Original research article
This study investigates the effects of organic management systems (OMS) on soil microbial communities and their activities, comparing them with conventional management systems (CMS) and wild systems (WS) in chestnut orchards across the Tamba region of Japan. Soil samples were collected from four distinct locations: Wachi, Ayabe, Fukuchiyama, and Sasayama. Microbial activity was assessed by analyzing nine enzyme types, while the microbial community, including bacteria and arbuscular mycorrhizal fungi (AMF), was characterized using amplicon sequencing analysis. The results revealed that in general soils under WS exhibited the highest enzyme activities followed by the OMS and then by CMS, with special regard to invertase activity. The relative abundance data indicated that Alphaproteobacteria and Betaproteobacteria were the dominant bacterial classes in orchards under OMS and CMS, while Bacilli were more prevalent under WS. Among AMF, Claroideoglomus was notably abundant in soils under OMS in Ayabe and Wachi. The bacterial richness, here represented by the number of Operational Taxonomic Units (OTUs) and Shannon-Wiener index (SW) indicated that it was higher under OMS than under conventional management systems (CMS) in certain areas. Predicted metabolic functions highlighted greater values to those related to nitrogen cycling activity in OMS-managed soils, whereas the majority of those representing the carbon cycling was more pronounced under WS followed by the OMS. The study also identified relationships between specific enzyme activities and microbial community composition, which were influenced by OMS practices. This research provides valuable insights into the impacts of different cultivation practices on soil health, emphasizing the importance of sustainable agricultural management for maintaining soil ecosystems.
Alkorta I, Aizpurua A, Riga P, Albizu I, Amézaga I, Garbisu C. 2003. Soil enzyme activities as biological indicators of soil health. Reviews on environmental health. 18:65-73. https://doi.org/10.1515/REVEH.2003.18.1.65
10.1515/REVEH.2003.18.1.65Ambrosini A, Souza R, Passaglia LMP. 2016. Ecological role of bacterial inoculants and their potential impact on soil microbial diversity. Pl. and Soil 400:193-207. https://doi.org/10.1007/s11104-015-2727-7
10.1007/s11104-015-2727-7Antonious GF, Turley ET, Dawood MH. 2020. Monitoring soil enzymes activity before and after animal manure application. Agric. 10:166. https://doi.org/10.3390/agriculture10050166
10.3390/agriculture10050166Bogati K, Walczak M. 2022. The impact of drought stress on soil microbial community, enzyme activities and plants. Agron. 12:189. https://doi.org/10.3390/agronomy12010189
10.3390/agronomy12010189Böhme L, Langer U, Böhme F. 2005. Microbial biomass, enzyme activities and microbial community structure in two european long-term field experiments. Agric. Ecos. Env. 109:141-152. https://doi.org/10.1016/j.agee.2005.01.017
10.1016/j.agee.2005.01.017Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet C, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F. et al., 2018. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. Nat. Biot. 37:852-857. https://doi.org/10.1038/s41587-019-0209-9
10.1038/s41587-019-0209-931341288PMC7015180Brown RW, Chadwick DR, Bending GD, Collins CD, Whelton HL, Daulton E, Covington JA, Bull ID, Jones DL. 2022. Nutrient (C, N and P) enrichment induces significant changes in the soil metabolite profile and microbial carbon partitioning. Soil Biol. Biochem. 172:108779. https://doi.org/10.1016/j.soilbio.2022.108779
10.1016/j.soilbio.2022.108779Cruz AF, Hamel C, Hanson K, Selles F, Zentner RP. 2009. Thirty-seven years of soil nitrogen and phosphorus fertility management shapes the structure and function of the soil microbial community in a Brown chernozem. Pl. Soil 315:173-184. https://doi.org/10.1007/s11104-008-9742-x
10.1007/s11104-008-9742-xCruz AF, Ishii T. 2012. Arbuscular mycorrhizal fungal spores host bacteria that affect nutrient biodynamics and biocontrol of soil‐borne plant pathogens. Biol Open 1:52-57. https://doi.org/10.1242/bio.2011014
10.1242/bio.201101423213368PMC3507164Dilzahan HA, Okamura A, Calubaquib MA, Organo ND, Kobayashi M, Cruz AF. 2021. Function and characterization of fungal communities in chestnut soils (Castanea crenata) of Kansai region, Japan. Asian J. Soil Sci. Pl. Nut. 7:7-19. https://doi.org/10.9734/ajsspn/2021/v8i130123
10.9734/ajsspn/2021/v8i130123Gamage A, Gangahagedara R, Gamage J, Jayasinghe N, Kodikara N, Suraweera P, Merah O. 2023. Role of organic farming for achieving sustainability in agriculture. Farm. Syst. 1:100005. https://doi.org/10.1016/j.farsys.2023.100005
