Isolation, identification, and detection of ACC deaminase gene-encoding rhizobacteria from rhizosphere of stressed pineapple
Dori Kusuma Jaya(1), Giyanto Giyanto(2*), Novik Nurhidayat(3), Sarjiya Antonius(4)
(1) Graduate School of Soil and Environmental Biotechnology, Department of Soil Science and Landresources, Faculty of Agriculture, Bogor Agricultural University, Jalan Ulin, Babakan, Kampus IPB Dramaga, Bogor 16680, Indonesia
(2) Department of Plant Protection, Faculty of Agriculture, Bogor Agricultural University, Jalan Kamper, Babakan, Kampus IPB Dramaga, Bogor 16680, Indonesia
(3) Research Center for Botany and Microbiology, Indonesian Institute of Sciences, Jalan Raya Bogor Km 46, Cibinong, Bogor 16911, Indonesia
(4) Research Center for Botany and Microbiology, Indonesian Institute of Sciences, Jalan Raya Bogor Km 46, Cibinong, Bogor 16911, Indonesia
(*) Corresponding Author
Abstract
ACC deaminase is a microbial cytoplasmic enzyme that cleaves ACC, a precursor of ethylene, in the stressed plant. The aims of this study were to isolate, identify, and detect the presence of ACC deaminase gene-encoding rhizobacteria from the rhizospheric soil of pineapple plants that have been exposed to abiotic and biotic stress, specifically herbicide, flooding, and Phytophthora spp. stress. A total of 49 rhizobacterial isolates were obtained, seven of which were observed for their growth on DF medium containing 3 mM L-1 ACC. The four best-growing isolates were selected for genomic DNA extraction. They were molecularly identified as Stenotrophomonas maltophilia (3), Burkholderia territorii (2A), Pseudomonas oryzihabitans (5B), and Bacillus tropicus (1E). A set of primers, 105F-acdS 5’-TGCCAAGCGTGAAGACTGC-3’ and 244R-acdS 5’-GGGTCTGGTTCGACTGGAT-3’, were constructed to amplify the ACC deaminase gene (acdS). Based on melt peak curve analysis, four products appeared to show a specific single peak at 86, 89, 87, and 89.5°C, indicating a single product was produced. In addition, a Blast search showed that these four products met the ACC deaminase feature and their acdS sequences were clustered into an ancestral group compared with the bacterial strains deposited in GenBank. These results suggest that ACC deaminase gene-encoding rhizobacteria from a pineapple plantation of tropical origin may affect the acdS sequences and may contribute to the host plant’s stress tolerance.
Keywords
Full Text:
PDFReferences
Bal HM, Das S, Dangar TK, Adhya TK. 2013. ACC deaminase and IAA producing growth promoting bacteria from the rhizosphere soil of tropical rice plants. Journal of Basic Microbiology. 53, 972-984.
Bray EA, Bailey-Serres J, Weretilnyk E. 2000. “Responses to abiotic stresses,” in Biochemistry and Molecular Biology of Plants, eds W. Gruissem, B. Buchannan, and R. Jones Rockville MD: American Society of Plant Physiologists. 1158-1249.
Dorak MT. 2006. Real time PCR. Newcastle (GB): Taylor and Francis Group, UK.
Duan J, Müller KM, Charles TC, Vesely S, Glick BR. 2009. 1-Aminocyclopropane-1-carboxylate (ACC) deaminase genes in rhizobia from southern Saskatchewan. Microbial Ecology. 57:423–436.
Dwight Z, Palais R, Wittwer CT. 2011. uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application. Bioinformatics. 27(7):1019–1020.
Glick BR, Penrose DM, Li J. 1998. A model for the lowering of plant ethylene concentrations by plant growth-promoting bacteria. Journal of Theoritical Biology. 190:63-68.
Glick BR, Cheng Z, Czarny J, Duan J. 2007. Promotion of plant growth by ACC deaminase-producing soil bacteria. European Journal of Plant Pathology. 119:329-339.
Glick BR. 2014. Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiological Research. 169:30-39.
Hanna SE, Connor CJ, Wang HH. 2005. Real-time polymerase chain reaction for the food microbiologist: technologies, applications, and limitations. Journal of Food Science. 70:49–53.
Honma M, Shimomura T. 1978. Metabolism of 1-aminocyclopropane-1-carboxylate deaminase. Agricultural Biology and Chemistry. 42:1825-1831.
