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In Situ Dynamics of Microbial Communities during Decomposition of Wheat, Rape, and Alfalfa Residues

  • Environmental Microbiology
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Abstract

Microbial communities are of major importance in the decomposition of soil organic matter. However, the identities and dynamics of the populations involved are still poorly documented. We investigated, in an 11-month field experiment, how the initial biochemical quality of crop residues could lead to specific decomposition patterns, linking biochemical changes undergone by the crop residues to the respiration, biomass, and genetic structure of the soil microbial communities. Wheat, alfalfa, and rape residues were incorporated into the 0–15 cm layer of the soil of field plots by tilling. Biochemical changes in the residues occurring during degradation were assessed by near-infrared spectroscopy. Qualitative modifications in the genetic structure of the bacterial communities were determined by bacterial-automated ribosomal intergenic spacer analysis. Bacterial diversity in the three crop residues at early and late stages of decomposition process was further analyzed from a molecular inventory of the 16S rDNA. The decomposition of plant residues in croplands was shown to involve specific biochemical characteristics and microbial community dynamics which were clearly related to the quality of the organic inputs. Decay stage and seasonal shifts occurred by replacement of copiotrophic bacterial groups such as proteobacteria successful on younger residues with those successful on more extensively decayed material such as Actinobacteria. However, relative abundance of proteobacteria depended greatly on the composition of the residues, with a gradient observed from alfalfa to wheat, suggesting that this bacterial group may represent a good indicator of crop residues degradability and modifications during the decomposition process.

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Acknowledgement

This ECOGER project was supported by an ECCO grant from the French National Research Agency (ANR). N. Pascault received a grant from the Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME), and the Burgundy region. The authors are grateful to the CEMAGREF of Grenoble and S. De Danieli and J.J. Brun for the NIR analysis. Thanks are also extended to C. Faivre, S. Dequiedt, and F. Bastian for their technical help.

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Authors and Affiliations

  1. UMR Microbiologie du Sol et de l’Environnement, INRA/Université de Bourgogne, CMSE, BP 86510, 17 rue de Sully, 21065, Dijon Cedex, France

    Noémie Pascault, Catherine Hénault, Amadou Sarr, Lionel Ranjard & Pierre-Alain Maron

  2. UMT GES-N2O, CETIOM Paris-Grignon, Avenue Lucien Brétignières, 78850, Thiverval-Grignon, France

    Lauric Cécillon

  3. UMR 5561Biogéosciences, CNRS/Université de Bourgogne, Université de Bourgogne, 6 bd Gabriel, 21000, Dijon, France

    Olivier Mathieu & Jean Lévêque

  4. Unité Expérimentale, Domaine d’Epoisses, INRA Dijon, 21110, Bretenière, France

    Pascal Farcy

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  1. Noémie Pascault
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  2. Lauric Cécillon
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  9. Pierre-Alain Maron
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Correspondence to Pierre-Alain Maron.

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Figure S1

Supplemental data. Loading matrices of PC1 and PC2 for principal component analysis of NIR fingerprints of all residues (a, b); wheat (c, d); rape (e, f); and alfalfa (g, h) residues. Gray gradation represents loading values from −1 (black) to +1 (white). Threshold values of −0.8 and +0.8 were used for the identification of wavebands explanatory for each principal component represented in Table 1. Wavenumbers are expressed per centimeter. (DOC 602 kb)

Figure S2

Supplemental data. Rarefaction curves for wheat, rape, and alfalfa resides at T22 and T254 day after incorporation to soil, respectively. (DOC 54 kb)

Figure S3

Supplemental data. Microbial C-biomass determined by analysis of the total soil fatty acid (PLFA) content in the soil after incorporation of wheat, rape, and alfalfa residue. (DOC 72 kb)

Figure S4

Supplemental data. Rainfall (mm) and atmospheric temperature (°C) during the experiment. (DOC 78 kb)

Table S1

Supplemental data. Closest affiliations of 16S rDNA sequences cloned from DNA extracted from wheat, rape, and alfalfa residue for July 2006 and March 2007 (22 and 254 days after incorporation, respectively). The accession numbers for the 16S rDNA gene sequences were deposited in the GeneBank database (from GQ379348 to GQ379673). (DOC 451 kb)

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Pascault, N., Cécillon, L., Mathieu, O. et al. In Situ Dynamics of Microbial Communities during Decomposition of Wheat, Rape, and Alfalfa Residues. Microb Ecol 60, 816–828 (2010). https://doi.org/10.1007/s00248-010-9705-7

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