10.1016/j.farsys.2023.100005García-Ruiz, R., Ochoa V, Hinojosa MB, Carreira JA. 2008. Suitability of enzyme activities for the monitoring of soil quality improvement in organic agricultural systems. Soil Biol. Bioch. 40:2137-2145. https://doi.org/10.1016/j.soilbio.2008.03.023
10.1016/j.soilbio.2008.03.023Gomiero T, Pimentel D, Paoletti MG. 2011. Environmental impact of different agricultural management practices: Conventional vs. Organic agriculture. Crit. Rev. Pl. Sci. 30:95-124. https://doi.org/10.1080/07352689.2011.554355
10.1080/07352689.2011.554355Hamel C, Hanson K, Selles F, Cruz AF, Lemke R, McConkey B, Zentner R. 2006. Seasonal and long-term resource-related variations in soil microbial communities in wheat-based rotations of the Canadian prairie. Soil Biol. Bioch. 38:2104-2116. https://doi.org/10.1016/j.soilbio.2006.01.011
10.1016/j.soilbio.2006.01.011Han Y, Yuan G, Yang X, Fang L, Liang Y, Zhou B, Wei Z. 2025. Arbuscular mycorrhizal fungi enhance soil nutrient cycling by regulating soil bacterial community structures in mango orchards with different soil fertility rates. Front. Microb. 16. 1615694. https://doi.org/10.3389/fmicb.2025.1615694
10.3389/fmicb.2025.161569440657501PMC12245812Kageyama K, Komatsu T, Suga H. 2003. Refined PCR protocol for detection of plant pathogens in soil. J Gen Plant Pathol 69:153-160.
Kim K, Neuberger P, Daly EJ, Gorzelak M, Hernandez-Ramirez G. 2022. Arbuscular mycorrhizal fungi community linkages to soil nutrient availability across contrasting agroecosystems. Appl. Soil Ecol. 176:104464. https://doi.org/10.1016/j.apsoil.2022.104464
10.1016/j.apsoil.2022.104464Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. 2013. Evaluation of general 16s ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucl. Acids Res. 41:e1. https://doi.org/10.1093/nar/gks808
10.1093/nar/gks80822933715PMC3592464Lammel DR, Barth G, Ovaskainen O, Cruz LM, Zanatta JA, Ryo M, Souza EM, Pedrosa FO. 2018. Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures. Microbiome 6:1-13. https://doi.org/10.1186/s40168-018-0482-8
10.1186/s40168-018-0482-829891000PMC5996553Louca S, Parfrey LW, Doebeli M. 2016. Decoupling function and taxonomy in the global ocean microbiome. Science 353:1272-1277. https://doi.org/10.1126/science.aaf4507
10.1126/science.aaf4507Mierzwa-Hersztek M, Gondek K, Klimkowicz-Pawlas A, Chmiel MJ, Dziedzic K, Taras H. 2019. Assessment of soil quality after biochar application based on enzymatic activity and microbial composition. Int. Agrop. 33:331-336. https://doi.org/10.31545/intagr/110807
10.31545/intagr/110807Mohan A, Yichao Y, Jung L, Sharma AR. 2021. Soil microbial diversity in organic and non-organic pasture systems. PeerJ9:e11184. https://doi.org/10.7717/peerj.11184
10.7717/peerj.1118433981494PMC8071071Neemisha, Sharma S. 2022. Soil enzymes and their role in nutrient cycling in structure and functions of pedosphere. Singapore: Springer Nat. Singapore. 173-188. https://doi.org/10.1007/978-981-16-8770-9_8
10.1007/978-981-16-8770-9_8Nishio S, Yamamoto T, Terakami S, Sawamura Y, Takada N, Saito T. 2011. Genetic diversity of Japanese chestnut cultivars assessed by SSR markers. Breed. Sci. 61:109-120. https://doi.org/10.1270/jsbbs.61.109
10.1270/jsbbs.61.109Niwa R., Koyama T, Sato T, Adachi K, Tawaraya K, Sato S, Hirakawa H, Yoshida S, Ezawa T. 2018. Dissection of niche competition between introduced and indigenous arbuscular mycorrhizal fungi with respect to soybean yield responses. Scient. Rep. 8:7419. https://doi.org/10.1038/s41598-018-25701-4
10.1038/s41598-018-25701-429743529PMC5943277Öpik M, Vanatoa A, Vanatoa E, Moora M, Davison J, Kalwij JM, Reier Ü, Zobel M. 2010. The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytol. 188:223-241. https://doi.org/10.1111/j.1469-8137.2010.03334.x
10.1111/j.1469-8137.2010.03334.xOuyang Y, Reeve JR, Norton JM. 2022. The quality of organic amendments affects soil microbiome and nitrogen-cycling bacteria in an organic farming system. Front. Soil Sci. 2 869136. doi:10.3389/fsoil.2022.869136
10.3389/fsoil.2022.869136Pereira-Lorenzo S, Ballester A, Corredoira E, Vieitez AM, Agnanostakis S, Costa R, Bounous G, Botta R, Beccaro GL, Kubisiak TL. 2012. Chestnut In: Fruit Breeding, Springer, Boston, MA. 729-69. https://doi.org/10.1007/978-1-4419-0763-9_19
10.1007/978-1-4419-0763-9_19Philippot L, Chenu C, Kappler A, Rillig MC, Fierer N. 2024. The interplay between microbial communities and soil properties. Nat. Rev. Microb. 22:226-239. https://doi.org/10.1038/s41579-023-00980-5
10.1038/s41579-023-00980-5Palmer JM, Lindner DL, Volk TJ. 2008. Ectomycorrhizal characterization of an American chestnut (Castanea dentata) dominated community in Western Wisconsin. Mycorrhiza. 19:27-36. https://doi.org/10.1007/s00572-008-0200-7.
