Identifikasi dan Kekerabatan Rhizobia Pohon Mangium dan Sengon Berdasarkan nodD1 dan nifH
Rhizobia from legumes Acacia mangium (Mangium) and Paraserianthes falcataria (Sengon) have often been isolated and studied for their applications to plants, but studies on the nod and nif genes are still lacking. Even though this plant were often used as a source of paper raw materials and reforestation plants. The aim of this study was to define the genetic relationship of a group of potential strains isolated from tropical legume trees in terms of 16S rRNA, nodD1, and nifH genes. This research method includes the selection of isolates based on the main character of Rhizobiales, to isolate the 16S rRNA, nodD1, and nifH genes from the selected isolates, and to construct a phylogeny tree based on the isolated genes. Two rhizobia were selected based on a selection test, namely DCM 212 from A. mangium and DF13 from P. falcataria. DCM 212 isolate was identified as having the closest similarity to Rhizobium multihospitium CC-13H. The isolate of DF13 had high similarity with Bradyrhizobium elkanii based on 16S rRNA, nodD1, and nifH. The degenerative primer pairs used in this study could not detect nodD1 gene from DCM 212 isolate.
Keywords: Bradyrhizobium, phylogeny, rhizobium
Akter Z, Pageni BB, Lupwayi NZ, Balasubramanian PM. 2014. Biological nitrogen fixation and nifH gene expression in dry beans (Phaseolus vulgaris L.). Canadian Journal Plant Science. 94: 203-212. https://doi.org/10.4141/cjps2013-200
Bala A, Giller KE. 2001. Symbiotic specificity of tropical tree rhizobia for host legumes. New Phytologist. 149(3):495-507. https://doi.org/10.1046/j.1469-8137.2001.00059.x
Bergey, David H. (1994). Bergey's manual of determinative bacteriology (9th ed.). Lippincott Williams & Wilkins. USA.
Bisseling T, Geurts R. 2020. Specificity in legume nodule symbiosis. Science 369(6504):620–621. https://doi.org/10.1126/science.abd3857
Buxton. 2016. Blood agar plates and hemolysis protocols. American society for microbiology. USA. 1-9 pp. https://doi.org/10.1101/pdb.rec088567
Clapp JP, Mansur I, Dodd JC, Jeffries P. 2001. Ribotyping of rhizobia nodulating Acacia mangium and Paraserianthes falcataria from different geographical areas in Indonesia using PCR-RFLP-SSCP (PRS) and sequencing. Environmental Microbiology 3(4):273–280. https://doi.org/10.1046/j.1462-2920.2001.00191.x
Del Cerro P, Rolla-Santos AA, Gomes DF, Marks BB, Pérez-Montaño F, Rodríguez-Carvajal MÁ, Nakatani AS, Gil-Serrano A, Megías M, Ollero FJ, et al.. 2015. Regulatory nodD1 and nodD2 genes of Rhizobium tropici strain CIAT 899 and their roles in the early stages of molecular signaling and host-legume nodulation. BMC Genomics 16(1):251. https://doi.org/10.1186/s12864-015-1458-8
Del Cerro P, Pérez-Montaño F, Gil-Serrano A, López-Baena FJ, Megías M, Hungria M, Ollero FJ. 2017. The Rhizobium tropici CIAT 899 NodD2 protein regulates the production of Nod factors under salt stress in a flavonoid-independent manner. Scientific Reports 7(46712): 1-10. https://doi.org/10.1038/srep46712
Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 5: 113
Fahy PC, Persley GJ. 1983. Plant bacterial diseases; a diagnostic guide. Academic Press, Australia. 393 p.
