Long-term application of organic matter improves soil properties and plant growth-promoting bacteria in soil communities of oil palm plantation

References

• Ali, S. S., M. Kornaros, A. Manni, R. Al-Tohamy, A. E. R. El-Shanshoury, I. M. Matter, T. Elsamahy, M. Sobhy, and J. Sun. 2021. “Advances in Microorganisms-Based Biofertilizers: Major Mechanisms and Applications.” Biofertilizers 1:371–385. https://doi.org/10.1016/B978-0-12-821667-5.00023-3
   Google Scholar
• Babu, S., and R. Rengasamy. 2017. “Isolation and Identification of Bacillus sp. from Seaweed Liquid Fertilizer (SLF.” Journal of Marine Biosciences 3:167–174.
   Google Scholar
• Balasundram, S. K., P. C. Robert, D. J. Mulla, and D. L. Allan. 2006. “Relationship Between Oil Palm Yield and Soil Fertility As Affected by Topography in an Indonesian Plantation.” Communications in Soil Science & Plant Analysis 37:1321–1337. https://doi.org/10.1080/00103620600626817.
   Web of Science ®Google Scholar
• Berkelmann, D., D. Schneider, N. Hennings, A. Meryandini, and R. Daniel. 2020. “Soil Bacterial Community Structures in Relation to Different Oil Palm Management Practices.” Scientific Data 7:421. https://doi.org/10.1038/s41597-020-00752-3.
   PubMed Web of Science ®Google Scholar
• Boafo, D. K., B. Kraisornpornson, S. Panphon, B. E. Owusu, and P. N. Amaniampong. 2020. “Effect of Organic Soil Amendments on Soil Quality in Oil Palm Production.” Applied Soil Ecology 147:103358. https://doi.org/10.1016/j.apsoil.2019.09.008.
   Web of Science ®Google Scholar
• Boberg, J. B., K. Ihrmark, and B. D. Lindahl. 2011. “Decomposing Capacity of Fungi Commonly Detected in Pinus sylvestris Needle Litter.” Fungal Ecology 4:110–114. https://doi.org/10.1016/j.funeco.2010.09.002.
   Web of Science ®Google Scholar
• Boratyn, G. M., J. Thierry-Mieg, D. Thierry-Mieg, B. Busby, and T. L. Madden. 2019. “Magic-Blast, an Accurate RNA-Seq Aligner for Long and Short Reads.” BMC Bioinformatics 20:405. https://doi.org/10.1186/s12859-019-2996-x.
   PubMed Web of Science ®Google Scholar
• Breitkreuz, C., A. Heintz-Buschart, F. Buscot, S. F. M. Wahdan, M. Tarkka, and T. Reitz. 2021. “Can We Estimate Functionality of Soil Microbial Communities from Structure-Derived Predictions? A Reality Test in Agricultural Soils.” Microbiology Spectrum 9 (1): e00278–21. https://doi.org/10.1128/Spectrum.00278-21.
   Web of Science ®Google Scholar
• Bremner, J. M. 1965. Total Nitrogen, In: Methods of Soil Analysis: Part 2 Chemical and Microbiological Properties., 1149–1178. Ames, Iowa, USA: American Society of Agronomy, Inc.
   Google Scholar
• Brinkmann, N., D. Schneider, J. Sahner, J. Ballauff, N. Edy, H. Barus, B. Irawan, et al. 2019. “Intensive Tropical Land Use Massively Shifts Soil Fungal Communities.” Scientific Reports 9:3403. https://doi.org/10.1038/s41598-019-39829-4.
   PubMed Web of Science ®Google Scholar
• Budianta, D., N. Gofar, and G. A. Andika. 2013. “Improvement of Sand Tailing Fertility Derived from Post Tin Mining Using Leguminous Crop Applied by Compost and Mineral Soil.” Journal of Tropical Soils 18 (3): 217–223. https://doi.org/10.5400/jts.2013.18.3.217.
   Google Scholar
• Caporaso, J. G., J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K. Costello, N. Fierer, et al. 2010. “QIIME Allows Analysis of High-Throughput Community Sequencing Data.” Nature Methods 7 (5): 335–336. https://doi.org/10.1038/nmeth.f.303.
