Changes in Essential Soil Nutrients and Soil Disturbance Directly Affected Soil Microbial Community Structure: A Metagenomic Approach

• Autorzy: Wiryawan Adam , Eginarta Wahyu Satria , Hermanto Feri Eko , Ustiatik Reni , Dinira Layta , Mustafa Irfan

Identyfikatory

DOI

10.12911/22998993/149972

• Języki publikacji: EN

Abstrakty

EN

Soil environment, both biotic (e.g., microbial community) and abiotic (e.g., nutrients and water availability) factors determine soil fertility and health and are directly affected by soil management systems. However, only limited studies evaluate the combined effect of nutrients availability and soil disturbance on the soil bacteria community structure, especially in conventional agricultural practices, on the forests converted to agricultural land. This study aimed to provide a viewpoint of the effect of different soil management systems, i.e., forest soil (natural process) and tilled land, on soil bacteria community structure on forest converted to agricultural land, according to a metagenomics approach. Moreover, each land use was sampled to identify the bacterial community using 16S gene as a biomarker. The sequencing was performed using MinION (Oxford Nanopore Technologies) to read the DNA sequence from each soil sample. Principle Component Analysis (PCA) was performed to comprehend the relationship between availability of nutrients and bacterial diversity. The results revealed that the concentrations of soil micronutrients, such as iron, zinc, and magnesium, were significantly higher in forest soil than in tilled land. According to diversity indices, soil bacteria were more diverse in forest soil than in tilled land. Forest soil had more distinctive taxa than tilled land. Several species comprised the most abundant taxa, such as Candidatus Koribacter versatilis, Candidatus Solibacter usiatus, Rhodoplanes sp., Luteitalea pratensis, and Betaproteobacteria bacterium, were more scarce in tilled land. On the distinctive taxa in each soil sample, Anseongella ginsenosidimutans and Janthinobacterium sp. were the most abundant species in forest and tilled land, respectively. According to PCA analysis, soil management system affected the soil micro-and macronutrients also microbial community structure between forest and tilled land. In conclusion, soil management influences the essential nutrient content and bacterial community structure of soil. Better management should be adopted to maintain soil quality near forest soil.

Słowa kluczowe

EN

forest soil; metagenome; soil bacteria; soil nutrients; tilled land

• Wydawca: Polskie Towarzystwo Inżynierii Ekologicznej ; Lublin University of Technology
• Czasopismo: Journal of Ecological Engineering
• Rocznik: 2022
• Tom: Vol. 23, nr 7
• Strony: 238--245
• Opis fizyczny: Bibliogr. 35 poz., rys., tab.

Twórcy

autor

Wiryawan Adam

• Department of Chemistry, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jl. Veteran, Malang, East Java, 65145, Indonesia

autor

Eginarta Wahyu Satria

• Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jl. Veteran, Malang, East Java, 65145, Indonesia

autor

Hermanto Feri Eko

• Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jl. Veteran, Malang, East Java, 65145, Indonesia

autor

Ustiatik Reni

• Department of Soil Science, Faculty of Agriculture, Brawijaya University, Jl. Veteran, Malang, East Java, 65145, Indonesia

• https://orcid.org/0000-0001-7703-1874

autor

Dinira Layta

• Department of Chemistry, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jl. Veteran, Malang, East Java, 65145, Indonesia

autor

Mustafa Irfan

• Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jl. Veteran, Malang, East Java, 65145, Indonesia

