K2 a Newly Isolated Strain of Bacillus amyloliquefaciens Regulates Responsive Proteins for Its Survival and Promotes Plant Growth of Rice Seedlings against Bacterial Leaf Blight and Salt Stresses
Keywords:Halophilic bacteria, Phylogenetic analysis, Xanthomonas oryzae pv. oryzae, High-throughput proteome analysis
Soil salinity limits the growth and productivity of crop plants worldwide including Thailand. Plant growth promoting rhizobacteria (PGPR) can elicit plant tolerance against both biotic and abiotic (adverse-environmental effects) stresses that may become an alternative process in crop management system. In this study, a new PGPR strain is hypothesized whether it can adapt to high salt concentrations and promote seedling growth of rice against Xanthomonas oryzae pv. oryzae (Xoo), causal organism of bacterial leaf blight, under salt stress that might correlate with its biosynthesis of stress-responsive proteins production. Forty eight bacteria were isolated from different salt -soil lands, and strain K2 (obtained from mangrove plant rhizosphere at Bangkrachao, Samut Prakan) was selected for further investigation based on its superior in biocontrol activity and survival in nutrient broth (NB) plus 12% NaCl which indicated that K2 was a halophilic bacterium. Strain K2 was identified using physiological and biochemical properties, 16s rRNA and gyrB nucleotide sequencing analysis revealed that K2 was placed in Bacillus amyloliquefaciens. Culture filtrates of strain K2 grown in NB with or without 5%NaCl for 24 h were subjected to proteomic analysis. Strain K2 and its culture filtrates exhibited a good performance in Xoo suppression shown by plate assay, and increased growth enhancement of rice seedlings (root length and shoot height) under both normal and salt-stress conditions. Of the shotgun proteomic LC-MS/MS identified proteins, the specific proteins were up-regulated in K2 – salinity grown cells. A key role for proteins predominantly expressed in above analysis was likely mediating plant health tolerated to Xoo and salt stresses. Those involving proteins included the iron scavenging and transport, defense mechanism, the synthesis and transport of compatible solutes, protein expression in protecting K2 survival and adaptation, biocontrol activity, plant growth promotion, and induced salt tolerance was discussed.
Amin, M., Z. Rakhisi, and A. Z. Ahmady. 2015. Isolation and identification of Bacillus species from soil and evaluation of their antibacterial properties. Avicenna J. Clin. Microbiol. Infect. 2(1): e23233.
Amoozegar, M. A., C. Sa´nchez-Porro, R. Rohban, M. Hajighasemi, and A. Ventosa. 2009. Bacillus persepolensis sp. nov., a moderately halophilic bacterium from a hypersaline lake. Int. J. Syst. Evol. Microbiol. 59: 2352–2358.
Arahal, D.R., R.H. Vreeland, and C.D. Litchfield.2007. Recommended minimal standards for describing new taxa of the family Halomonadaceae. Int J Syst Evol Microbiol. 57(10): 2436-2446.
Ash, C., J.A.E. Farrow, S. Wallbanks, and M.D. Collins. 1991. Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small‐subunit‐ribosomal RNA sequences. Lett. Appl. Microbiol. 13(4): 202-206.
Ausubel, F. M., R. Brent, R. E. Kingston, D.D. Moore, J.G. Seidman, J. A. Smith, and
K. Struh. 1987. Current protocols in molecular biology. John Wiley and Sons, Inc., Media, PA.
Bano, A. and M. Fatima. 2009. Salt tolerance in Zea mays (L.) following inoculation with Rhizobium and Pseudomonas. Biol. Fertility Soils. 45: 405-413.
Belbahri L., F. N. Alenezi, L. Luptakova, M. E. Rateb, and S. Woodward. 2015. Complete genome sequence of Aneurinibacillus migulanus E1, a Gramicidin S- and D-phenylalanyl-l-propyl diketopiperazine-deficient mutant. Genome Announc. 3: 1441–1415.
Boottanun P., C. Potisap, J. G. Hurdle, and H.R. Sermswan. 2017. Secondary metabolites from Bacillus amyloliquefaciens isolated from soil can kill Burkholderia pseudomallei. AMB Express. 7:16 doi.org/10.1186/s13568-016-0302-0.