   PubMed Web of Science ®Google Scholar
• Comte, I., F. Colin, J. K. Whalen, O. Grünberger, and J.-P. Caliman. 2012. “Agricultural Practices in Oil Palm Plantations and Their Impact on Hydrological Changes, Nutrient Fluxes and Water Quality in Indonesia.” In Advances in Agronomy, 71–124. Elsevier. https://doi.org/10.1016/B978-0-12-394277-7.00003-8.
   Google Scholar
• Diacono, M., and F. Montemurro. 2010. “Long-Term Effects of Organic Amendments on Soil Fertility. a Review.” Agronomy for Sustainable Development 30:401–422. https://doi.org/10.1051/agro/2009040.
   Web of Science ®Google Scholar
• Directorate General of Estate Crops. 2020. Statistical of National Leading Estate Crops Commodity 2019-2021. Secretariate of Directorate General of Estate Crops, Ministry of Agriculture Republic of Indonesia.
   Google Scholar
• Du, T.-Y., H.-Y. He, Q. Zhang, L. Lu, W.-J. Mao, and M.-Z. Zhai. 2022. “Positive Effects of Organic Fertilizers and Biofertilizers on Soil Microbial Community Composition and Walnut Yield.” Applied Soil Ecology 175:104457. https://doi.org/10.1016/j.apsoil.2022.104457.
   Web of Science ®Google Scholar
• Edgar, M., A. Levi, C. Percy, and L. Gaddafi. 2018. “Analysis of Nitrifying Microbial Community for Organic Hydroponics.” African Journal of Microbiology Research 12 (1): 1–8. https://doi.org/10.5897/AJMR2017.8635.
   Google Scholar
• Esitken, A., H. E. Yildiz, S. Ercisli, M. Figen Donmez, M. Turan, and A. Gunes. 2010. “Effects of Plant Growth Promoting Bacteria (PGPB) on Yield, Growth and Nutrient Contents of Organically Grown Strawberry.” Scientia Horticulturae 124:62–66. https://doi.org/10.1016/j.scienta.2009.12.012.
   Web of Science ®Google Scholar
• Farda, B., A. Mattedi, R. Djebaili, L. Pace, M. Del Gallo, and M. Pellegrini. 2022. “Microbial Community Investigation of Wild Brambles with Root Nodulation from a Calcareous Nitrogen-Deficient Soil.” Soil Systems 6:96. https://doi.org/10.3390/soilsystems6040096.
   Web of Science ®Google Scholar
• Foong, S. Z. Y., C. K. M. Goh, C. V. Supramaniam, and D. K. S. Ng. 2019. “Input–Output Optimisation Model for Sustainable Oil Palm Plantation Development.” Sustainable Production and Consumption 17:31–46. https://doi.org/10.1016/j.spc.2018.08.010.
   Web of Science ®Google Scholar
• Galeano, R. M. S., D. G. Franco, P. O. Chaves, G. C. Giannesi, D. C. Masui, R. Ruller, B. O. Corrêa, M. da Silva Brasil, and F. F. Zanoelo. 2021. “Plant Growth Promoting Potential of Endophytic Aspergillus niger 9-P Isolated from Native Forage Grass in Pantanal of Nhecolândia Region, Brazil.” Rhizosphere 18:100332. https://doi.org/10.1016/j.rhisph.2021.100332.
   Web of Science ®Google Scholar
• Gee, G. W., and D. Or. 2002. Particle-Size Analysis, In: Methods of Soil Analysis, Part 4: Physical Methods., 255–293. Madison, WI, USA: Soil Science Society of America, Inc.
   Google Scholar
• Goh, Y. K., M. Z. H. M. Zoqratt, Y. K. Goh, Q. Ayub, and A. S. Y. Ting. 2020. “Determining Soil Microbial Communities and Their Influence on Ganoderma Disease Incidences in Oil Palm (Elaeis guineensis) via High-Throughput Sequencing.” Biology 9:424. https://doi.org/10.3390/biology9120424.
