Skip to main content

Effects of cover crop in an apple orchard on microbial community composition, networks, and potential genes involved with degradation of crop residues in soil


Changes in the soil microbial communities and networks were monitored after planting the cover crop for 9 years. The field experiment included plots with a cover crop and without a cover crop but with weed control, and two subplots with or without chemical fertilizer (192 kg N ha−1, 108 kg P2O5 ha−1, and 168 kg K2O ha−1 each year). After applying the cover crop and chemical fertilizer for 9 years, the composition and activity of bacterial and fungal communities changed significantly (p < 0.05), with the cover crop had greater effects than the chemical fertilizer on the composition of the soil microbial community. The relative abundances of 22 selected genera (in Firmicutes and Bacteroidetes) and two selected classes (Ascomycota) related to cover crop residue degradation increased significantly in the presence of the cover crop (p < 0.05). Network analysis showed that the cover crop decreased the number of positive links between bacterial and fungal taxa by 25.33%, and increased the negative links by 22.89%. The positive links among bacterial taxa increased by 16.63% with the cover crop, mainly among Proteobacteria (increase of 39), Firmicutes (16), Actinobacteria (five), and Bacteroidetes (10). The links among fungal taxa were less than among bacterial taxa and were not significantly affected by cover crop. Taxa such as Thaumarchaeota, unidentified_Nitrospiraceae, unidentified_Nitrosomonadaceae, Faecalibacterium, Coprococcus_3, and Ruminococcaceae_NK4A214_group dominated the network without the cover crop but they were not dominant with the cover crop. The relative abundances of potential genes involved with the degradation of cellulose, hemicellulose, and cello-oligosaccharides increased significantly with the cover crop. Therefore, the SOC and TN contents were enhanced by the cover crop with the increase of the soil enzyme activities. Thus, the apple yield was improved by the cover crop.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6


Download references


This study was supported by the Special Fund for Agro-scientific Research in the Public Interest of China (201303104, 201103005-9), Agriculture Science Technology Achievement Transformation Fund of Shaanxi (NYKJ-2015-17), the Science and Technology Innovation Project of Shaanxi Province (2011KTZB02-02-05).

Author information

Authors and Affiliations


Corresponding authors

Correspondence to Bingnian Zhai or Ziyan Li.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Zheng, W., Zhao, Z., Gong, Q. et al. Effects of cover crop in an apple orchard on microbial community composition, networks, and potential genes involved with degradation of crop residues in soil. Biol Fertil Soils 54, 743–759 (2018).

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:


  • Grass cover
  • Mulch
  • Soil enzyme
  • Soil microbial community
  • Soil network
  • Soil organic matter