Microbial Ecology

, Volume 77, Issue 4, pp 931–945 | Cite as

Crop Residues in Wheat-Oilseed Rape Rotation System: a Pivotal, Shifting Platform for Microbial Meetings

  • Lydie Kerdraon
  • Marie-Hélène Balesdent
  • Matthieu Barret
  • Valérie LavalEmail author
  • Frédéric SuffertEmail author
Environmental Microbiology


Crop residues are a crucial ecological niche with a major biological impact on agricultural ecosystems. In this study, we used a combined diachronic and synchronic field experiment based on wheat-oilseed rape rotations to test the hypothesis that plant is a structuring factor of microbial communities in crop residues, and that this effect decreases over time with their likely progressive degradation and colonisation by other microorganisms. We characterised an entire fungal and bacterial community associated with 150 wheat and oilseed rape residue samples at a plurennial scale by metabarcoding. The impact of plant species on the residue microbiota decreased over time and our data revealed turnover, with the replacement of oligotrophs, often plant-specific genera (such as pathogens) by copiotrophs, belonging to more generalist genera. Within a single cropping season, the plant-specific genera and species were gradually replaced by taxa that are likely to originate from the soil. These changes occurred more rapidly for bacteria than for fungi, known to degrade complex compounds. Overall, our findings suggest that crop residues constitute a key fully-fledged microbial ecosystem. Taking into account this ecosystem, that has been neglected for too long, is essential, not only to improve the quantitative management of residues, the presence of which can be detrimental to crop health, but also to identify groups of beneficial microorganisms. Our findings are of particular importance, because the wheat-oilseed rape rotation, in which no-till practices are frequent, is particularly widespread in the European arable cropping systems.


Community succession Microbial diversity Oilseed rape Residue microbiota Wheat 



This study was performed in collaboration with the GeT core facility, Toulouse, France ( and was supported by France Génomique National Infrastructure, funded as part of ‘Investissement d’avenir’ program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). We thank Martial Briand (INRA, UMR IRHS) and Dr. Gautier Richard (INRA, UMR IGEPP) for assistance with bioinformatic analyses, and Dr. Thierry Rouxel (INRA, UMR BIOGER) for improving and clarifying this manuscript. We thank Julie Sappa for her help correcting our English. We finally thank the reviewers for their insightful comments on the paper, as these comments led us to improve the correctness of several analyses.

Authors’ Contributions

LK, FS, VL, MHB and MB conceived the study, participated in its design, and wrote the manuscript. LK conducted the experiments and analysed the data. FS and VL supervised the project. All authors read and approved the final manuscript.


This study was supported by a grant from the European Union Horizon Framework 2020 Program (EMPHASIS Project, Grant Agreement No. 634179) covering the 2015–2019 period.

Supplementary material

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ESM 14 Bacterial 16S sequence dataset (also deposited in GitHub: (RDATA 26533 kb)
ESM 15 ・Fungal ITS sequence dataset (also deposited in GitHub: (RDATA 5952 kb)
ESM 16 – R scripts used to analyze the bacterial 16S sequence dataset (also deposited in GitHub: (R 9 kb)
ESM 17 – R scripts used to analyze the fungal ITS sequence dataset (also deposited in GitHub: (R 8 kb)


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Authors and Affiliations

  1. 1.UMR BIOGER, INRA, AgroParisTechUniversité Paris-SaclayThiverval-GrignonFrance
  2. 2.UMR IRHS, INRA, Agrocampus OuestUniversité d’AngersBeaucouzéFrance

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