Canovas D., C. Vargas, S. Kneip, M.J. Moron, A. Ventosa, E. Bremer, and J.J. Nieto. 2000. Genes for the synthesis of the osmoprotectant glycine betaine from choline in the moderately halophilic bacterium Halomonas elongate DSM 3043. Microbiol.146:455–463.
Cappuccino, J.C. and N. Sherman. 2004. A Laboratory Manual. Microbiology 7th. Pearson Education Publication, New Dehli, India.
Chauhan, P.S., C. Lata, S. Tiwari, A.S. Chauhan, S.M. Kumar, L. Agrawal, D. Chakrabarty, and C. S. Nautiyal. 2019. Transcriptional alterations reveal Bacillus amyloliquefaciens-rice cooperation under salt stress. Sci Rep 9: 11912. https://doi.org/10.1038/s41598-019-48309-8.
Chen, T. H. and N. Murata. 2011. Glycine betaine protects plants against abiotic stress: mechanisms and biotechnological applications. Plant Cell Environ. 34: 1–20.
Chen, X. H., A. Koumoutsi, R. Scholz, A. Eisenreich, K. Schneider, I. Heinemeyer, B. Morgenstern, B. Voss, W. R. Hess, O. Reva, H. Junge, B. Voigt, P. R. Jungblut, J. Vater, R. Süssmuth, H. Liesegang, A. Strittmatter, G. Gottschalk, and R. Borriss. 2007. Comparative analysis of the complete genome sequence of the plant growth–promoting bacterium Bacillus amyloliquefaciens FZB42. Nat. Biotechnol. 25(9): 1007-1014.
Christensen, K.K., H.S. Jensen, F.Ø. Andersen, C. Wigand, and M. Holmer. 1998. Interferences between root plaque formation and phosphorus availability for isoetids in sediments of oligotrophic lakes. Biogeochem. 43: 107–128.
Cole, J. R., K. Konstantinidis, R.J. Farris, and J.M. Tiedje. 2010.Microbial diversity and phylogeny: extending from rRNAs to genomes. Environmental Molecular Microbiology. pp.1-20. Ed. by W.T. Liu and J. K. Jansson. Calster Academic Press Norfolk UK.
Dodd, I.C and F. Perez-Alfocea. 2012. Microbial alleviation of crop salinity. J. Exp. Bot. 63: 3415-3428.
Egamberdieva, D., S. Wirth, S. D. Bellingrath-Kimura, J. Mishra, and N. K. Arora. 2019. Salt-tolerant plant growth promoting rhizobacteria for enhancing crop productivity of saline soils. Front. Microbiol. 10: 2791.
Ertekin, O., M. Kutnu, A.A. Taşkin, M. Demir, A. Y. Karatas, and G. Ozcengiz. 2020. Analysis of a bac operon-silenced strain suggests pleiotropic effects of bacilysin in Bacillus subtilis. J Microbiol. 58, 297–313
FAO and ITPS. 2015. Status of world’s soil Resources (SWSR) – Main Report. Rome: Food and Agriculture Organization of the United Nations and Intergovernmental Technical Panel on Soils.
Ferreira, L.J., V. Azevedo, J. Maroco, M. M. Oliveira, and A. P. Santos. 2015. Salt tolerant and sensitive rice varieties display differential methylome flexibility under salt stress. PLoS ONE 10(5): e0124060.
Genuchten, M.T. and S.K. Gupta, 1993. A reassessment of the crop tolerance response function. J. Indian Soc. Soil Sci. 41(4): 730–737.
Grover, M., Ali, S. Z., Sandhya, V., Rasul, A., and Venkateswarlu, B. 2011. Role of microorganisms in adaptation of agriculture crops to abiotic stresses. World J. Microbiol. Biotechnol. 27, 1231–1240.
