pest insects. J Stored Prod Res. 2012; 51: 33-40.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30: 772-780.
Maddison W, Maddison D. Mesquite: a modular system for evolutionary analysis. Version 3.10. 2015; Avaliable from: http://mesquiteproject.
Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE, A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015; 32: 268-274.
Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006; 23(2): 254-267.
Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004; 14(6): 1188-1190.
Flandrois JP, Perriére G, Gouy M. leBIBIQBPP: a set of database and a webtool for automatic phylogenetic analysis of prokaryotic sequences. BMC Bioinformatics, 2015; 16, 10.1186/s12859-015-0692-z.
Forsyth G, Logan NA. Isolation of Bacillus thuringiensis from Northern Victoria Land, Antarctica. Appl Microbiol. 2000; 30: 263-266.
Apaydin O, Yenidunya AF, Harsa S, Gunes H. Isolation and characterization of Bacillus thuringiensis strains from different grain habitats in Turkey. World J Microbiol Biotechnol. 2004; 21: 285-292.
Cinar C, Apaydin O, Yenidunya AF, Harsa S, Gunes H. Isolation and characterization of Bacillus thuringiensis strains from olive-related habitats in Turkey. J Appl Microbiol. 2008; 515-525.
Drobniewski FA. Bacillus cereus and related species. Clin Microbiol Rev. 1993; 6: 324-338.
Ash C, Farrow JAE, Dorsch M, Stackebrandt E, Collins MD. Comparative analysis of Bacillus anthracis, Bacillus cereus, and related species on the basis of reverse transcriptase sequencing of 16S rRNA. Int J Syst Evol Microbiol. 1991; 41:343–346.
von Wintzingerode F, Rainey FA, Kroppenstedt RM, Stackebrandt E. Identification of environmental strains of Bacillus mycoides by fatty acid analysis and species-specific 16S rDNA oligonucleotide probe. FEMS Microbiol Ecol. 1997; 24(3): 201-209.
Bourque SN, Valero JR, Mercier J, Lavoie MC, Levesque RC. Multiplex polymerase chain reaction for detection and differentiation of the microbial insecticide Bacillus thuringiensis. Appl Environ Microbiol. 1993; 59:523-527.
te Giffel MC, Beumer RR, Granum PE, Rombouts FM. Isolation and characterisation of Bacillus cereus from pasteurized milk in household refrigerators in The Netherlands. Int J Food Microbiol. 1997; 34: 307-318.
Debode F, Janssen E, Bragard C, Berben G. Detection by real-time PCR and pyrosequencing of the Cry1Ab and Cry1Ac genes introduced in GM constructs. Food Addit Contam Part A. 2017; 34(8): 1-23.
El-kersh TA, Al-sheikh YA, Al-akeel RA, Alsayed AA. Isolation and characterization of native Bacillus thuringiensis isolates from Saudi Arabia. Afr J Biotechnol. 2012; 11(8):1924-1938.
Banik A, Chattopadhyay A, Ganguly S, Mukhopadhyay SK. Characterization of a tea pest specific Bacillus thuringiensis and identification of its toxin by MALDI-TOF mass spectrometry. Ind Crops Prod. 2019; 137: 549-556.
Camacho-Millána R, Aguilar-Medina EM, Quezada H, Medina-Contreras Ó, Patino-López G, Cárdenas-Cota, HM, Ramos-Payán R. Characterization of Cry toxins from autochthonous Bacillus thuringiensis isolates from Mexico. Bol Med Hosp Infant Mex. 2017; 74(3): 193-199.
Elleuch J, Tounsi S, B Ben Hassen, N, Lacoix MN, Chandre F, Jaoua S, Zghal RZ. Characterisation of novel Bacillus thuringiensis isolates against Aedes aegypti (Diptera: Culicidae) and Ceratitis capitata (Diptera: Tephridae). J Invertebr Pathol. 2015; 124: 90-97.
Selvakumar G, Sushi SN, Stanley J, Mohan M. Brevibacterium frigoritolerans a novel entomopathogen of Anomala dimidiata and Holotrichia longipennis (Scarabaeidae: Coleoptera). Biocontrol Sci Technol. 2011; 21(7): 821-827.
Han Y, Chen F, Li N, Zhu B, Li X. Bacillus marcorestinctum sp. nov., a novel soil acylhomocerine lactone quorum-sensing sinal quenching bacterium. Int. J. Mol. Sci. 2010; 11(2): 507-520.
