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Long-term organic fertilization changes soil active bacterial composition and multifunctionality: RNA-based bacterial community and qPCR-based SmartChip analysis

  • Soils, Sec 1 • Soil Organic Matter Dynamics and Nutrient Cycling • Research Article
  • Published:
Journal of Soils and Sediments Aims and scope Submit manuscript

Abstract

Purpose

Organic amendments greatly influence soil functions and biochemical processes that are driven by soil active microbiota. Yet, how organic fertilization impacts transcriptionally active microbes and impacts soil ecosystem functions is still largely unknown. In this study, the variations of RNA-based soil active bacteria and multifunctionality in response to long-term organic fertilization were investigated.

Methods

We selected an experimental observation station with the application of organic fertilizers for 30 years. High-throughput sequencing and qPCR-based SmartChip assays were employed to explore the abundance, diversity, composition, and function of soil active microorganisms under different application regimes.

Results

Organic fertilization increased soil transcriptionally active bacterial abundances significantly, and changed their compositions compared to control treatment. Of the differentially active bacteria, Bacillus was the most abundant genus which was increased by organic fertilization dramatically. Unexpectedly, however, the impacts of organic fertilization on the active communities did not demonstrate a dose-dependent response at the RNA level. SmartChip analysis further indicated that organic fertilization significantly increased the abundances of 25 functional genes associated with energy metabolism, organic matter degradation, denitrification, phosphorus solubilization, sulfur oxidation, and sulfate reduction processes. In addition, soil multifunctionality was also promoted by organic fertilization, and such promotion had a strong relationship with the differentially active bacteria, suggesting that the variations of soil ecosystem functions could be mainly regulated by differentially active bacterial communities.

Conclusion

Organic fertilization impacted the abundances and compositions of soil active bacteria, and increased soil multifunctionality. Understanding dynamic changes in soil active microbes is therefore crucial for managing application regimes of organic fertilizers in agricultural practices and evaluating element biogeochemical cycling in soil.

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Funding

This study was funded by the National Youth Science Foundation of China (41701299), and the China Postdoctoral Science Foundation (2019M662253).

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Authors and Affiliations

  1. Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China

    Xiaoxuan Su, Gang Li, Lai Wei, Ting Pan & Kai Ding

  2. Zhejiang Key Lab of Urban Environment Process and Pollution Control, Ningbo Urban Environment Observation and Research Station—NUEORS, Chinese Academy of Sciences, Ningbo, 315830, China

    Gang Li

  3. Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, 55108, USA

    James B. Cotner

  4. College of Civil Engineering, Fuzhou University, Fuzhou, 350116, China

    Yingmu Wang

  5. University of Chinese Academy of Sciences, Beijing, 100049, China

    Ting Pan

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  1. Xiaoxuan Su
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  4. Lai Wei
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  7. Kai Ding
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Correspondence to Kai Ding.

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Su, X., Li, G., Cotner, J.B. et al. Long-term organic fertilization changes soil active bacterial composition and multifunctionality: RNA-based bacterial community and qPCR-based SmartChip analysis. J Soils Sediments 21, 799–809 (2021). https://doi.org/10.1007/s11368-020-02854-2

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  • DOI: https://doi.org/10.1007/s11368-020-02854-2

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