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

Xiaoxuan Su, Gang Li, James B. Cotner, Lai Wei, Yingmu Wang, Ting Pan, Kai Ding

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)799-809
Number of pages11
JournalJournal of Soils and Sediments
Issue number2
StatePublished - Jan 7 2021

Bibliographical note

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

Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature.


  • Active microbes
  • Bacterial community
  • Biochemical process
  • Functional genes
  • Organic fertilization


Dive into the research topics of 'Long-term organic fertilization changes soil active bacterial composition and multifunctionality: RNA-based bacterial community and qPCR-based SmartChip analysis'. Together they form a unique fingerprint.

Cite this