Soil fungal diversity profile of the sugarcane plantations in Lampung and South Sumatra, Indonesia
DOI:
https://doi.org/10.22302/iribb.jur.mp.v94i1.707Keywords:
Metagenomics Analysis, Soil Fungal Profile, SugarcaneAbstract
As a high-value commodity, sugarcane harvesting areas in Indonesia have been declining year after year. Metagenomic studies on sugarcane plantation land are expected to provide an overview of land suitability for sustainable sugarcane production. This study investigated soil fungal communities in two sugarcane plantations, Bunga Mayang (BUMA) and Cinta Manis (CIMA), in Lampung and South Sumatra, respectively, using high-throughput ITS1 gene sequencing. Chemical and biological analyses were conducted on soils with depths of 0-20 cm and 20- 40 cm on plant cane (PC) and ratoon cane (RC) categories. The results showed that plantation land in South Sumatra (CIMA) had higher organic carbon and total nitrogen concentrations than in Lampung (BUMA). However, in several other parameters, such as P2O5, K2O, and microbial population, the BUMA farm has higher values with lower pH. Metagenomic analysis revealed the differences in microbial dominance between the plantation areas. Sugarcane fields in Lampung were dominated by the genus Protrudomyces, Coralloidiomyces, and Spizellomyces, while South Sumatra was dominated by the genus Lichtheimia, Phyctochytrium, and Spizellomyces. In the RC category, Lichtheimia corymbifera is the most dominant species in both the BUMA (RC-B) and CIMA (RC-C) plantations. However, in the PC category, BUMA (PC-B) is dominated by Protrudomyces lateralis, meanwhile CIMA (PC-C) is dominated by Phlyctochytrium californicum. The alpha diversity values of the two areas did not significantly different, with low Trichoderma populations. Thus, sugarcane fields in the two locations differ in microbial composition, which is thought to be influenced by different technical cultures and environmental conditions.
Downloads
References
Ajilogba, C.F., Olanrewaju, O.S., & Babalola, O.O. (2022). Plant growth stage drives the temporal and spatial dynamics of the bacterial microbiome in the rhizosphere of Vigna subterranea. Frontiers in Microbiology. 13, 825377. https://doi.org/10.3389/fmicb.2022.825377
Aziz, M.A., Fitriyah, F., Wahyuni, S., Arisandy, P., Fadila, H., Siregar, V.M.R., Sulastri, Luktyansyah, I.M., Priyono, & Siswanto (2024). Humic acid enriched with urea and NPK factory by-products promoted the growth and yield of Saccharum officinarum L. Agricultural Science, 9(1), 9-21
Balai Penelitian Tanah, (2009). Petunjuk Teknis Edisi 2: analisis kimia tanah, tanaman, air, dan pupuk. Bogor: Balai Penelitian Tanah
Bamisile, B.S., Akutse, K.S., Siddiqui, J.A., & Xu, Y. (2022). Model application of entomophatogenic fungi as alternatives to chemical pesticides: Prospects, challenges, and insights for next-generation sustainable agriculture. Front. Plant. Sci., 12. https://doi.org/10.3389/fpls.2021.741804
Bello, A., Wang, B., Zhao, Y., Yang, W., Ogundeji, A., Deng, L., Egbaegu, U.U., Yu, S., Zhao, L., Li, D., & Xu, X. (2021). Composted biochar affects structural dynamics, function and co-occurrence network patterns of fungal communities. Science of the Total Environment, 775, 145672. https://doi.org//10.1016/j.scitotenv.2021.145672
Breidenbach, B., Blaser, M.B., Klose, M., & Conrad, R. (2016). Crop rotation of flooded rice with upland maize impacts the resident and active methanogenic microbial community. Environmental Microbiology, 18(9), 2868-85. https://doi.org/10.1111/1462-2920.13041
Coster, W.D., D'Hert, S., Schultz, D.T., Cruts, M., & Broeckhoven C.V. (2018). NanoPack: visualizing and processing long-read sequencing data. Bioinformatics, 34(15), 2666-2669. https://doi.org/10.1093/bioinformatics/bty149
Diacono, M., & Montemurro, F. (2021). Long-term effects of organic amendments on soil fertility. Sustainable Agriculture, 30(2), 401-422. https://doi.org/10.1007/978-94-007-0394-0_34
Fallah. N., Pang, Z., Zhang, C., Tayyub, M., Yang, Z., & Lin, Z. (2023). Complementary effects of biochar, secondary metabolites, and bacteria biocontrol agents rejuvenate ratoon sugarcane traits and stimulate soil fertility. Industrial Crops Products, 202, 117081. https://doi/10.1016/j.indcrop.2023.117081
Galitskaya, P., Biktasheva, L., Saveliev, A., Grigoryeva, T., Boulygina, E., & Selivanovskaya, S. (2017). Fungal and bacterial successions in the process of co-composting of organic wastes as revealed by 454 pyrosequencing. Plos One, 12(10):e186051. https://doi/10.1371/journal.pone.0186051
Gschwend, F., Aregger, K., Gramlich, A., Walter, T., Widmer, F. (2020). Periodic waterlogging consistently shapes agricultural soil microbiomes by promoting specific taxa. Applied Soil Ecology, 155,103623. https://doi.org/10.1016/j.apsoil.2020.103623
