Mapping and predictive variations of soil bacterial richness across France

PLoS One. 2017 Oct 23;12(10):e0186766. doi: 10.1371/journal.pone.0186766. eCollection 2017.

Abstract

Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and determinants of such diversity on a nationwide scale. The overall objectives of this study were i) to describe the bacterial taxonomic richness variations across France, ii) to identify the ecological processes (i.e. selection by the environment and dispersal limitation) influencing this distribution, and iii) to develop a statistical predictive model of soil bacterial richness. We used the French Soil Quality Monitoring Network (RMQS), which covers all of France with 2,173 sites. The soil bacterial richness (i.e. OTU number) was determined by pyrosequencing 16S rRNA genes and related to the soil characteristics, climatic conditions, geomorphology, land use and space. Mapping of bacterial richness revealed a heterogeneous spatial distribution, structured into patches of about 111km, where the main drivers were the soil physico-chemical properties (18% of explained variance), the spatial descriptors (5.25%, 1.89% and 1.02% for the fine, medium and coarse scales, respectively), and the land use (1.4%). Based on these drivers, a predictive model was developed, which allows a good prediction of the bacterial richness (R2adj of 0.56) and provides a reference value for a given pedoclimatic condition.

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • France
  • Polymerase Chain Reaction
  • RNA, Ribosomal, 16S / genetics
  • Soil Microbiology*

Substances

  • RNA, Ribosomal, 16S

Grants and funding

This study was granted by ADEME (French Environment and Energy Management Agency) and by “France Génomique” through involvement of the technical facilities of Genoscope (project number ANR-10-INBS-09-08). In addition, due to the involvement of technical facilities at the GenoSol platform of the infrastructure ANAEE France, it also received a grant from the French state through the National Agency for Research under the program “Investments for the Future” (reference ANR-11-INBS-0001). RMQS soil sampling and physico-chemical analyses were supported by a French Scientific Group of Interest on soils: the “GIS Sol”, involving the French Ministry of Ecology, Sustainable Development and Energy (MEEM), the French Ministry of Agriculture (MAP), the French Institute for Environment (IFEN), the Environment and Energy Management Agency (ADEME), the French Institute for Research and Development (IRD) and the National Institute for Agronomic Research (INRA).