Seki T, Chung CK, Mikami H, Oshima Y. Deoxyribonucleic acid homology and taxonomy of the genus Bacillus. Int J Syst Evol Microbiol. 1978; 28: 182-189.
Granum PE, Brynestad S, Kramer JM. Analysis of enterotoxin production by Bacillus cereus from dairy products, food poisoning incidents and non-gastrointestinal infections. Int J Food Microbiol. 1993; 17: 269-279.
Yamada S, Ohashi E, Agata N, Venkateswaran K. Cloning and Nucleotide Sequence Analysis of gyrB of Bacillus cereus, B. thuringiensis, B. mycoides, and B. anthracis and their application to the detection of B. cereus in rice. Appl Environ Microbiol. 1999; 65(4): 1483-1490.
_||_References
Ibarra JE, Del Rincon MC, Orduz S, Noriega D, Benintende G, Monnerat R, Regis L, De Oliveira CM, Lanz H, Rodriguez MH, Sanchez J, Pena G, Bravo A. Diversity of Bacillus thuringiensis strains from Latin America with insecticidal activity against different mosquito species. Appl Environ Microbiol. 2003; 69: 5269-5274.
Crickmore N, Zeigler DR, Schnepf E, Van Rie J, Lereclus D, Baum J, Bravo A, Dean DH. Revision of the nomenclature for the Bacillus thuringiensis pesticidal crystal proteins. Microbiol Mol Biol Rev. 2004; 62 (3): 807–813.
Nazarian A, Jahangiri R, Salehi Jouzani Gh, Seifinejad A, Soheilivand S, Bagheri O, Keshavarzi M, Alamisaeid Kh. Coleopteran-specific and putative novel cry genes in Iranian native Bacillus thuringiensis collection. J invertebr pathol. 2009; 102: 101-109.
Beron CM, Curatti L, Salerno GL. New strategy for identification of novel cry-type genes from Bacillus thuringiensis strains. Appl Environ Microbiol. 2005; 71 (2): 761–765.
Tamez-Guerra P, Damas G, Iracheta MM, Oppert B, Gomez-Flores R, Rodriguez-Padilla C. Differences in susceptibility and physiological fitness of Mexican field Trichoplusia ni strains exposed to Bacillus thuringiensis. J Econ Entomol. 2006; 99: 937–945.
Woo PCY, Lau SKP, Teng JLL, Tse H, Yuen KY. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect. 2008; 14: 908-934.
Goto K, Jiang W, Zheng Q, Oku Y, Kamiya H, Itoh T, Ito M. Epidemiology of Helicobacter infection in wild rodents in the Xinjiang-Uygur autonomous region of China. Curr Microbiol. 2004; 49: 221-223.
Ticknor LO, Kolstø AB, Hill KK, Keim P, Laker MT, Tonks M, Jackson PJ. Fluorescent amplified fragment length polymorphism analysis of Norwegian Bacillus cereus and Bacillus thuringiensis soil isolates. Appl Environ Microbiol. 2001; 67:4863-73.
Devulder G, Perrie`re G, Baty F, Flandrois JP. BIBI, a bioinformatics bacterial identification tool. J Clin Microbiol. 2003; 41: 1785–1787.
Travers RS, Martin PAW, Reichelderfer CF. Selective process for efficient isolation of soil Bacillus spp. Appl Environ Microbiol. 1987; 53(6): 1263-1266.
Yılmaz S, Ayvaz A, Akbulut M, Azizoglu U, Karabörklü S. A novel Bacillus thuringiensis strain and its pathogenicity against three important pest insects. J Stored Prod Res. 2012; 51: 33-40.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30: 772-780.
Maddison W, Maddison D. Mesquite: a modular system for evolutionary analysis. Version 3.10. 2015; Avaliable from: http://mesquiteproject.
Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE, A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015; 32: 268-274.
Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006; 23(2): 254-267.
Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004; 14(6): 1188-1190.
Flandrois JP, Perriére G, Gouy M. leBIBIQBPP: a set of database and a webtool for automatic phylogenetic analysis of prokaryotic sequences. BMC Bioinformatics, 2015; 16, 10.1186/s12859-015-0692-z.
Forsyth G, Logan NA. Isolation of Bacillus thuringiensis from Northern Victoria Land, Antarctica. Appl Microbiol. 2000; 30: 263-266.