Gunarto, L. (2000). Rhizosphere microbes: their roles and potential. Journal of Agricultural Research and Development, 19(2), 39-48
Jacoby, R., Peukert, M., Succurro, A., Koprivova, A., & Kopriva, S. (2017). The role of soil microorganisms in plant mineral nutrition-current knowledge and future directions. Frontiers in Plant Science, 8(1617). https://doi.org/10.3389/fpls.2017.01617
Kim, D., Song, L., Breitwieser, F.P., & Salzberg, S.L. (2016). Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research, 26(12), gr.210641.116. https://doi.org/10.1101/gr.210641.116
Leelastwattanagul, O., Sutheeworapong, S., Khoiri, A.N., Dulsawat, S., Wattanachaisaereekul, S., Tachaleat, A., Duangfoo, T., Paenkaew, P., Prommeenate, P., Cheevadhanarak, S., & Jirakkakil, J. (2023). Soil microbiome analysis reveals effects of periodicwaterlogging stress on sugarcane growth. PLoS ONE, 18(11), https://doi.org/10.1371/journal.pone.0293834
Li, R., Khafipour, E., Krause, D.O., Entz, M.H., Kievit, T.R., & Fernando, W.G.D. (2012). Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities. PLoS One, 7(12), e51897. https://doi.org/10.1371/journal.pone.0051897
Li, Y., & Yang, L.T. (2015). Sugarcane agriculture and sugar industry in China. Sugar Tech, 17, 9-12. https://doi.org/10.1007/s12355-014-0342-1
Liu, Q., Pang, Z., Yang, Z., Nyumah, F., Hu, C., Lin, W., & Yuan, Z. (2022). Bio-fertilizer affects structural dynamics, function, and network patterns of the sugarcane rhizospheric microbiota. Microbial Ecology, 84, 1195-1211. https://doi.org/10.1007/s00248-021-01932-3
Liu, Q., Xie, S., Zhao, X., Liu, Y., Xing, Y., & Dao, J. (2021). Drought sensitivity of sugarcane cultivars shapes rhizosphere bacterial community patterns in response to water stress. Frontiers in Microbiology, 12, 732989. https://doi.org/10.3389/fmicb.2021.732989
Malviya, M.K., Solanki, M.K., Li, C.N., Wang, Z., Zeng, Y., Verma, K.K., Singh, R.K., Singh, P., Huang, H.R., Yang, L.T., Song, X.P., & Li, Y.R. (2021). Sugarcane-legume intercropping can enrich the soil microbiome and plant growth. Frontiers In Sustainable Food Systems, 5, 606595. https://doi.org/10.3389/fsufs.2021.606595
Monela, A.P.C., Carvalho, L.A.L., Teheran-Sierra, L.G., Funnicelli, M.I.G., & Pinheiro, D.G. (2022). Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure. Scientific Reports, 12, 19174. https://doi.org/10.1038/s41598-022-23562-6
Morais, T.P.D., Barbosa P.M.G., Garcia, N.F.L., & Rosa, N.G.D. (2018). Catalytic and thermodynamic properties of β-glucosidases produced by Lichtheimia corymbifera and Byssochlamys spectabilis. Preparative Biochemistry & Biotechnology, 48(9). https://doi.org/10.1080/10826068.2018.1509083
Nygaard, A.B., Tunsjo, H.S., Meisal, R., & Charnock, C. (2020). A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes. Scientific Report, 10(1), 1-10. https://doi.org/10.1038/s41598-020-59771-0
Pang, Z., Dong, F., Liu, Q., Lin, W., Hu, C., & Yuan, Z. (2021). Soil metagenomics reveals effects of continuous sugarcane cropping on the structure and functional pathway of rhizospheric microbial community. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.627569
Pusdatin (Pusat Data dan Sistem Informasi Pertanian) (2022). Sugarcane plantation commodity outlook. Jakarta: Ministry of Agriculture
Singh, A., Sarma, B.K., Upadhyay, R.S., & Singh, H.B. (2013). Compatible rhizosphere microbes mediated alleviation of biotic stress in chickpea through enhanced antioxidant and phenylpropanoid activities. Microbiological Research, 168(1), 33-40. https://doi.org/10.1016/j.micres.2012.07.001
Wick, R.R., Judd, L.M., & Holt, K.E. (2019). Performance of neural network basecalling tools for Oxford Nanopore Sequencing. Genome Biology, 20(1), 129. https://doi.org/10.1186/s13059-019-1727-y
Yi, H., Heil, M., Adame-Alvarez, R.M., Ballhorn, D.J., & Ryu, C. (2009). Airborne induction and priming of plant defenses against a bacterial pathogen. Plant Physiology, 151, 2152- 2161. https://doi.org/10.1104/pp.109.144782
Zhang, F., Huo, Y., Cobb, A.B., Luo, G., Zhou, J., & Yang, G. (2018). Trichoderma biofertilizer links to altered soil chemistry, altered microbial communities, and improved grassland biomass. Frontiers in Microbiology, 9. https://doi.org/10.3389/fmicb.2018.00848
Zhang, Q., Guo, T., Li, H., Wang, Y., & Zhou, W. (2020). Identification of fungal populations assimilating rice root residue-derived carbon by DNA stable-isotope probing. Applied Soil Ecology, 147,103374. https://doi.org/10.1016/j.apsoil.2019.103374
Downloads
Published
Issue
Section
License
Copyright (c) 2026 Muhammad Abdul Aziz, Donny Nugroho Kalbuadi, Galuh Wening Permatasari, Happy Widiastuti

This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.