   PubMed Web of Science ®Google Scholar
• Gondwe, R. L., R. Kinoshita, T. Suminoe, D. Aiuchi, J. P. Palta, and M. Tani. 2020. “Available Soil Nutrients and NPK Application Impacts on Yield, Quality, and Nutrient Composition of Potatoes Growing During the Main Season in Japan.” American Journal of Potato Research 97:234–245. https://doi.org/10.1007/s12230-020-09776-2.
   Web of Science ®Google Scholar
• Guan, Y. L. 2019. “Enhancing Sustainable Oil Palm Cultivation Using Compost.” Journal of Oil Palm Research 31:412–421. https://doi.org/10.21894/jopr.2019.0037.
   Web of Science ®Google Scholar
• Guillaume, T., A. M. Holtkamp, M. Damris, B. Brümmer, and Y. Kuzyakov. 2016. “Soil Degradation in Oil Palm and Rubber Plantations Under Land Resource Scarcity.” Agriculture, Ecosystems and Environment 232:110–118. https://doi.org/10.1016/j.agee.2016.07.002.
   Web of Science ®Google Scholar
• Hasputri, R., Sudradjat and Sugiyanta. 2017. “The Roles of Organic and NPK Compound Fertilizers for Four Year Old Mature Oil Palm (Elaeis guineensis Jacq).” The International Journal of Science 36:213–225.
   Google Scholar
• Hidayat, F., R. Farrasati, I. Pradiko, E. Listia, M. Syarovy, S. Rahutomo, and Winarna. 2021. “Preliminary Study on the Bacterial Community Structure of Ganoderma Soil Under Oil Palm Plantation.” In Advances in Biological Sciences Research. Presented at the 10th International Seminar and 12th Congress of Indonesian Society for Microbiology (ISISM 2019), 49–53. Surakarta, Indonesia: Atlantis Press International B.V. https://doi.org/10.2991/absr.k.210810.010.
   Google Scholar
• Hou, Q., S. Lin, Y. Ni, L. Yao, S. Huang, T. Zuo, J. Wang, and W. Ni. 2022. “Assembly of Functional Microbial Communities in Paddy Soil with Long-Term Application of Pig Manure Under Rice-Rape Cropping System.” Journal of Environmental Management 305:114374. https://doi.org/10.1016/j.jenvman.2021.114374.
   PubMed Web of Science ®Google Scholar
• Hu, Y., D. Li, Y. Wu, S. Liu, L. Li, W. Chen, S. Wu, Q. Meng, H. Feng, and K. H. M. Siddique. 2023. “Mitigating Greenhouse Gas Emissions by Replacing Inorganic Fertilizer with Organic Fertilizer in Wheat–Maize Rotation Systems in China.” Journal of Environmental Management 344:118494. https://doi.org/10.1016/j.jenvman.2023.118494.
   PubMed Web of Science ®Google Scholar
• Inayah, M. N., Y. Lestari, and A. Meryandini. 2022. “Community of Soil Actinobacteria in PTPN VI Oil Palm Plantation Jambi (Sumatra, Indonesia) Based on Amplicon Sequencing of 16S rRNA Gene.” Hayati Journal of Bioscience 29 (3): 389–398. https://doi.org/10.4308/hjb.29.3.389-398.
   Google Scholar
• Karácsony, Z., D. G. Knapp, S. Lengyel, G. M. Kovács, and K. Z. Váczy. 2021. “The Fungus Kalmusia longispora Is Able to Cause Vascular Necrosis on Vitis vinifera.” PLOS ONE 16:e0258043. https://doi.org/10.1371/journal.pone.0258043.
   PubMed Web of Science ®Google Scholar
• Khan, A. L., M. Hamayun, Y.-H. Kim, S.-M. Kang, J.-H. Lee, and I.-J. Lee. 2011. “Gibberellins Producing Endophytic Aspergillus fumigatus sp. LH02 Influenced Endogenous Phytohormonal Levels, Isoflavonoids Production and Plant Growth in Salinity Stress.” Process Biochemistry 46:440–447. https://doi.org/10.1016/j.procbio.2010.09.013.
   Web of Science ®Google Scholar
• Ko, W.-H., C.-H. Yang, M.-J. Lin, C.-Y. Chen, and Y.-J. Tsou. 2011. “Humicola phialophoroides sp. Nov. from Soil with Potential for Biological Control of Plant Diseases.” Botanical Studies 52:197–202.
