Strong agricultural management effects on soil microbial community in a non-experimental agroecosystem

Jing ZHOU, Jonathan J. FONG*

*Corresponding author for this work

Research output: Journal PublicationsJournal Article (refereed)peer-review

19 Citations (Scopus)


Soil microbial communities are indicators of soil health and are affected by factors such as agricultural management, plant selection and soil compartment. It remains unclear how these factors interact and affect microbial community structure and function in non-experimental agroecosystems. In this study, we take a holistic approach to investigate the composition and function of the bacterial and fungal communities associated with different agricultural management systems (organic/conventional) of two crop species (cabbage/lettuce) in two soil compartments (rhizosphere/bulk) using Illumina sequencing. Microbial alpha diversity indices were higher in soils from the organic compared to conventional system. Microbial beta diversities were significantly affected by both individual [agricultural management (M) and plant selection (P)] and interactive (M × P) effects. Bacterial and fungal community composition were more strongly influenced by agricultural management (explained 26.0% and 18.0%, respectively) compared to plant selection (8.5% and 12.0%), soil compartment (2.4% and 1.1%) and interactions between factors (0.1–2.4%). Soils from the organic system had higher pH, organic matter concentration and available phosphorus, and pH was identified as having the largest influence on bacterial and fungal communities. Taxonomic and functional analyses identified potential benefits of soils from the organic system, such as having higher levels of plant disease suppression (Streptomyces) and nutrient cycling (enriched metabolism, higher proportion of taxa in order Rhizobiales). Network analyses inferred that bacterial and fungal networks in soils from the organic system compared to the conventional system are more connected and centralized. Our findings suggest that organic management practices have a large effect increasing diversity, promoting healthier soils via beneficial microbial taxa and functions and supporting more complex bacterial networks.
Original languageEnglish
Article number103970
Number of pages12
JournalApplied Soil Ecology
Early online date16 Mar 2021
Publication statusPublished - 1 Sept 2021

Bibliographical note

We would like to thank Sze Chung CHOW (Sangwoodgoon) and Mr. TSE for allowing access to their farms and information on the history of the region. This research has benefitted from financial support of Lingnan University, Hong Kong Special Administrative Region, China under the Faculty Research Grant Scheme (Project No.: 102173), the Croucher Chinese Visitorship and National Natural Science Foundation of China (No. 41807053), the Young Talents Invitation Program of Shandong Provincial Colleges and Universities (No. 2019-6-1).


  • Bulk soil
  • Conventional farming
  • Organic farming
  • Plant selection
  • Rhizosphere
  • Soil compartment


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