file={Texte intégral:/home/acottin/Zotero/storage/VGETRU3D/Djemiel et al. - 2023 - Biogeographical patterns of the soil fungalbacter.pdf:application/pdf},
}
@article{gardi_soil_2009,
title={Soil biodiversity monitoring in {Europe}: ongoing activities and challenges},
volume={60},
issn={1351-0754, 1365-2389},
shorttitle={Soil biodiversity monitoring in {Europe}},
abstract={The increasing interest in soil biodiversity and its protection includes both the biodiversity conservation issues and the mostly unknown economic and ecological values of services provided by soil biodiversity. Inventory and monitoring are necessary tools for the achievement of an adequate level of knowledge regarding soil biodiversity status and for the detection of biodiversity hot spots as well as areas where current levels of biodiversity are under threat of decline. In this paper the main tools and methodological approaches for soil biodiversity measurement are presented. Technical aspects related to the inventory and monitoring activities at a large spatial scale are discussed. A short review of some current experiences of soil biodiversity monitoring at the European level is also presented.},
language={en},
number={5},
urldate={2023-11-07},
journal={European Journal of Soil Science},
author={Gardi, C. and Montanarella, L. and Arrouays, D. and Bispo, A. and Lemanceau, P. and Jolivet, C. and Mulder, C. and Ranjard, L. and Römbke, J. and Rutgers, M. and Menta, C.},
@@ -67,24 +67,27 @@ This dataset allows for in-depth studies of soil microbial ecology at biogeograp
\section*{Background \& Summary}
Soil is the support of many ecosystem services, such as soil fertility, carbon storage waste decomposition, pest control or water retention \cite{guerra_global_2022}.
All these services are mainly supported by the important reservoir of soil microbial biodiversity, encompassing diverse lineages of life, e.g. bacteria, archaea or fungi.
But, soil microbial communities are constantly subjected to various stresses, like human activities through deforestation, land use intensification and global warming.
These stresses have a significant influence on these communities and lead to an overall impact on soil functions.
Soil is the support of many ecosystem services, such as soil fertility, carbon storage, waste decomposition, pest control and pathogens control or water retention \cite{guerra_global_2022}.
All these services are mainly supported by the important reservoir of soil microbial biodiversity, encompassing diverse taxa, e.g. bacteria, archaea or fungi.
However, soil microbiota is constantly subjected to various natural or anthropogenic stresses, associated to deforestation, land use intensification and global warming.
These disturbances have a significant influence on these soil microbial communities and lead to an overall impact on soil functions.
For an efficient conservation of soils, it is essential to be able to detect the emergence and trends of these changes at an early stage.
For the past 15 years, the RMQS ("Réseau de Mesures de la Qualité des Sols" - French Soil Quality Monitoring Network) has been meeting these goals of long-term assessment and monitoring of soil quality in France \cite{imbert_rmqs_2021}.
The RMQS network is based on the monitoring of 2,240 sites representative of French soils and their land use, spread over the whole French territory along a systematic square grid of 16 km x 16 km cells \cite{imbert_rmqs_2021}.
Soil samples, measurements and observations are taken every 10 to 15 years at the center of each grid cell.
As it is, the RMQS is probably one of the most intensive and extensive sampling strategy at the national scale.
The RMQS network is based on the monitoring of 2,240 sites spread over the whole French territory along a systematic square grid of 16 km x 16 km cells, to be representative of the different types of French soils and of their land use\cite{imbert_rmqs_2021}.
Soil sampling, characterization and observations are taken every 15 years at the center of each grid cell.
The RMQS is probably one of the most intensive and extensive sampling strategy at a national scale in Europe \cite{gardi_soil_2009}.
The first sampling campaign in mainland France took place from 2000 to 2009, while the second campaign is currently ongoing (2016 to 2027).
The first campaign focused on soil contamination assessment and made it possible to map key soil parameters (i.e. 28 variables such as pH, carbon organic content or texture) as well as several trace metal elements and persistent organic pollutants \cite{dequiedt_rmqs_2020}.
The first campaign focused on soil contamination assessment and made it possible to map key soil parameters (i.e. 28 variables such as pH, carbon organic content or texture) as well as several trace metal elements and persistent organic pollutants \cite{dequiedt_rmqs_2020}\todo{LR indique citation Jolivet et.al. ?}\url{https://www.gissol.fr/}.
Thanks to the use of various molecular tools, a substantial body of scientific knowledge on soil microbial communities has been already produced \cite{dequiedt_biogeographical_2011, terrat_mapping_2017, karimi_biogeography_2018, karimi_biogeography_2020,djemiel_biogeographical_2023}.
Thanks to the use of various molecular tools, a substantial body of scientific knowledge on RMQS soil microbiota has been already produced \cite{dequiedt_biogeographical_2011, terrat_mapping_2017, karimi_biogeography_2018, karimi_biogeography_2020,djemiel_biogeographical_2023}.
Moreover, several technical developments were conducted to standardize each method and the whole process \cite{terrat_molecular_2012, terrat_meta-barcoded_2015, terrat_reclustor_2020, djemiel_biocom-pipe_2020}.
We therefore decided to perform a reorganization of all available microbiological RMQS datasets (i.e. molecular microbial biomass, fungal:bacterial density ratio, bacterial richness, bacterial taxonomical characterization, bacterial habitat definition and beta-diversity through OTU matrix) to improve the reusage of these datasets, with a focus on easing its linking with other soil measurements from the RMQS.
Indeed, and although France is only the 50th largest country in the world by its total area, France is the third-largest European country, exhibits the third-highest pedological diversity across the world, according to the WRB classification \cite{minasny_global_2010} and France is also known as an extremely diversified territory in terms of land use, climate conditions and biodiversity \cite{karimi_biogeography_2020}. Consequently, these datatsets provides an extensive and relevant playground for successfully improving our understanding on soil microbial communities and their importance in various soil functions.
These datasets will be further enriched through current and future analyses (e.g. fungi microbial datasets, second sampling survey of the RMQS) and we expect that the provided datasets will ease the improvement of our knowledge on soil microbial communities by the whole scientific community.
We therefore decided to perform a reorganization of all available microbiological RMQS datasets (i.e. molecular microbial biomass, fungal:bacterial ratio and densities, bacterial richness, bacterial taxonomic characterization, bacterial habitat definition and beta-diversity through OTU matrix) to improve the reuse of these datasets, with a focus on easing its linking with other soil measurements from the RMQS.
Although France is only the 50th largest country in the world by its total area, it is the third-largest European country, exhibits the third-highest pedological diversity across the world, according to the WRB classification \cite{minasny_global_2010}.
Moreover, France is also known as an extremely diversified territory in terms of land use, climate conditions and biodiversity \cite{karimi_biogeography_2020}.
Consequently, these datasets provide an extensive and relevant playground for successfully improving our understanding on soil microbial communities and performing the monitoring of soil microbial quality.
These datasets will be further enriched through current and future analyses (e.g. fungal microbial datasets, second sampling survey of the RMQS) and we expect that the provided datasets will ease the improvement of our knowledge on soil microbial communities by the whole scientific community.
