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Different microbial communities in paddy soils under organic and nonorganic farming

  • Soil and Agricultural Microbiology - Research Paper
  • Published:
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Abstract  

Organic agriculture is a farming method that provides healthy food and is friendly to the environment, and it is developing rapidly worldwide. This study compared microbial communities in organic farming (Or) paddy fields to those in nonorganic farming (Nr) paddy fields based on 16S rDNA sequencing and analysis. The predominant microorganisms in both soils were Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, and Nitrospirota. The alpha diversity of the paddy soil microbial communities was not different between the nonorganic and organic farming systems. The beta diversity of nonmetric multidimensional scaling (NMDS) revealed that the two groups were significantly separated. Distance-based redundancy analysis (db-RDA) suggested that soil pH and electrical conductivity (EC) had a positive relationship with the microbes in organic paddy soils. There were 23 amplicon sequence variants (ASVs) that showed differential abundance. Among them, g_B1-7BS (Proteobacteria), s_Sulfuricaulis limicola (Proteobacteria), g_GAL15 (p_GAL15), c_Thermodesulfovibrionia (Nitrospirota), two of f_Anaerolineaceae (Chloroflexi), and two of g_S085 (Chloroflexi) showed that they were more abundant in organic soils, whereas g_11-24 (Acidobacteriota), g__Subgroup_7 (Acidobacteriota), and g_Bacillus (Firmicutes) showed differential abundance in nonorganic paddy soils. Functional prediction of microbial communities in paddy soils showed that functions related to carbohydrate metabolism could be the major metabolic activities. Our work indicates that organic farming differs from nonorganic farming in terms of microbial composition in paddy soils and provides specific microbes that might be helpful for understanding soil fertility.

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Acknowledgements

The authors would like to thank Chien-Ni Wei for her correction on English writing.

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Authors and Affiliations

  1. Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung, 94450, Taiwan

    Jimmy Kuo

  2. Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, 94450, Taiwan

    Jimmy Kuo

  3. Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan

    Daniel Liu, Wei Hao Wen & Chorng-Horng Lin

  4. Department of Bioresources, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan

    Ching Yuan Chiu, Wanyu Chen & Yun Wen Wu

  5. Department of Medicinal Botanicals and Foods On Health Applications, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan

    Fang-Ting Lai

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Contributions

All authors contributed to the study conception and design. Material preparation, data collection, and analysis were performed by W.H.W., C.Y.C., W.C., Y.W.W., F.-T.L., and C.-H.L. The first draft of the manuscript was written by J.K., D.L., and C.-H.L. All authors read and approved the final manuscript.

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Kuo, J., Liu, D., Wen, W.H. et al. Different microbial communities in paddy soils under organic and nonorganic farming. Braz J Microbiol 55, 777–788 (2024). https://doi.org/10.1007/s42770-023-01218-5

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