Hashem, A., E.F. Abd_Allah, A.A. Alqarawi, A. Al Huqail Asma, D. Egamberdieva, and S. Wirth. 2016. Alleviation of cadmium stress in Solanum lycopersicum L. by arbuscular mycorrhizal fungi via induction of acquired systemic tolerance. Saudi J. Biol. Sci. 23(2): 271–281.
Hillmann, F., R.J. Fischer and H. Bahl. 2006. The rubrerythrin-like protein Hsp21 of
Clostridium acetobutylicum is a general stress protein. Arch. Microbiol. 185: 270-276.
Holt, J.G., N.R. Krieg, P.H.A. Sneath, J.T. Staley and S.T. Williams. 1994. Bergey’s Manual of Determinative Bacteriology 9th. Baltimore: The Williams and Wilkins Co.
Huang J., R. Hirji, L. Adam, K.L. Rozwadowski, J.K. Hammerlindl, W.A. Keller and G. Selvaraj. 2000. Genetic engineering of glycinebetaine production toward enhancing stress tolerance in plants: metabolic limitations. J. Plant Physiol.122:747–756.
Idriss, E.E., O. Makarewicz, F. Abd-ElAziem, D. Kristin, G. Ralf, B. Helmut, and R. Thomas. 2002. Extracellular phytase activity of Bacillus amyloliquefaciens FZB45 contributes to its plant-growth-promoting effect. Microbiol. 148(7): 2097-2109.
Joung, K. B. and J. C. Cote. 2002. A single phylogenetic analysis of Bacillus thuringiensis strains and bacilli species inferred from 16S rRNA gene restriction fragment length polymorphism is congruent with two independent phylogenetic analyses. J. Appl. Microbiol. 93: 1075–1082.
Kannan, N. 2002. Laboratory Manual in General Microbiology, Pima publishing In Co. New Delhi, India.
Kheoruenromne, I. 2007. Saline Soil in Thailand. KU Press. Bangkok (In Thai)
Kloepper, J.W. and M. N. Schroth. 1981. Relationship of vitro antibiosis of plant growth – promoting rhizobacteria to plant growth and the displacement of root microflora. Phytopathol. 71: 1020 -1024.
Krasensky, J. and C. Jonak. 2012. Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks. J. Exp. Bot. 63 (4): 1593-608.
Li, R., T. Chaicherdsakul, V. Kunathigan, S. Roytrakul, A. Paemanee, and S. Kittisenachai. 2020. Shotgun proteomic analysis of germinated rice (Oryza sativa L.) under salt stress. Appl. Sci. Eng. Progress. 13(1): 76-85.
Ludwig, W., E. Dumont, M. Meybeck, M. Meybeck, S. Heussner, and S. Heussner. 2009. River discharges of water and nutrients to the Mediterranean and Black Sea: Major drivers for ecosystem changes during past and future decades?. PROG OCEANOGR 80(3): 199-217.
Lugtenberg, B. and F. Kamilova. 2009. Plant-growth-promoting rhizobacteria. Ann. Rev. Microbiol. 63(1): 541-556.
Lutts, S., J.M. Kinet and J. Bouharmont. 1995. Changes in plant response to NaCl during development of rice (Oryza sativa L.) varieties differing in salinity resistance. J. Exp. Bot. 46:1843–1852.
Mark A. Schneegurt. 2012. Media and conditions for the growth of halophilic and halotolerant bacteria and archaea. Advances in Understanding the Biology of Halophilic Microorganisms. R. H. Vreeland (ed.) USA.
Mendpara, J., V. Parekh, S. Vaghela, A. Makasana, P. D.Kunjadia, G. Sanghvi, D.Vaishnav, and G.S. Dave. 2013. Isolation and characterization of high salt tolerant bacteria from agricultural soil. Euro. J. Exp. Bio. 3(6):351-358.
Miethke, M., O. Klotz, U. Linne, J. J. May, C. L. Beckering, and M. A. Marahiel. 2006. Ferri-bacillibactin uptake and hydrolysis in Bacillus subtilis. Mol. Microbiol. 61(6): 1413–1427.
Murray, R. G. E., R. N. Doetsch, and F. Robinow. 1994. Determinative and cytological light microscopy. Methods for General and Molecular Bacteriology, pp. 21–41. Washington, DC. USA.