   Web of Science ®Google Scholar
• Kong, Z., and H. Liu. 2022. “Modification of Rhizosphere Microbial Communities: A Possible Mechanism of Plant Growth Promoting Rhizobacteria Enhancing Plant Growth and Fitness.” Frontier in Plant Science 13:920813. https://doi.org/10.3389/fpls.2022.920813.
   PubMed Web of Science ®Google Scholar
• Langille, M. G. I., J. Zaneveld, J. G. Caporaso, D. McDonald, D. Knights, J. A. Reyes, J. C. Clemente, et al. 2013. “Predictive Functional Profiling of Microbial Communities Using 16S rRNA Marker Gene Sequences.” Nature Biotechnology 31:814–821. https://doi.org/10.1038/nbt.2676.
   PubMed Web of Science ®Google Scholar
• Lee-Cruz, L., D. P. Edwards, B. M. Tripathi, and J. M. Adams. 2013. “Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo.” Applied & Environmental Microbiology 79 (23): 7290–7297. https://doi.org/10.1128/AEM.02541-13.
   PubMed Web of Science ®Google Scholar
• Lei, S., L. Wang, L. Liu, Y. Hou, Y. Xu, M. Liang, J. Gao, Q. Li, and S. Huang. 2019. “Infection and Colonization of Pathogenic Fungus Fusarium proliferatum in Rice Spikelet Rot Disease.” Rice Science 26 (1): 60–68. https://doi.org/10.1016/j.rsci.2018.08.005.
   Web of Science ®Google Scholar
• Liang, Q., H. Chen, Y. Gong, M. Fan, H. Yang, R. Lal, and Y. Kuzyakov. 2012. “Effects of 15 Years of Manure and Inorganic Fertilizers on Soil Organic Carbon Fractions in a Wheat-Maize System in the North China Plain.” Nutrient Cycling in Agroecosystems 92:21–33. https://doi.org/10.1007/s10705-011-9469-6.
   Web of Science ®Google Scholar
• Liem, L. T. T., Y. Tashiro, P. V. T. Tinh, and K. Sakai. 2022. “Reduction in Greenhouse Gas Emission from Seedless Lime Cultivation Using Organic Fertilizer in a Province in Vietnam Mekong Delta Region.” Sustainability 14:6102. https://doi.org/10.3390/su14106102.
   Web of Science ®Google Scholar
• Liu, C. M., S. Kachur, M. G. Dwan, A. G. Abraham, M. Aziz, P.-R. Hsueh, Y.-T. Huang, J. D. Busch, et al. 2012. “FungiQuant: A Broad-Coverage Fungal Quantitative Real-Time PCR Assay.” BMC Microbiology 12:255. https://doi.org/10.1186/1471-2180-12-255.
   PubMed Web of Science ®Google Scholar
• Liu, H., D. Li, Y. Huang, Q. Lin, L. Huang, S. Cheng, S. Sun, and Z. Zhu. 2023. “Addition of Bacterial Consortium Produced High-Quality Sugarcane Bagasse Compost As an Environmental-Friendly Fertilizer: Optimizing Arecanut (Areca catechu L.) Production, Soil Fertility and Microbial Community Structure.” Applied Soil Ecology 188:104920. https://doi.org/10.1016/j.apsoil.2023.104920.
   Web of Science ®Google Scholar
• Liu, J., A. Shu, W. Song, W. Shi, M. Li, W. Zhang, Z. Li, et al. 2021. “Long-Term Organic Fertilizer Substitution Increases Rice Yield by Improving Soil Properties and Regulating Soil Bacteria.” Geoderma 404:115287. https://doi.org/10.1016/j.geoderma.2021.115287.
   Web of Science ®Google Scholar
• Liu, Z., X. Ma, N. He, J. Zhang, J. Wu, and C. Liu. 2020. “Shifts in Microbial Communities and Networks Are Correlated with the Soil Ionome in a Kiwifruit Orchard Under Different Fertilization Regimes.” Applied Soil Ecology 149:103517. https://doi.org/10.1016/j.apsoil.2020.103517.
