Mapping and Predictive Variations of Soil Bacterial Richness across French National Territory

doi:10.15468/k3589t

Mapping and Predictive Variations of Soil Bacterial Richness across French National Territory

Citation

MGnify (2020). Mapping and Predictive Variations of Soil Bacterial Richness across French National Territory. Sampling event dataset https://doi.org/10.15468/k3589t accessed via GBIF.org on 2024-12-13.

Description

Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and the determinism of such diversity on a wide scale. The overall objectives of this study were i) to describe the bacterial taxonomic richness variations across French national territory, ii) to identify the ecological processes (i.e. selection by the environment and dispersal limitation) and environmental filters most 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 rDNA genes directly amplified from DNA of all soil samples 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 111 km, where the main drivers were the soil physico-chemical properties, the spatial descriptors and the land use. 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.

Sampling Description

Sampling

Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and the determinism of such diversity on a wide scale. The overall objectives of this study were i) to describe the bacterial taxonomic richness variations across French national territory, ii) to identify the ecological processes (i.e. selection by the environment and dispersal limitation) and environmental filters most 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 rDNA genes directly amplified from DNA of all soil samples 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 111 km, where the main drivers were the soil physico-chemical properties, the spatial descriptors and the land use. 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.

Method steps

Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/5.0

Taxonomic Coverages

Geographic Coverages

Bibliographic Citations

Djemiel C, Dequiedt S, Karimi B, Cottin A, Girier T, El Djoudi Y, Wincker P, Lelièvre M, Mondy S, Chemidlin Prévost-Bouré N, Maron PA, Ranjard L, Terrat S. 2020. BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons. BMC Bioinformatics vol. 21 - DOI:10.1186/s12859-020-03829-3
Karimi B, Dequiedt S, Terrat S, Jolivet C, Arrouays D, Wincker P, Cruaud C, Bispo A, Chemidlin Prévost-Bouré N, Ranjard L. 2019. Biogeography of Soil Bacterial Networks along a Gradient of Cropping Intensity. Sci Rep vol. 9 - DOI:10.1038/s41598-019-40422-y
Karimi B, Terrat S, Dequiedt S, Saby NPA, Horrigue W, Lelièvre M, Nowak V, Jolivet C, Arrouays D, Wincker P, Cruaud C, Bispo A, Maron PA, Bouré NCP, Ranjard L. 2018. Biogeography of soil bacteria and archaea across France. Sci Adv vol. 4 - DOI:10.1126/sciadv.aat1808
Terrat S, Horrigue W, Dequiedt S, Saby NPA, Lelièvre M, Nowak V, Tripied J, Régnier T, Jolivet C, Arrouays D, Wincker P, Cruaud C, Karimi B, Bispo A, Maron PA, Chemidlin Prévost-Bouré N, Ranjard L. 2017. Mapping and predictive variations of soil bacterial richness across France. PLoS One vol. 12 - DOI:10.1371/journal.pone.0186766

Contacts

originator
The French National Sequencing Center (Genoscope)
Le Ponant Building D - 25 rue Leblanc
PARIS - RCS B 775 685 019
75015
FR
Telephone: +33 (0) 1 64 50 20 59

metadata author
The French National Sequencing Center (Genoscope)
Le Ponant Building D - 25 rue Leblanc
PARIS - RCS B 775 685 019
75015
FR
Telephone: +33 (0) 1 64 50 20 59

administrative point of contact
The French National Sequencing Center (Genoscope)
Le Ponant Building D - 25 rue Leblanc
PARIS - RCS B 775 685 019
75015
FR
Telephone: +33 (0) 1 64 50 20 59