Apaydin O, Yenidunya AF, Harsa S, Gunes H. Isolation and characterization of Bacillus thuringiensis strains from different grain habitats in Turkey. World J Microbiol Biotechnol. 2004; 21: 285-292.
Cinar C, Apaydin O, Yenidunya AF, Harsa S, Gunes H. Isolation and characterization of Bacillus thuringiensis strains from olive-related habitats in Turkey. J Appl Microbiol. 2008; 515-525.
Drobniewski FA. Bacillus cereus and related species. Clin Microbiol Rev. 1993; 6: 324-338.
Ash C, Farrow JAE, Dorsch M, Stackebrandt E, Collins MD. Comparative analysis of Bacillus anthracis, Bacillus cereus, and related species on the basis of reverse transcriptase sequencing of 16S rRNA. Int J Syst Evol Microbiol. 1991; 41:343–346.
von Wintzingerode F, Rainey FA, Kroppenstedt RM, Stackebrandt E. Identification of environmental strains of Bacillus mycoides by fatty acid analysis and species-specific 16S rDNA oligonucleotide probe. FEMS Microbiol Ecol. 1997; 24(3): 201-209.
Bourque SN, Valero JR, Mercier J, Lavoie MC, Levesque RC. Multiplex polymerase chain reaction for detection and differentiation of the microbial insecticide Bacillus thuringiensis. Appl Environ Microbiol. 1993; 59:523-527.
te Giffel MC, Beumer RR, Granum PE, Rombouts FM. Isolation and characterisation of Bacillus cereus from pasteurized milk in household refrigerators in The Netherlands. Int J Food Microbiol. 1997; 34: 307-318.
Debode F, Janssen E, Bragard C, Berben G. Detection by real-time PCR and pyrosequencing of the Cry1Ab and Cry1Ac genes introduced in GM constructs. Food Addit Contam Part A. 2017; 34(8): 1-23.
El-kersh TA, Al-sheikh YA, Al-akeel RA, Alsayed AA. Isolation and characterization of native Bacillus thuringiensis isolates from Saudi Arabia. Afr J Biotechnol. 2012; 11(8):1924-1938.
Banik A, Chattopadhyay A, Ganguly S, Mukhopadhyay SK. Characterization of a tea pest specific Bacillus thuringiensis and identification of its toxin by MALDI-TOF mass spectrometry. Ind Crops Prod. 2019; 137: 549-556.
Camacho-Millána R, Aguilar-Medina EM, Quezada H, Medina-Contreras Ó, Patino-López G, Cárdenas-Cota, HM, Ramos-Payán R. Characterization of Cry toxins from autochthonous Bacillus thuringiensis isolates from Mexico. Bol Med Hosp Infant Mex. 2017; 74(3): 193-199.
Elleuch J, Tounsi S, B Ben Hassen, N, Lacoix MN, Chandre F, Jaoua S, Zghal RZ. Characterisation of novel Bacillus thuringiensis isolates against Aedes aegypti (Diptera: Culicidae) and Ceratitis capitata (Diptera: Tephridae). J Invertebr Pathol. 2015; 124: 90-97.
Selvakumar G, Sushi SN, Stanley J, Mohan M. Brevibacterium frigoritolerans a novel entomopathogen of Anomala dimidiata and Holotrichia longipennis (Scarabaeidae: Coleoptera). Biocontrol Sci Technol. 2011; 21(7): 821-827.
Han Y, Chen F, Li N, Zhu B, Li X. Bacillus marcorestinctum sp. nov., a novel soil acylhomocerine lactone quorum-sensing sinal quenching bacterium. Int. J. Mol. Sci. 2010; 11(2): 507-520.
Seki T, Chung CK, Mikami H, Oshima Y. Deoxyribonucleic acid homology and taxonomy of the genus Bacillus. Int J Syst Evol Microbiol. 1978; 28: 182-189.
Granum PE, Brynestad S, Kramer JM. Analysis of enterotoxin production by Bacillus cereus from dairy products, food poisoning incidents and non-gastrointestinal infections. Int J Food Microbiol. 1993; 17: 269-279.
Yamada S, Ohashi E, Agata N, Venkateswaran K. Cloning and Nucleotide Sequence Analysis of gyrB of Bacillus cereus, B. thuringiensis, B. mycoides, and B. anthracis and their application to the detection of B. cereus in rice. Appl Environ Microbiol. 1999; 65(4): 1483-1490.