Fuentes-Romero F, Navarro-Gómez P, Ayala-García P, Moyano-Bravo I, López-Baena F-J, Pérez-Montaño F, Ollero-Márquez F-J, Acosta-Jurado S, Vinardell J-M. 2022. The nodD1 gene of Sinorhizobium fredii HH103 restores nodulation capacity on bean in a Rhizobium tropici CIAT 899 nodD1/nodD2 mutant but the secondary symbiotic regulators nolR, nodD2 or syrM prevent HH103 to nodulate with this legume. Microorganisms 10(1):139. https://doi.org/10.3390/microorganisms10010139
Geneious Prime. 2021.1.1.(https://www.geneious.com)
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology 59(3):307–321. https://doi.org/10.1093/sysbio/syq010
Hernandez-Lucas I, Segovia L, Martinez-Romero E, Pueppke SG. 1995. Phylogenetic relationships and host range of Rhizobium spp. that nodulate Phaseolus vulgaris L. Applied and Environmental Microbiology 61 (7) : 2775-2779. https://doi.org/10.1128/aem.61.7.2775-2779.1995
Hakim S, Imran A, Mirza MS. 2021. Phylogenetic diversity analysis reveals Bradyrhizobium yuanmingense and Ensifer aridi as major symbionts of mung bean (Vigna radiata L.) in Pakistan. Brazilian Journal of Microbiology. 52: 311–324. https://doi.org/10.1007/s42770-020-00397-9
Kaneko T, Maita H, Hirakawa H, Uchiike N, Minamisawa K, Watanabe A, Sato S. 2011. Complete genome sequence of the soybean symbiont Bradyrhizobium japonicum strain USDA6T. Genes 2(4):763-87. https://doi.org/10.3390/genes2040763
Lekatompessy S, Nurjanah L, Sukiman H. 2019. Study of cross inoculation of Rhizobium tropici with other potential soil microbes on their ability to support the growth of soybean. IOP Conference Series: Earth and Environmental Sciences 308. https://doi.org/10.1088/1755-1315/308/1/012041
Mahmud K, Makaju S, Ibrahim R, Missaoui A. 2020. Current progress in nitrogen fixing plants and microbiome research. Plants 9(1):97. https://doi.org/10.3390/plants9010097
Morón B, Soria-Díaz ME, Ault J, Verroios G, Noreen S, Rodríguez-Navarro DN, Gil-Serrano A, Thomas-Oates J, Megías M, Sousa C. 2005. Low pH changes the profile of nodulation factors produced by Rhizobium tropici CIAT899. Chemistry & Biology (9):1029-40. https://doi.org/10.1016/j.chembiol.2005.06.014
Okon Y, Albrecht SL, Burris RH. 1977. Methods for growing Spirillum lipoferum and for counting it in pure culture and in association with plants. Applied Environmental Microbiology 33 (1):85-88. https://doi.org/10.1128/aem.33.1.85-88.1977
Ormeño-Orrillo E, Menna P, Almeida LG, Ollero FJ, Nicolás MF, Pains Rodrigues E, Shigueyoshi Nakatani A, Silva Batista JS, Oliveira Chueire LM, Souza RC, Ribeiro Vasconcelos AT, Megias M, Hungria M, Martínez-Romero E. 2012. Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.). BMC Genomics 13: 735 - 735. https://doi.org/10.1186/1471-2164-13-735
Peck MC, Fisher RF, Long SR. 2006. Diverse flavonoids stimulate nodD1 binding to nod gene promoters in Sinorhizobium meliloti. Journal of Bacteriology 188(15):5417-5427. https://doi.org/10.1128/JB.00376-06
Perrineau MM, Le Roux C, De Faria SM, De Carvalho Balieiro F, Galiana A, Prin Y, Béna G. 2011. Genetic diversity of symbiotic Bradyrhizobium elkanii populations recovered from inoculated and non-inoculated Acacia mangium field trials in Brazil. Systematic and Applied Microbiology 34 (5):376-384. https://doi.org/10.1016/j.syapm.2011.03.003
Purwaningsih R. 2004. Effect of microbe as fertilizer on the growth of Acacia mangium on the sand sterile in green house. Biodiversitas Journal of Biological Diversity 5(2): 85-88. https://doi.org/10.13057/biodiv/d050209
Reeve W, van Berkum P, Ardley J, Tian R, Gollagher M, Marinova D, Elia P, Reddy TBK, Pillay M, Varghese N, Seshadri R, Ivanova N, Woyke T, Baeshen MN, Baeshen NA, Kyrpides N. 2017. High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr. Standards in Genomic Sciences 12:26. https://doi.org/10.1186/s40793-017-0238-2
Risal CP, Djedidi S, Dhakal D, Ohkama-Ohtsu N, Sekimoto H, Yokoyama T. 2012. Phylogenetic diversity and symbiotic functioning in mungbean (Vigna radiata L. Wilczek) bradyrhizobia from contrast agro-ecological regions of Nepal. Systematic and Applied Microbiology 35: 45–53. https://doi.org/10.1016/j.syapm.2011.06.004
Tamura K, Kumar S, Stecher G. 2016. MEGA 7: Molecular evolutionary genetics analysis version 7.0 for bigger data sets. Molecular Biology and Evolution 33: 1870-1874. https://doi.org/10.1093/molbev/msw054
Vincent JM. 1970. A Manual of the Practical study of the root nodule bacteria international biological programme. London. Handbook No 15. 164 p.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. NonCommercial — You may not use the material for commercial purposes.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).