Additional file 1 of Experimental community coalescence sheds light on microbial interactions in soil and restores impaired functions

Additional file 1: Supplementary Table 1. Number of OTUs significantly differentially abundant among all treatments as estimated using a generalized linear mixed model, among the 515 most abundant 16S rRNA OTUs and the 439 most abundant 18S rRNA OTUs. Supplementary Figure 1. Abundances of total bacteria and total fungi. Quantification of 16S rRNA (a and c) and ITS (b and d) gene copy numbers in the original soil, the removal treatments and the control (Step 1; a and b) and in the coalescence treatment, the self-mixed removal treatment and the control samples (Step 2; c and d) (mean ± s.e. of log10-transformed data expressed as gene copy g-1 dry soil). Letters indicate significantly differen…

Deciphering biotic interactions and their role in soil microbial community assembly

National audience; Soil microbial communities play key roles in ecosystem functioning. Yet, little is known aboutthe importance of microbe-microbe interactions in soil microbial community assembly andfunctions. To address this knowledge gap, the objective of my thesis is to assess the role ofinteractions between micro-organisms in soil microbial communities. For this purpose, we willmanipulate the interactions between microorganisms within complex soil microbialcommunities by (i) removing different members of the soil community, (ii) adding microbialtaxa to the soil community and (iii) increasing the physical distance between members of thesoil community. How shifts in microbial interaction…

Unraveling biotic interactions determining soil microbial community assembly and functioning

National audience; Microbial communities are at the heart of all ecosystems and yet, a sound understanding of the ecological processes governing the assembly of these communities in the environment is missing. To address the role of biotic interactions in assembly and functioning of the soil microbiota, we used a top down manipulation approach based on the removal of various populations in a natural microbial community. Suspensions of the soil microbiota were subjected to various biocidal and filtration treatments before being inoculated into the same sterilized soil. We hypothesized that if biotic interactions are an important shaping force of the microbiota assembly, removal of microbial …

Predicting pesticide biodegradation potential from microbial community composition: new tools for bioremediation

Bioaugmentation is receiving increasing attention as a green technology to treat contaminatedareas by inoculating specific biodegrading microorganisms. However, our understanding of therole of microbial community composition and structure in the expression of contaminantdegradation potential is yet to improve. It could help making wise choice for microorganisms –community or specific strain – to be inoculated in contaminated soils with consideration to theirindigeneous microbiota.Here we tried to predict the microbial degradation of two herbicides, glyphosate andisoproturon by means of penalized regression and machine learning methods routinely used ingenomic selection. To this end, we cond…

Les herbicides β-tricétones : devenir et impact écotoxicologique dans les sols agricoles et caractérisation de souches bactériennes dégradantes

P-triketone herbicides : fate and ecotoxicological impact in arable soils and characterization of degrading bacterial strains abstract :This work aims to describe the ecodynamics of synthetic (sulcotrione and mesotrione) and natural (leptospermone) -triketone herbicides and to estimate their ecotoxicological impact on the bacterial community in arable soils. The processes involved in the dissipation of these herbicides (adsorption and biodegradation) have been studied in soil microcosms. Two bacterial strains, Bradyrhizobium sp. SRl able to degrade sulcotrione and mesotrione, and Methylophilus sp. LS1 degrading leptospermone, have been isolated. A bank of 12 ooo mutants of Bradyrhizobium sp…

Predicting pesticide biodegradation potential from microbial community composition : new tools for bioremediation

Bioaugmentation is receiving increasing attention as a green technology to treat contaminated areas by inoculating specific biodegrading microorganisms. However, our understanding of the role of microbial community composition and structure in the expression of contaminant degradation potential is yet to improve. It could help making wise choice for microorganisms – community or specific strain – to be inoculated in contaminated soils with consideration to their indigeneous microbiota. Here we tried to predict the microbial degradation of two herbicides, glyphosate and isoproturon by means of penalized regression and machine learning methods routinely used in genomic selection. To this end,…

Biodegradation of synthetic β-triketone herbicide

Experimental community coalescence sheds light on microbial interactions in soil and restores impaired functions

Abstract Background Microbes typically live in communities where individuals can interact with each other in numerous ways. However, knowledge on the importance of these interactions is limited and derives mainly from studies using a limited number of species grown in coculture. Here, we manipulated soil microbial communities to assess the contribution of interactions between microorganisms for assembly of the soil microbiome. Results By combining experimental removal (taxa depletion in the community) and coalescence (mixing of manipulated and control communities) approaches, we demonstrated that interactions between microorganisms can play a key role in determining their fitness during soi…

Fate, biodegradation and ecotoxicological impact of the bioherbicide leptospermone on soil bacterial community

International audience

Impact of Leptospermone, a Natural β-Triketone Herbicide, on the Fungal Composition and Diversity of Two Arable Soils

Impact of leptospermone, a β-triketone bioherbicide, was investigated on the fungal community which supports important soil ecological functions such as decomposition of organic matter and nutrients recycling. This study was done in a microcosm experiment using two French soils, Perpignan (P) and Saint-Jean-de-Fos (SJF), differing in their physicochemical properties and history treatment with synthetic β-triketones. Soil microcosms were treated with leptospermone at recommended dose and incubated under controlled conditions for 45 days. Untreated microcosms were used as control. Illumina MiSeq sequencing of the internal transcribed spacer region of the fungal rRNA revealed significant chang…

Impact of land use, pesticide application and agricultural management practices on the phosphorus foraging capacity of mycorrhizal fungi in 217 european agricultural soils

More than 80% of vascular plants form symbiotic associations with arbuscular mycorrhizal fungi (AMF). Several studies have shown the potential of AMF to provide plants with phosphorus (P) via their hyphal network. Most of these studies have been performed in the greenhouse under controlled conditions using standardized soil mixtures. However, few studies have investigated hyphal P transfer in natural soils, severely limiting our understanding of the main drivers of P transfer by AMF in real agricultural soils. As a consequence, the potential of using AMF as a tool to increase crop yield remains a mystery. Using agricultural soils from a large field observation study in Europe, we aimed at a…

Impact of Leptospermone, a Natural β-Triketone Herbicide, on the Fungal Composition and Diversity of Two Arable Soils

International audience; Impact of leptospermone, a β-triketone bioherbicide, was investigated on the fungal community which supports important soil ecological functions such as decomposition of organic matter and nutrients recycling. This study was done in a microcosm experiment using two French soils, Perpignan (P) and Saint-Jean-de-Fos (SJF), differing in their physicochemical properties and history treatment with synthetic β-triketones. Soil microcosms were treated with leptospermone at recommended dose and incubated under controlled conditions for 45 days. Untreated microcosms were used as control. Illumina MiSeq sequencing of the internal transcribed spacer region of the fungal rRNA re…