10.1007/s00572-008-0200-7Purin S, Filho OK, Stürmer SL. 2006. Mycorrhizae activity and diversity in conventional and organic apple orchards from Brazil. Soil Biol. Bioch. 38:1831-1839. https://doi.org/10.1016/j.soilbio.2005.12.008
10.1016/j.soilbio.2005.12.008Rao MA, Scelza R, Gianfreda L. 2014. Soil Enzymes. Enzymes in Agricultural Sciences. Foster City: OMICS Group EBooks, 10-43.
Reeve JR, Hoagland LA, Villalba JJ, Carr PM, Atucha A, Cambardella C, Davis DR, Delate K. 2016. Organic farming, soil health, and food quality: Considering possible links. Adv. Agron. 137:319-367. https://doi.org/10.1016/bs.agron.2015.12.003
10.1016/bs.agron.2015.12.003Rodríguez-Espinosa T, Papamichael I, Voukkali I, Gimeno AP, Candel MBA, Navarro-Pedreño J, Zorpas AA, Lucas IG. 2023. Nitrogen management in farming systems under the use of agricultural wastes and circular economy. Sci Total Env. 876:162666. https://doi.org/10.1016/j.scitotenv.2023.162666
10.1016/j.scitotenv.2023.162666Schinner F, von Mersi W. 1990. Xylanase-, Cm-cellulase-and invertase activity in soil: An improved method. Soil Biol. Bioch. 22:511-515. https://doi.org/10.1016/0038-0717(90)90187-5
10.1016/0038-0717(90)90187-5Tabatabai MA. 1994. Soil Enzymes. Methods of Soil Analysis: Part 2 Microbiological and Biochemical Properties 5: 775-833. https://doi.org/10.2136/sssabookser5.2.c37
10.2136/sssabookser5.2.c37van Bruggen AHC, Gamliel A, Finckh MR. 2016. Plant disease management in organic farming systems.” Pest Man. Sci. 72:30-44. https://doi.org/10.1002/ps.4145
10.1002/ps.4145Yamagata M, Nakagawa K, Ae N. 1997. Difference of protease activity between crops in rhizosphere. Soil Sci. Plant Nut. 68:295-300. https://doi.org/10.20710/dojo.68.3_295
10.20710/dojo.68.3_295Yu T, Yang R, Jie X, Lian T, Zang H, Zeng Z, Yang Y. 2024. Organic management improved the multifunctionality in recolonization soil by increasing microbial diversity and function. Funct. Ecol. 38:2207-2219. https://doi.org/10.1111/1365-2435.14637
10.1111/1365-2435.14637Zhang X, Davidson EA, Mauzerall DL, Searchinger TD, Dumas P, Shen Y. 2015. Managing nitrogen for sustainable development. Nature 528:51-59. https://doi.org/10.1038/nature15743
10.1038/nature15743- Publisher :Korean Society of Soil Science and Fertilizer
- Publisher(Ko) :한국토양비료학회
- Journal Title :Korean Journal of Soil Science and Fertilizer
- Journal Title(Ko) :한국토양비료학회 학회지
- Volume : 59
- No :1
- Pages :12-24
- Received Date : 2025-08-26
- Revised Date : 2025-12-14
- Accepted Date : 2025-12-24
- DOI :https://doi.org/10.7745/KJSSF.2026.59.1.012
Korean Journal of Soil Science and Fertilizer
