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Stimulation of Different Functional Groups of Bacteria by Various Plant Residues as a Driver of Soil Priming Effect

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Abstract

The turnover of organic matter in soil depends on the activity of microbial decomposers. However, little is known about how modifications of the diversity of soil microbial communities induced by fresh organic matter (FOM) inputs can regulate carbon cycling. Here, we investigated the decomposition of two 13C labeled crop residues (wheat and alfalfa) and the dynamics of the genetic structure and taxonomic composition of the soil bacterial communities decomposing 13C labeled FOM and native unlabeled soil organic matter (SOM), respectively. It was achieved by combining the stable isotope probing method with molecular tools (DNA genotyping and pyrosequencing of 16S rDNA). Although a priming effect (PE) was always induced by residue addition, its intensity increased with the degradability of the plant residue. The input of both wheat and alfalfa residues induced a rapid dynamics of FOM-degrading communities, corresponding to the stimulation of bacterial phyla which have been previously described as copiotrophic organisms. However, the dynamics and the identity of the bacterial groups stimulated depended on the residue added, with Firmicutes dominating in the wheat treatment and Proteobacteria dominating in the alfalfa treatment after 3 days of incubation. In both treatments, SOM-degrading communities were dominated by Acidobacteria, Verrucomicrobia, and Gemmatimonadetes phyla which have been previously described as oligotrophic organisms. An early stimulation of SOM-degrading populations mainly belonging to Firmicutes and Bacteroidetes groups was observed in the alfalfa treatment whereas no change occurred in the wheat treatment. Our findings support the hypothesis that the succession of bacterial taxonomic groups occurring in SOM- and FOM-degrading communities during the degradation process may be an important driver of the PE, and consequently of carbon dynamics in soil.

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Acknowledgments

This study was financially supported by the Agence de l’Environnement et de la Maîtrise de l’Energie (ADEME), the French National Agency ANR (DIMIMOS project), the Burgundy region, and the European EcoFinders project. We thank Christopher Hunter (EMG, EMBL-EBI, Cambridge, UK) for his help in submitting sequences to SRA–EBI database.

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Authors and Affiliations

  1. UMR Agroecology, INRA/Université de Bourgogne, CMSE, BP 86510, 17 rue de Sully, 21065, Dijon Cedex, France

    Noémie Pascault, Lionel Ranjard, Aurore Kaisermann, Sébastien Terrat, Christophe Mougel, Catherine Henault, Philippe Lemanceau & Pierre-Alain Maron

  2. INRA, Plateforme GenoSol, UMR1347 Agroécologie, BP 86510, 21000, Dijon, France

    Lionel Ranjard, Sébastien Terrat & Pierre-Alain Maron

  3. Laboratoire de Biologie Virtuelle, Centre de Biochimie, Parc Valose, Université de Nice et CNRS UMR 6543, 06108, Nice, France

    Dipankar Bachar & Richard Christen

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

    Olivier Mathieu & Jean Lévêque

  5. CEA, DSV, IBEB, Group Rech Appl Phytotechol, UMR 6191 CEA/CNRS/Université Aix-Marseille, 13108, Saint-Paul-lez-Durance, France

    Michel Péan & Séverine Boiry

  6. UR874 Unité de Recherche sur l’Ecosystème Prairial, INRA, 234 avenue du Brézet, 63100, Clermont-Ferrand, France

    Sébastien Fontaine

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  1. Noémie Pascault
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Correspondence to Pierre-Alain Maron.

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Author Contributions

NP performed the research; NP and AK jointly conducted the incubations; DB, RC, and CM performed bioinformatic analysis; OM and JL performed 13C analysis; CH performed PLFA analysis; MP labeled the plants; PL and SF commented on the manuscript, the modeling and the statistical analyses; PAM and LR designed the study; PAM wrote the first version of the manuscript. All the authors contributed substantially to revisions.

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10021_2013_9650_MOESM1_ESM.tif

Figure 1S. Example of B-ARISA profile obtained from light and heavy DNA fractions of wheat amended microcosms after 3, 7, 14, 28, 60 and 120 days of incubation. Molecular mass (in base pairs) is indicated on the left (TIF 1500 kb)

10021_2013_9650_MOESM2_ESM.tif

Figure 2S. Principal component analysis (PC1xPC2) plots generated from B-ARISA profiles obtained from DNA extracted from the heavy fractions of wheat- and alfalfa-amended microcosms. Grey labels represent the alfalfa treatment; black labels represent the wheat treatment. Numbers represent days of incubation. Lines correspond to the three replicate samples performed for each sampling point (TIF 270 kb)

10021_2013_9650_MOESM3_ESM.tif

Figure 3S. Rarefaction curves determined by pyrosequencing of the 16S rDNA gene obtained for the heavy and light DNA fractions from wheat (A) and alfalfa (B) amended microcosms after 3, 14, and 60 days of incubation. Rarefaction curves were determined using clustering at K = 3 differences (TIF 863 kb)

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Pascault, N., Ranjard, L., Kaisermann, A. et al. Stimulation of Different Functional Groups of Bacteria by Various Plant Residues as a Driver of Soil Priming Effect. Ecosystems 16, 810–822 (2013). https://doi.org/10.1007/s10021-013-9650-7

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