Kaur G, Kumar S, Nayyar H, Upadhyaya HD. 2008. Cold stress injury during the pod-filling phase in chickpea (Cicer arietinum L.): effects on quantitative and qualitative components of seeds. Jorunal of Agronomy and Crop Science. 194(6):457-464.
Kende H. 1993. Ethylene biosynthesis. Annual Review of Plant Physiology and Molecular Biology. 44:283-307.
Kwak MJ, Song JY, Kim SY, Jeong H, Kang SG, Kim BK, Kwon SK, Lee CH, Yu DS, Park SH, Kim JF. 2012. Complete genome sequence of the endophytic bacterium Burkholderia sp. strain KJ006. Journal of Bacteriology. 24:1385-1391.
Lane DJ. 1991. 16S/23S rRNA sequencing. In Stackebrandt E, Good fellow M (eds). Nucleic Acid Techniques in Bacterial Systematics. New York: John Wiley and Sons. 115-75.
Li Z, Siping C, Shuting Y, Mingyue C, Li L, Yuanyuan L, Shuying L, Qianli A. 2015. Differentiation of 1-aminocycylopropane-1-carboxylate (ACC) deaminase from its homologs is the key for identifying bacteria producing ACC deaminase. FEMS Microbiology Ecology. Vol 91, No. 10.
Ma W, Guniel FC, Glick BR. 2003. Rhizobium leguminosorum biovarviciae 1-aminocyclopropane-1-carboxylate deaminase promotes nodulation of pea plants. Applied Environmental Microbiology. 69:4396-4402.
Mehnaz S, Baig DN, Lazarovits G. 2010. Genetic and phenotypic diversity of plant growth promoting rhizobacteria isolated from sugarcane plants growing in Pakistan. Journal of Microbiology and Biotechnology. 20:1614-1623.
Misra S, Vijay KD, Mohammad HK, Shashank KM, Gyanendra D, Sumit Y, Alok L, Puneet SC. 2017. Exploitation of agro-climate environment for selection of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase producing salt tolerant indigenous plant growth promoting rhizobacteria. Microbiological Research. 205:25-34.
Nascimento FX, Rossi MJ, Soares CRFS, McConkey BJ, Glick BR. 2014. New insights into 1-aminocyclopropane-1-carbocylate (ACC) deaminase phylogeny, evolution and ecological significance. PLoS ONE. 9:e99168.
Penrose DM, Glick BR. 2003. Methods for isolating and characterizing ACC deaminase-producing plant growth-promoting rhizobacteria. Physiologia Plantarum. 118:10–5.
Poritz MA, Ririe KM. 2014. Getting Things Backwards to Prevent Primer Dimers. Journal of Molecular Diagnostic. 16(2):159-62.
Singh RP, Ganesh MS, Anil K, Prabhat NJ. 2015. Biochemistry and genetics of ACC deaminase: a weapon to “stress ethylene” produced in plants. Frontier in Microbiology. Vol. 6, No. 937.
Singh RP, Jha PN. 2017. The PGPR Stenotrophomonas maltophilia SBP-9 Augments Resistence against Biotic and Abiotic Stress in Wheat Plants. Plants Frontier Microbiology. 8:1945.
Taghavi S, Garafola C, Monchy S, Newman L, Hoffman A, Weyens N, Barac T, Vangronsveld J, vander Lelie D. 2009. Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees. Applied Environmental Microbiology. 75:748–757.
Thakur P, Kumar S, Malik JA, Berger JD, Nayyar H. 2010. Cold stress effects on reproductive development in grain crops: an overview. Environmental and Experimental Botany. 67(3):429-443.
Timmusk S, Paalme V, Pavlicek T, Bergquist J, Vangala A, Danilas T, Nevo E. 2011. Bacterial distribution in the rhizosphere of wild barley under contrasting microclimates. PLoS ONE 6:e17968.
Toouli CD, Turner DR, Grist SA. 2000. The effect of cycle number and target size on polymerase chain reaction amplification of polymorphic repetitive sequences. Analytical Biochemistry. 280:324–326.
Varma A, Lynette A, Dietrich W, Rudiger H. 2004. Plant Surface Microbiology. Springer-Verlag Berlin Heidelberg.
Weilharter A, Mitter B, Shin MV, Chain PS, Nowak J, Sessitsch A. 2011. Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN. Journal of Bacteriology. 193:3383-3384.
DOI: https://doi.org/10.22146/ijbiotech.39018
Article Metrics
Abstract views : 5597 | views : 3864Refbacks
- There are currently no refbacks.
Copyright (c) 2019 The Author(s)
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.