Bibliografia

• 1. Allen K., Corre M.D., Kurniawan S., Utami S.R., Veldkamp E. 2016. Spatial variability surpasses land-use change effects on soil biochemical properties of converted lowland landscapes in Sumatra, Indonesia. Geoderma, 284, 42–50.
• 2. Alvarez R., Steinbach H.S. 2009. A review of the effects of tillage systems on some soil physical properties, water content, nitrate availability and crops yield in the Argentine Pampas. Soil and Tillage Research, 104, 1–15.
• 3. Bargaz A., Lyamlouli K., Chtouki M., Zeroual Y., Dhiba D. 2018. Soil Microbial Resources for Improving Fertilizers Efficiency in an Integrated Plant Nutrient Management System. Frontiers in Microbiology, 9.
• 4. Breitwieser F.P., Salzberg S.L. 2020. Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification. Bioinformatics, 36, 1303–1304.
• 5. Busari M.A., Kukal S.S., Kaur A., Bhatt R., Dulazi A.A. 2015. Conservation tillage impacts on soil, crop and the environment. International Soil and Water Conservation Research, 3, 119–129.
• 6. Dang C., Kellner E., Martin G., Freedman Z.B., Hubbart J., Stephan K., Kelly C. N., Morrissey E. M. 2021. Land use intensification destabilizes stream microbial biodiversity and decreases metabolic efficiency. Science of the Total Environment, 767.
• 7. De Coster W., D’Hert S., Schultz D. T., Cruts M., Van Broeckhoven C. 2018. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics, 34, 2666–2669.
• 8. Dubey A., Malla M.A., Khan F., Chowdhary K., Yadav S., Kumar A., Sharma S., Khare P.K., Khan M.L. 2019. Soil microbiome: a key player for conservation of soil health under changing climate. Biodiversity and Conservation, 28, 2405–2429.
• 9. Durrer A., Gumiere T., Zagatto M.R.G., Feiler H.P., Silva A.M.M., Longaresi R.H., Homma S. K., Cardoso E.J.B.N. 2021. Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields. PeerJ, 9, 1–24.
• 10. Fortier J., Truax B., Gagnon D., Lambert F. 2019. Abiotic and biotic factors controlling fine root biomass, carbon and nutrients in closed-canopy hybrid poplar stands on post-agricultural land. Scientific Reports, 9, 1–15.
• 11. Giweta M. 2020. Role of litter production and its decomposition, and factors affecting the processes in a tropical forest ecosystem: A review. Journal of Ecology and Environment, 44, 1–9.
• 12. Holden S.R., Treseder K.K. 2013. A meta-analysis of soil microbial biomass responses to forest disturbances. Frontiers in Microbiology, 4, 1–17.
• 13. Issaka F., Zhang Z., Zhao Z.Q., Asenso E., Li J.H., Li Y.T., Wang J.J. 2019. Sustainable conservation tillage improves soil nutrients and reduces nitrogen and phosphorous losses in maize farmland in southern China. Sustainability (Switzerland), 11.
• 14. 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, 1–19.
• 15. Jin J., Wang L., Müller K., Wu J., Wang H., Zhao K., Berninger F., Fu W. 2021. A 10-year monitoring of soil properties dynamics and soil fertility evaluation in Chinese hickory plantation regions of southeastern China. Scientific Reports, 11, 1–13.
• 16. Kim D., Song L., Breitwieser F.P., Salzberg S.L. 2016. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res., 26, 1721–1729.
• 17. Koorem K., Gazol A., Öpik M., Moora M., Saks Ü., Uibopuu A., Sõber V., Zobel M. 2014. Soil nutrient content influences the abundance of soil microbes but not plant biomass at the small-scale. PLoS ONE, 9, 1–9.
• 18. Koshila Ravi R., Anusuya S., Balachandar M., Muthukumar T. 2019. Microbial Interactions in Soil Formation and Nutrient Cycling. Mycorrhizosphere and Pedogenesis, 363–382.
• 19. Kurniawan S., Corre M. D., Utami S. R., Veldkamp E. 2018. Soil biochemical properties and nutrient leaching from smallholder oil palm plantations, Sumatra-Indonesia. Agrivita, 40, 257–266.
• 20. Kurniawan S., Utami S. R., Mukharomah M., Navarette I. A., Prasetya B. 2019. Land use systems, soil texture, control carbon and nitrogen storages in the forest soil of ub forest, Indonesia. Agrivita, 41, 416–427.
• 21. Lehmann J., Bossio D.A., Kögel-Knabner I., Rillig M.C. 2020. The concept and future prospects of soil health. Nature Reviews Earth and Environment, 1, 544–553.
• 22. Madegwa Y.M., Uchida Y. 2021. Land use and season drive changes in soil microbial communities and related functions in agricultural soils. Environmental DNA, 3, 1214–1228.
• 23. Oliveira H.B. de, Rocha E., Teles T., Florentino L.A. 2022. Microbial Activity in the Agricultural and Forestry System. Research, Society and Development, 11, e56211226184.
• 24. Page K.L., Dang Y.P., Dalal R.C. 2020. The Ability of Conservation Agriculture to Conserve Soil Organic Carbon and the Subsequent Impact on Soil Physical, Chemical, and Biological Properties and Yield. Frontiers in Sustainable Food Systems, 4, 1–17.
• 25. Saleem M., Hu J., Jousset A. 2019. More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health. Annual Review of Ecology, Evolution, and Systematics, 50, 145–168.
• 26. de Santiago A., Quintero J.M., Delgado A. 2008. Long-term effects of tillage on the availability of iron, copper, manganese, and zinc in a Spanish Vertisol. Soil and Tillage Research, 98, 200–207.
• 27. Shiwakoti S., Zheljazkov V.D., Gollany H.T., Kleber M., Xing B. 2019. Micronutrients decline under long-term tillage and nitrogen fertilization. Scientific Reports, 9, 1–9.
• 28. Singh J.S., Gupta V.K. 2018. Soil microbial biomass: A key soil driver in management of ecosystem functioning. Science of the Total Environment, 634, 497–500.
• 29. Sui X., Zhang R., Frey B., Yang L., Li M.H., Ni H. 2019. Land use change effects on diversity of soil bacterial, Acidobacterial and fungal communities in wetlands of the Sanjiang Plain, northeastern China. Scientific Reports, 9, 1–14.
• 30. Szostek M., Szpunar-Krok E., Pawlak R., Stanek-Tarkowska J., Ilek A. 2022. Effect of Different Tillage Systems on Soil Organic Carbon and Enzymatic Activity. Agronomy, 12, 1–16.
• 31. Tibbett M., Fraser T.D., Duddigan S. 2020. Identifying potential threats to soil biodiversity. PeerJ, 8, e9271.
• 32. Ustiatik R., Nuraini Y., Suharjono S., Jeyakumar P., Anderson C.W.N., Handayanto E. 2021. Mercury resistance and plant growth promoting traits of endophytic bacteria isolated from mercury-contaminated soil. Bioremediation Journal, 0, 1–20.
• 33. Wang X., He T., Gen S., Zhang X. Q., Wang X., Jiang D., Li C., Li C., Wang J., Zhang W., Li C. 2020. Soil properties and agricultural practices shape microbial communities in flooded and rainfed croplands. Applied Soil Ecology, 147, 103449.
• 34. Wick R.R., Judd L.M., Holt K. E. 2019. Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biology, 20, 129.
• 35. Willy D.K., Muyanga M., Mbuvi J., Jayne T. 2019. The effect of land use change on soil fertility parameters in densely populated areas of Kenya. Geoderma, 343, 254–262.