   Web of Science ®Google Scholar
• Lo, R. K. S., and K. P. Chong. 2020. “Metagenomic Data of Soil Microbial Community in Relation to Basal Stem Rot Disease.” Data in Brief 31:106030. https://doi.org/10.1016/j.dib.2020.106030.
   PubMed Web of Science ®Google Scholar
• Maestre, S. E., J. Mora, V. Hernandis, and J. L. Todolí. 2003. “A System for the Direct Determination of the Nonvolatile Organic Carbon, Dissolved Organic Carbon, and Inorganic Carbon in Water Samples Through Inductively Coupled Plasma Atomic Emission Spectrometry.” Analytical Chemistry 75:111–117. https://doi.org/10.1021/ac025980f.
   PubMed Web of Science ®Google Scholar
• Makinde, E. A., L. S. Ayeni, and S. O. Ojeniyi. 2011. “Effects of Organic, Organomineral and NPK Fertilizer Treatments on the Nutrient Uptake of Amaranthus cruentus (L) on Two Soil Types in Lagos, Nigeria.” Journal of Central European Agriculture 12 (1): 114–123. https://doi.org/10.5513/JCEA01/12.1.887.
   Google Scholar
• Maza-Márquez, P., R. Vílchez-Vargas, A. González-Martínez, J. González-López, and B. Rodelas. 2018. “Assessing the Abundance of Fungal Populations in a Full-Scale Membrane Bioreactor (MBR) Treating Urban Wastewater by Using Quantitative PCR (qPCR).” Journal of Environmental Management 223:1–8. https://doi.org/10.1016/j.jenvman.2018.05.093.
   PubMed Web of Science ®Google Scholar
• Mc Lean, E. O., M. E. Watson, and S. S. S. A. Books. 2015. “Soil Measurements of Plant-Available Potassium.” In edited by R. D. Munson), C. ASA, 277–308. Madison, WI, USA: American Society of Agronomy, Crop Science Society of America, Soil Science Society of America. https://doi.org/10.2134/1985.potassium.c10.
   Google Scholar
• Monzon, J. P., M. A. Slingerland, S. Rahutomo, F. Agus, T. Oberthür, J. F. Andrade, A. Couëdel, et al. 2021. “Fostering a Climate-Smart Intensification for Oil Palm.” Nature Sustainability 4:595–601. https://doi.org/10.1038/s41893-021-00700-y.
   Web of Science ®Google Scholar
• Mukhtar, I., X. Quan, T. Chou, Q. Huang, J. Yan, B. Chen, S. Jiang, F. Liu, Z. Wen, and B. Xie. 2019. “First Report of Talaromyces funiculosus Causing Fruit Core Rot of Peach (Prunus persica) in China.” Plant Disease 103:2124–2125. https://doi.org/10.1094/PDIS-11-18-2050-PDN.
   Web of Science ®Google Scholar
• Nishi, E., Y. Tashiro, and K. Sakai. 2015. “Discrimination Among Individuals Using Terminal Restriction Fragment Length Polymorphism Profiling of Bacteria Derived from Forensic Evidence.” International Journal of Legal Medicine 129:425–433. https://doi.org/10.1007/s00414-014-1092-z.
   PubMed Web of Science ®Google Scholar
• Osono, T. 2020. “Functional Diversity of Ligninolytic Fungi Associated with Leaf Litter Decomposition.” Ecological Research 35:30–43. https://doi.org/10.1111/1440-1703.12063.
   Web of Science ®Google Scholar
• Ozlu, E., and S. Kumar. 2018. “Response of Soil Organic Carbon, pH, Electrical Conductivity, and Water Stable Aggregates to Long‐Term Annual Manure and Inorganic Fertilizer.” Soil Science Society of America Journal 82:1243–1251. https://doi.org/10.2136/sssaj2018.02.0082.
   Web of Science ®Google Scholar
• Pierzynski, G. M. 2000. Methods of Phosphorus Analysis for Soils, Sediments, Residuals, and Waters. North Carolina: North Carolina State University.