Oleg, N. R., C. Dixelius, J. Meijer, F. G. Priest. 2004. Taxonomic characterization and plant colonizing abilities of some bacteria related to Bacillus amyloliquefaciens and Bacillus subtilis, FEMS Microbiol. Eco. 48(2) 249–259.
Prathuangwong, S. and N. Buensanteai. 2007. Bacillus amyloliquefaciens induced systemic resistance against bacterial pustule pathogen with increased phenols, peroxides, and 1,3-ᵦ-glucanase in soybean plant. Acta Phytopathol. Entomol. Hung. 42: 321-330.
Prathuangwong, S., W. Chuaboon, S. Kasem, D. Athinuwat, K. Suyama, and H. Negishi. 2009. Potential for application time of Pseudomonas fluorescens SP007s and biofertilizer for alternaria leaf spot management of Chinese kale. In Proc. of the ISSAAS International Congress. Feb. 23 -27, 2009. Bangkok.
Prathuangwong, S., W. Chuaboon., T. Chatnaparat., L. Kladsuwan., M. Choorin and S. Kasem. 2012. Induction of Disease and Drought Resistance in Rice by Pseudomonas fluorescens SP007s. CMU J. Nat. Sci. 11(1):45-56.
Prathuangwong, S., D. Athinuwat, W. Chuaboon, T. Chatnaparat and N. Buensanteai. 2013. Bioformulation Pseudomonas fluorescens SP007s against dirty panicle disease of rice. Afr. J. Microbiol. Res. 7(4): 5274-5283.
Priest, F. G., M. Goodfellow, and C. Todd. 1988. A numerical classification of the genus Bacillus. J Gen Microbiol 134: 1847–1882.
Roberts, M.F. 2005. Organic compatible solutes of halotolerant and halophilic microorganism. Saline Systems 1: 1-30.
Rubiano-Labrador, C., C., Bland, G. Miotello, J. Armengaud, S. Baena. 2015. Salt stress induced changes in the exoproteome of the halotolerant bacterium Tistlia consotensis deciphered by proteogenomics. PLoS ONE 10(8): e0135065.
Saengsanga, T., C. Aukaew, and K. Rodsanthia. 2017. Effects of Salt Stress on the Germination and Early Seedling Growth of Rice (Oryza sativa L.). NUJST. 25(1): 92-101.
Sakamoto, A., N. Murata. 2002. The role of glycine betaine in the protection of plants from stress: clues from transgenic plants. Plant Cell Environ. 25:163–171.
Sangwanna, M., P. Seeniang and S. Patarapuwadol. 2018. Survey of Bacterial Blight Disease and the Need of Knowledge in Disease Management in Organic Rice System in Roi Et Province. Agri. Sci. J. 49(3): 230–240.
Singh M., N.K. Sharma, S.B. Prasad, S.S. Yadav, G. Narayan and A.K. Rai. 2013. The freshwater cyanobacterium Anabaena doliolum transformed with ApGSMT-DMT exhibited enhanced salt tolerance and protection to nitrogenase activity, but became halophilic. Microbiol. 159: 641–648.
Skerman, V.B., V. McGowan, and P.H.A. Sneath. 1989. Approved Lists of Bacterial Names. ASM Press. Washington (DC).
Sulaiman, A., S. Kasem and S. Prathuangwong. 2013. Heat Shock and Stress Response in Rice-Bacteria Interaction for Improving Seedling Vigor. 28-31 p. In Proc. Seminar on Natural Resources Adaptation to the Global Climate Change. Bangkok.
Tamura K., G. Stecher, D. Peterson , A. Filipski, and S. Kumar. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30: 2725–2729.
Timmusk, S., A. Islam, A El-Daim, L. Copolovici, T.Tanilas, A. Kännaste, L. Behers, E. Nevo, G. Seisenbaeva, E Stenström, and Ü. Niinemets. 2014. Drought-tolerance of wheat improved by rhizosphere bacteria from harsh environments: enhanced biomass production and reduced emissions of stress volatiles. PLOS ONE 9(5): e96086. doi:10.1371/journal.pone.0096086.
