Soil microbial communities in the face of changing farming practices: A case study in an agricultural landscape in France

Abstract

According to biogeography studies, the abundance and richness of soil microorganisms vary across multiple spatial scales according to soil properties and farming practices. However, soil microorganisms also exhibit poorly understood temporal variations. This study aimed at better understanding how soil microbial communities respond to changes in farming practices at a landscape scale over time. A regular grid of 269 sites was set up across a 1,200 ha farming landscape, and soil samples were characterized for their molecular microbial biomass and bacterial richness at two dates (2011 and 2016). A mapping approach highlighted that spatial microbial patterns were stable over time, while abundance and richness levels were modified. The drivers of these changes were investigated though a PLS-PM (partial least square path-modeling) approach. Soil properties were stable over time, but farming practices changed. Molecular microbial biomass was mainly driven by soil resources, whereas bacterial richness depended on both farming practices and ecological parameters. Previous-crop and management effects and a temporal dependence of the microbial community on the historical farming management were also highlighted.

Wheat Rhizosphere Microbiota Respond to Changes in Plant Genotype, Chemical Inputs, and Plant Phenotypic Plasticity

“…When noted, the effect of inputs was negative on microbial communities in terms of bacterial and fungal evenness, as well as mycorrhizal colonization intensity (likely without functional consequence since arbuscular development was maintained). The results are in line with the literature (Dunn et al, 2021) and support our second hypothesis that the presence of inputs decreases, although slightly, the microbial diversity in the rhizosphere. This decrease in diversity was expected for several reasons.…”

“…From another perspective, rhizosphere microbiota changes observed since the Green Revolution may be attributed to the field application of synthetic chemical inputs (e.g., fertilizers, herbicides, and fungicides, hereafter called "inputs"). Effects of inputs were linked with decreased microbial diversity while favoring only few taxa (Dunn et al, 2021). Among different inputs, fertilization is often reported in the literature for its impact on soil microbiota.…”

Soil microbial community structures are shaped by agricultural systems revealing little temporal variation

“…Soil microorganisms can, however, also exhibit temporal variation ( Hannula et al, 2019 ), and the importance of such temporal aspects into soil microbiome studies is being increasingly highlighted in the literature ( Geisen, 2021 ). Despite this, the extent of this influence on the structure of the soil microbial community in agricultural systems, as well as the stability of any differences in community structure between differently managed systems, remains poorly understood ( Dunn et al, 2021 ). This is a pertinent knowledge gap, and has potentially profound implications on the sampling strategy of studies relating to soil microbiology and for designing efficient monitoring systems for soil biodiversity.…”

Current Challenges and Pitfalls in Soil Metagenomics

“…Soil physicochemical properties play a crucial role in determining soil microbiome composition and function [ 20 , 21 ]. However, most soil microbiome studies either do not include soil physicochemical properties or limit measurements to pH, soil organic carbon (SOC), total nitrogen (TN), total carbon (TC), moisture, and/or temperature, which do not fully reflect the complex soil chemical matrix and its various constituent elements (e.g., N, C, K, P, Zn, Fe, Ca, Mn, Mg).…”