   Google Scholar
• Poly, F., S. Wertz, E. Brothier, and V. Degrange. 2008. “First Exploration of Nitrobacter Diversity in Soils by a PCR Cloning-Sequencing Approach Targeting Functional Gene nxrA.” FEMS Microbiology Ecology 63:132–140. https://doi.org/10.1111/j.1574-6941.2007.00404.x.
   PubMed Web of Science ®Google Scholar
• Pradana, A., I. Pujiastuti, and P. P. Paramita. 2019. “Regionalization of Agricultural Based Leading Sectors and Food Security in Indonesia.” IOP Conference Series: Earth Environmental Science 338:012015. https://doi.org/10.1088/1755-1315/338/1/012015.
   Google Scholar
• Punja, Z. K. 2021. “First Report of Fusarium proliferatum Causing Crown and Stem Rot, and Pith Necrosis, in Cannabis (Cannabis sativa L. Marijuana) Plants.” Canadian Journal of Plant Pathology 43 (2): 236–255. https://doi.org/10.1080/07060661.2020.1793222.
   Google Scholar
• Quezada, J. C., T. Guillaume, C. Poeplau, J. Ghazoul, and A. Buttler. 2022. “Deforestation‐Free Land‐Use Change and Organic Matter‐Centered Management Improve the C Footprint of Oil Palm Expansion.” Global Change Biology 28:2476–2490. https://doi.org/10.1111/gcb.16069.
   PubMed Web of Science ®Google Scholar
• Rahman, N., K. E. Giller, A. de Neergaard, J. Magid, G. van de Ven, and T. B. Bruun. 2021. “The Effects of Management Practices on Soil Organic Carbon Stocks of Oil Palm Plantations in Sumatra, Indonesia.” Journal of Environmental Management 278:111446. https://doi.org/10.1016/j.jenvman.2020.111446.
   PubMed Web of Science ®Google Scholar
• Ryadin, A. R., D. Janz, D. Schneider, A. Tjoa, B. Irawan, R. Daniel, and A. Polle. 2022. “Early Effects of Fertilizer and Herbicide Reduction on Root-Associated Biota in Oil Palm Plantations.” Agronomy 12:199. https://doi.org/10.3390/agronomy12010199.
   Google Scholar
• Samaddar, S., J. Truu, P. Chatterjee, M. Truu, K. Kim, S. Kim, S. Seshadri, and T. Sa. 2019. “Long-Term Silicate Fertilization Increases the Abundance of Actinobacterial Population in Paddy Soils.” Biology and Fertility of Soils 55 (2): 109–120. https://doi.org/10.1007/s00374-018-01335-6.
   Web of Science ®Google Scholar
• Schneider, D., M. Engelhaupt, K. Allen, S. Kurniawan, V. Krashevska, M. Heinemann, H. Nacke, et al. 2015. “Impact of Lowland Rainforest Transformation on Diversity and Composition of Soil Prokaryotic Communities in Sumatra (Indonesia).” Frontiers in Microbiology 6:1339. https://doi.org/10.3389/fmicb.2015.01339.
   PubMed Web of Science ®Google Scholar
• Situmorang, E. C., Y. A. Nugroho, A. Prameswara, E. A. Hartono, R. H. Setyobudi, N. Toruan-Mathius, and T. Liwang. 2016. “The Bacterial Diversity Investigation in Oil Palm Plantation Using Terminal Restriction Length Polymorphism.” Presented at The 4th International Conference on Biological Science, 020017. Yogyakarta, Indonesia. https://doi.org/10.1063/1.4953491.
   Google Scholar
• Smets, W., J. W. Leff, M. A. Bradford, R. L. McCulley, S. Lebeer, and N. Fierer. 2016. “A Method for Simultaneous Measurement of Soil Bacterial Abundances and Community Composition via 16S rRNA Gene Sequencing.” Soil Biology and Biochemistry 96:145–151. https://doi.org/10.1016/j.soilbio.2016.02.003.
   Web of Science ®Google Scholar
• Soil Survey Staff. 2014. “Soil Survey Field and Laboratory Methods Manual, in Soil Survey Investigations.” Report No. 51; Version 2. Nebraska, US: U.S. Department of Agriculture, pp. 184–189.