Todaka D., K. Nakashima , K. Maruyama, S. Kidokoro, Y. Osakabe, and Y. Ito. 2012. Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress. Proc. Natl. Acad. Sci. USA. doi:109 15947–15952 10.1073/pnas.1207324109.
Tunsagool, P., W. Jutidamrongphan, N. Phaonakrop, J. Jaresitthikunchai, S. Roytrakul, and W. Leelasuphakul. 2019. Insights into stress responses in mandarins triggered by Bacillus subtilis cyclic lipopeptides and exogenous plant hormones upon Penicillium digitatum infection. Plant Cell Reports 38(5) doi: 10.1007/s00299-019-02386-1.
Upadhyay, S.K., D.P. Singh, and R. Saikia. 2009. Genetic diversity of plant growth promoting rhizobacteria isolated from rhizospheric soil of wheat under saline condition. Curr. Microbiol.59: 489-496.
Vandamme, P., B. Pot, M. Gillis, P. de Vos, K.Kersters, and J. Swings. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev. 60(2): 407–438.
Ventosa, A., J. J. Nieto, and A. Oren. 1998. Biology of moderately halophilic aerobic bacteria. Microbiol. Mol. Biol. Rev. 62: 504–544.
Waditee R., M.N.H. Bhuiyan, V. Rai, K. Aoki, Y. Tanaka, T. Hibino, S. Suzuki, J. Takano, A.T. Jagendorf, and T. Takabe. 2005. Genes for direct methylation of glycine provide high levels of glycine betaine and abiotic-stress tolerance in Synechococcus and Arabidopsis. In Proc. The National Academy of Sciences of the United States of America 102:1318–1323.
Wang, Q. F., W. Li, Y. L. Liu, H. H. Cao, Z. Li, and G. Q. Guo. 2007. Bacillus qingdaonensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a crude sea-salt sample collected near Qingdao in eastern China. Int J Syst Evol Microbiol. 57: 1143–1147.
Wang, W., M. Sun, W. Liu, and B. Zhang. 2008. Purification and characterization of a psychrophilic catalase from Antarctic Bacillus. Can. J. Microb. 54(10):823-8.
Wargo, M.J. 2013. Homeostasis and catabolism of choline and glycine betaine: Lessons from Pseudomonas aeruginosa. Appl. Environ. Microbiol 79(7): 2112-2120.
Watt, P. M. and I. D. Hickson. 1994. Structure and function of type II DNA topoisomerases. Biochem. J. 303: 681-695.
Woese, C.R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. PNAS. 87(12): 4576-4579.
Woese, C. R. 1987. Bacterial evolution. Microbiol Rev. 51(2): 221–271.
Wu, L., H. Wu, L. Chen, S. Xie, H. Zang, R. Borriss, and X. Gao. 2014. Bacilysin from Bacillus amyloliquefaciens FZB42 has specific bactericidal activity against harmful algal bloom species. Appl Environ Microbiol. 80 (24): 7512-7520.
Wu, L., H. Wu, L. Chen, X. Yu, R. Borriss and X. Gao. 2015. Difficidin and bacilysin from Bacillus amyloliquefaciens FZB42 have antibacterial activity against Xanthomonas oryzae rice pathogens. Sci Rep. 5: 12975e.
Yamamoto, S. and S. Harayama. 1995. PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol. 61(10): 3768.
Yang, J., J. Kloepper, and C. Ryu. 2009. Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci. 14: 1–4.
Yoshida, S., S. Hiradate, T. Tsukamoto, K. Hatakeda, A. Shirata. 2001. Antimicrobial activity of culture filtrate of Bacillus amyloliquefaciens RC-2 isolated from mulberry leaves. Phytopathology 91(2):181-187.
Zaprasis, A., J. Brill, M. Thüring, G. Wünsche, M. Heun, H. Barzantny, T. Hoffmann, E. Bremer. 2012. Osmoprotection of Bacillus subtilis through import and proteolysis of proline-containing peptides. Appl Environ Microbiol. 79 (2): 576-587.
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