Full-Length 16S rRNA Gene Amplicon Profiling of Soil Bacterial Communities under Rubber–Canna Intercropping and Rubber Monoculture
DOI:
https://doi.org/10.36722/sst.v11i3.5253Keywords:
Canna Indica, Hevea Brasiliensis, Intercropping System, Rhizosphere BacteriaAbstract
Rubber-based intercropping may modify soil bacterial communities through changes in vegetation cover, root inputs and soil chemistry. This comparative observational study evaluated bacterial-community profiles in rubber–canna (Hevea brasiliensis–Canna indica) intercropping and rubber monoculture plots at PTPN VIII, Subang, West Java. Three spatial soil subsamples per system were collected from 0–20 cm depth. Community DNA was extracted from 0.25 g soil, near-full-length 16S rRNA genes were amplified with 27F/1492R primers and amplicons were sequenced using Oxford Nanopore GridION. Reads were profiled using a Centrifuge/Krona read-based workflow. Shannon diversity was higher in intercropping than monoculture (5.00 ± 0.16 versus 4.78 ± 0.21), whereas Chao1 richness was lower (1575.8 ± 145.8 versus 1778.8 ± 223.6), exploratory Mann–Whitney tests were not significant. The systems shared 2,221 classified taxonomic units, with 531 units only in intercropping and 375 only in monoculture. Proteobacteria relative abundance was higher in intercropping (49%) than monoculture (27%). Soil organic C, total N, available P, Mg and Ca were also descriptively higher in intercropping. These findings indicate contrasting plot-level bacterial and soil-chemical profiles, but independent plot replication and functional validation are needed before causal conclusions are made.
References
[1] Ali, M. I. Ghani, Y. Li, H. Ding, H. Meng, and Z. Cheng, “HiSeq-based molecular characterization of soil microbial community diversity, structure, and predictive functional profiling in continuous cucumber soil affected by diverse cropping systems,” Int. J. Mol. Sci., vol. 20, no. 11, p. 2619, 2019, doi: 10.3390/ijms20112619.
[2] A. Liu, M. Y. Liang, J. W. Tang, Y. Q. Jin, Z. B. Guo, and K. H. M. Siddique, “Challenges of the establishment of rubber-based agroforestry systems: decreases in the diversity and abundance of ground arthropods,” J. Environ. Manage., vol. 292, p. 112747, 2021, doi: 10.1016/j.jenvman.2021.112747.
[3] H. Y. Sasaerila, S. Sakinah, N. Noriko, and R. S. Wijihastuti, “Effects of light environments on leaf traits and phenotypic plasticity of Canna indica,” Biosaintifika, vol. 13, no. 2, pp. 169–177, 2021, doi: 10.15294/biosaintifika.v13i2.30175.
[4] P. N. Karungamye, “Potential of Canna indica in constructed wetlands for wastewater treatment: a review,” Conservation, vol. 2, no. 3, pp. 499–513, 2022, doi: 10.3390/conservation2030034.
[5] N. Ling, T. Wang, and Y. Kuzyakov, “Rhizosphere bacteriome structure and functions,” Nat. Commun., vol. 13, p. 836, 2022, doi: 10.1038/s41467-022-28448-9.
[6] Y. Effendi, N. Aini, A. Pambudi, and H. Y. Sasaerila, “Metagenomics analysis of soil microbial communities in plant agroforestry system rubber tree (Hevea brasiliensis)–Ganyong (Canna sp.),” IOP Conf. Ser. Earth Environ. Sci., vol. 468, p. 012045, 2020, doi: 10.1088/1755-1315/468/1/012045.
[7] W. De Coster, S. D’Hert, D. T. Schultz, M. Cruts, and C. Van Broeckhoven, “NanoPack: visualizing and processing long-read sequencing data,” Bioinformatics, vol. 34, no. 15, pp. 2666–2669, 2018, doi: 10.1093/bioinformatics/bty149.
[8] Kim, L. Song, F. P. Breitwieser, and S. L. Salzberg, “Centrifuge: rapid and sensitive classification of metagenomic sequences,” Genome Res., vol. 26, no. 12, pp. 1721–1729, 2016, doi: 10.1101/gr.210641.116.
[9] J. Gauthier and N. Derome, “Evenness-richness scatter plots: a visual and insightful representation of Shannon entropy measurements for ecological community analysis,” mSphere, vol. 6, no. 2, e01019-20, 2021, doi: 10.1128/mSphere.01019-20.
[10] J. G. Kers and E. Saccenti, “The power of microbiome studies: some considerations on which alpha and beta metrics to use and how to report results,” Front. Microbiol., vol. 12, p. 796025, 2022, doi: 10.3389/fmicb.2021.796025.
[11] M. Hartmann and J. Six, “Soil structure and microbiome functions in agroecosystems,” Nat. Rev. Earth Environ., vol. 4, pp. 4–18, 2023, doi: 10.1038/s43017-022-00366-w.
[12] K. D. Curry et al., “Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data,” Nat. Methods, vol. 19, pp. 845–853, 2022, doi: 10.1038/s41592-022-01520-4.
[13] H. Lin and S. D. Peddada, “Analysis of microbial compositions: a review of normalization and differential abundance analysis,” NPJ Biofilms Microbiomes, vol. 6, p. 60, 2020, doi: 10.1038/s41522-020-00160-w.
[14] K. Dang, X. Gong, G. Zhao, H. Wang, A. Ivanistau, and B. Feng, “Intercropping alters the soil microbial diversity and community to facilitate nitrogen assimilation: a potential mechanism for increasing proso millet grain yield,” Front. Microbiol., vol. 11, p. 601054, 2020, doi: 10.3389/fmicb.2020.601054.
[15] X. Tang et al., “Cassava/peanut intercropping improves soil quality via rhizospheric microbes and increased available nitrogen contents,” BMC Biotechnol., vol. 20, p. 13, 2020, doi: 10.1186/s12896-020-00606-1.
[16] F. Cassán et al., “Everything you must know about Azospirillum and its impact on agriculture and beyond,” Biol. Fertil. Soils, vol. 56, pp. 461–479, 2020, doi: 10.1007/s00374-020-01463-y.
[17] M. Numan et al., “Azospirillum spp. from plant growth-promoting bacteria to their use in bioremediation,” Microorganisms, vol. 10, no. 5, p. 1057, 2022, doi: 10.3390/microorganisms10051057.
[18] M. Akob et al., “Acetylenotrophic and diazotrophic Bradyrhizobium sp. strain I71 from TCE-contaminated soils,” Appl. Environ. Microbiol., vol. 88, no. 22, e01219-22, 2022, doi: 10.1128/aem.01219-22.
[19] M. Billah, M. Khan, A. Bano, T. U. Hassan, A. Munir, and A. R. Gurmani, “Phosphorus and phosphate-solubilizing bacteria: keys for sustainable agriculture,” Geomicrobiol. J., vol. 36, no. 10, pp. 904–916, 2019, doi: 10.1080/01490451.2019.1654043.
[20] S. Fahad et al., “Agroforestry systems for soil health improvement and maintenance,” Sustainability, vol. 14, no. 22, p. 14877, 2022, doi: 10.3390/su142214877.