   Google Scholar
• Stichnothe, H., and F. Schuchardt. 2011. “Life Cycle Assessment of Two Palm Oil Production Systems.” Biomass & Bioenergy 35:3976–3984. https://doi.org/10.1016/j.biombioe.2011.06.001.
   Web of Science ®Google Scholar
• Suman, J., A. Rakshit, S. D. Ogireddy, S. Singh, C. Gupta, and J. Chandrakala. 2022. “Microbiome As a Key Player in Sustainable Agriculture and Human Health.” Frontiers in Soil Science 2:821589. https://doi.org/10.3389/fsoil.2022.821589.
   Google Scholar
• Sun, T., X. Mao, Q. Ma, K. Han, X. Wang, Q. Cheng, X. Sheng, W. Mi, and L. Wu. 2023. “Response of Rice Yield to Organic Amendments Was Regulated by Soil Chemical Properties, Microbial Functional Genes and Bacterial Community Rather Than Fungal Community.” Applied Soil Ecology 188:104923. https://doi.org/10.1016/j.apsoil.2023.104923.
   Web of Science ®Google Scholar
• Syarifain, R. I., E. D. Anggrainy, R. Sudirja, E. T. Sofyan, and T. Simarmata. 2019. “The Change of Microbial Communities in Rhizomicrobiome Due to the Land Management.” IOP Conference Series: Earth and Environmental Science 393:012043. https://doi.org/10.1088/1755-1315/393/1/012043.
   Google Scholar
• Tao, H.-H., J. L. Snaddon, E. M. Slade, J.-P. Caliman, R. H. Widodo Suhardi, and K. J. Willis. 2017. “Long-Term Crop Residue Application Maintains Oil Palm Yield and Temporal Stability of Production.” Agronomy for Sustainable Development 37:33. https://doi.org/10.1007/s13593-017-0439-5.
   PubMed Web of Science ®Google Scholar
• Thomas, G. W. 1996. “Soil pH and Soil Acidity.” In SSSA Book Series, edited by D. L. Sparks, A. L. Page, P. A. Helmke, R. H. Loeppert, P. N. Soltanpour, M. A. Tabatabai, C. T. Johnston, and M. E. Sumner, 475–490. Madison, WI, USA: Soil Science Society of America, American Society of Agronomy. https://doi.org/10.2136/sssabookser5.3.c16.
   Google Scholar
• Tin, H. S., K. Palaniveloo, J. Anilik, M. Vickneswaran, Y. Tashiro, C. S. Vairappan, and K. Sakai. 2017. “Impact of Land-Use Change on Vertical Soil Bacterial Communities in Sabah.” Microbial Ecology 75:459–467. https://doi.org/10.1007/s00248-017-1043-6.
   PubMed Web of Science ®Google Scholar
• Toju, H., A. S. Tanabe, S. Yamamoto, and H. Sato. 2012. “High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples.” PLOS ONE 7:e40863. https://doi.org/10.1371/journal.pone.0040863.
   PubMed Web of Science ®Google Scholar
• Treseder, K. K., and J. T. Lennon. 2015. “Fungal Traits That Drive Ecosystem Dynamics on Land.” Microbiology & Molecular Biology Reviews 79:243–262. https://doi.org/10.1128/MMBR.00001-15.
   PubMed Web of Science ®Google Scholar
• Udagawa, S., Y. Tsuzaki, and H. Uehada. 1979. “Growth Damage Caused by Ascopore Dispersal of Arnium macrotheca from Cultivated Carnation.” Trans Mycol Soc Japan 20:357–369.
   Google Scholar
• Větrovský, T., and P. Baldrian. 2013. “Analysis of Soil Fungal Communities by Amplicon Pyrosequencing: Current Approaches to Data Analysis and the Introduction of the Pipeline SEED.” Biology and Fertility of Soils 49 (8): 1027–1037. https://doi.org/10.1007/s00374-013-0801-y.
   Web of Science ®Google Scholar
• Volpiano, C. G., B. B. Lisboa, J. F. B. D. S. José, A. Beneduzi, C. E. Granada, and L. K. Vargas. 2022. “Soil-Plant-Microbiota Interactions to Enhance Plant Growth.” Revista Brasileira de Ciencia do Solo 46:e0210098. https://doi.org/10.36783/18069657rbcs20210098.
   Web of Science ®Google Scholar
• Walling, E., and C. Vaneeckhaute. 2020. “Greenhouse Gas Emissions from Inorganic and Organic Fertilizer Production and Use: A Review of Emission Factors and Their Variability.” Journal of Environmental Management 276:111211. https://doi.org/10.1016/j.jenvman.2020.111211.
   PubMed Web of Science ®Google Scholar
• Wang, C., X. Ma, J. Shen, D. Chen, L. Zheng, T. Ge, Y. Li, and J. Wu. 2022. “Reduction in Net Greenhouse Gas Emissions Through a Combination of Pig Manure and Reduced Inorganic Fertilizer Application in a Double-Rice Cropping System: Three-Year Results.” Agriculture, Ecosystems and Environment 326:107799. https://doi.org/10.1016/j.agee.2021.107799.
   Web of Science ®Google Scholar
• Wang, F., Y. Liu, J. Wang, Y. Zhang, and H. Yang. 2012. “Influence of Growth Manner on Nitrifying Bacterial Communities and Nitrification Kinetics in Three Lab-Scale Bioreactors.” Journal of Industrial Microbiology & Biotechnology 39:595–604. https://doi.org/10.1007/s10295-011-1065-x.
   PubMed Web of Science ®Google Scholar
• Watanabe, K., E. Nishi, Y. Tashiro, and K. Sakai. 2019. “Mode and Structure of the Bacterial Community on Human Scalp Hair.” Microbes and Environments 34:252–259. https://doi.org/10.1264/jsme2.ME19018.
   PubMed Web of Science ®Google Scholar
• Wen, J., S. K. Okyere, S. Wang, J. Wang, L. Xie, Y. Ran, and Y. Hu. 2022. “Endophytic Fungi: An Effective Alternative Source of Plant-Derived Bioactive Compounds for Pharmacological Studies.” Journal of Fungi 8:205. https://doi.org/10.3390/jof8020205.
   Web of Science ®Google Scholar
• Wong, S. 2021. “Soil Fungal Composition and Diversity in Oil Palm Plantation at Sungai Asap, Sarawak, Malaysia.” Journal of Oil Palm Research 33:215–226. https://doi.org/10.21894/jopr.2021.0014.
   Web of Science ®Google Scholar
• Xiang, X., J. M. Adams, C. Qiu, W. Qin, J. Chen, L. Jin, C. Xu, and J. Liu. 2021. “Nutrient Improvement and Soil Acidification Inducing Contrary Effects on Bacterial Community Structure Following Application of Hairy Vetch (Vicia Villosa Roth L.) in Ultisol.” Agriculture, Ecosystems and Environment 312:107348. https://doi.org/10.1016/j.agee.2021.107348.
   Web of Science ®Google Scholar
• Yang, C.-H., M.-J. Lin, H.-J. Su, and W.-H. Ko. 2014. “Multiple Resistance-Activating Substances Produced by Humicola phialophoroides Isolated from Soil for Control of Phytophthora Blight of Pepper.” Botanical Studies 55:40. https://doi.org/10.1186/1999-3110-55-40.
   PubMed Web of Science ®Google Scholar
• Yoon, S.-H., S.-M. Ha, S. Kwon, J. Lim, Y. Kim, H. Seo, and J. Chun. 2017. “Introducing EzBiocloud: A Taxonomically United Database of 16S rRNA Gene Sequences and Whole-Genome Assemblies.” International Journal of Systematic and Evolutionary Microbiology 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755.
   PubMed Web of Science ®Google Scholar
• Zhang, M., Y. Tashiro, Y. Asakura, N. Ishida, K. Watanabe, S. Yue, M.-N. Akiko, and K. Sakai. 2021. “Lab-Scale Autothermal Thermophilic Aerobic Digestion Can Maintain and Remove Nitrogen by Controlling Shear Stress and Oxygen Supply System.” Journal of Bioscience and Bioengineering 132:293–301. https://doi.org/10.1016/j.jbiosc.2021.05.008.
   PubMed Web of Science ®Google Scholar