Biology subjects

Martin-Laurent, F.

Publications and source records attributed to Martin-Laurent, F..

7 recordsLinked to original sources

bioRxiv2026

Deciphering the microbial architecture of pesticide and antibiotics biodegradation

Understanding emerging functions at the scale of a bacterial community is a major challenge in microbial ecology and could lead up to promising tools for engineering microbial communities, for example in bioremediation. Here, through a top-down approach we obtained compositional variants of pesticide and antibiotics-degrading communities and further investigated communities features associated with their degradation abilities. We first tested whether diversity index or functional genes abundance could reliably be used as a proxy for this function, and obtained encouraging, albeit variable results. Further, through the use of statistical tools borrowed from the genomic selection literature, we were able to derive accurate prediction of the mineralisation potential of a bacterial community, based on its composition. However, the parallel between genotype-phenotype and community composition-mineralisation potential suffers a crucial caveat: bacterial abundances vary on a much wider scale than allele dosage at a given locus and are prone to change over time (particularly at the mineralisation scale). Here we observed that using presence/absence data instead of relative abundance can overcome these limitations and provide a clearer functional signal for mineralisation prediction through linear regression models. Random forest can also intrinsically deal with microbial data without transformation and select for significant predictors. We suggest drawing inspiration from the tools and concepts used in genotype-phenotype mapping to elucidate microbial functions at the community level while keeping in mind the significant differences between these two fields. This parallel is here exemplified by the concept of microbial architecture of degrading functions, akin to the genetic architecture of phenotypic traits.

microbiology↗

bioRxiv2025

Assessing the efficiency and the side effects of atrazine-degrading biocomposites amended to atrazine-contaminated soil

Even decades after being banned in Europe, atrazine and its main metabolites can still be found in soils. While bioaugmentation using pesticide-degrading bacteria is already employed as a strategy for remediating polluted soils, there is still a need to improve its efficiency. Therefore, investigating the application of carrier materials to deliver and stabilize pesticide-degrading microorganisms in situ emerges as an interesting approach for further exploration. Here, we generated atrazine-degrading biocomposites by cultivating either a single strain or a 4-species bacterial consortium as biofilms on zeolite, which serves as the carrier material. Using a microcosm experiment, we then evaluated their efficiency to mineralize 14C-atrazine in an agricultural soil comparing to free-living cells, and assessed the side effects of the two inoculation methods on the native soil bacterial community using 16S rDNA amplicon sequencing. We showed that, right after inoculation, the atrazine mineralization potential of the free-living cells was higher than that of the biocomposites. However, microcosms inoculated with the biocomposites displayed significantly higher atrazine mineralization potential than the ones inoculated with free-living cells after 15 and 45 days of incubation, not only indicating a higher efficiency but also a better stability in the soil environment, further confirmed by qPCR of the atz genes. We also showed that the inoculation of free-living cells and biocomposites differently influences the diversity and composition of the native microbial community, and that these effects are modulated by the scenario of atrazine contamination during soil inoculation. Altogether, our results provide a thorough evaluation of the efficiency and the ecotoxicological impact of atrazine-degrading biocomposites in soil.

microbiology↗

bioRxiv2025

Effects of a Sequential Application of Plant Protection Products on Soil Microbes and Free-Living Nematodes in a Field Experiment

During crop growth cycle, often several different plant protection products (PPPs) are applied, in combination or sequentially. Such sequential applications result in unintentional mixtures of residues that may affect ecosystem services supported by non-target organisms such as soil microbes and nematodes. This scenario of sequential PPP application is frequent in agricultural practice but rarely addressed experimentally at field scale with regard to environmental impacts. The objective of this study was to evaluate the effect of individual and sequential application of three PPPs (the herbicide clopyralid, the insecticide zeta-cypermethrin, and the fungicide pyraclostrobin) on soil microbial communities, and on the abundance of free-living nematode. Single applications (at 1x or 10x the agronomical dose) were made to triplicated field plots with each one of the PPPs or all three PPPs in sequence, with untreated plots serving as controls. Plots were sampled prior to each application, and 7 and 28 days thereafter. The fungal communitys composition and abundance were found to be more susceptible than the bacterial community to PPP applications, while the bacterial was mainly driven by the in-field heterogeneity of soil properties. Transient effects of PPP applications were detected on nematode abundance. Higher tier ecotoxicological studies offer greater ecological relevance compared to the standard laboratory tests but are challenged by environmental variations that should be accounted for when evaluating the ecotoxicity of pesticides on soil organisms.

ecology↗

bioRxiv2024

Generic workflow for a rapid and easy design of strain-specific PCR and qPCR primers, applied to the assessment of bacterial strains survival in soil

BackgroundDetecting bacteria at the strain level is crucial in microbiology. Although qPCR is widely used, designing strain-specific primers remains a challenge due to nucleotide sequence similarities among related strains. Methods and ResultsThis paper introduces a simplified, web-based workflow for designing strain-specific primers using publicly available microbial genomes. The method does not require advanced bioinformatics skills and can be applied using a basic computer. Primers designed using this workflow are applied to assess the survival of two close Bacillus strains in soil microcosms. ConclusionThe workflow offers an accessible solution for accurate bacterial strain detection, and fills a gap for researchers without specialized training in bioinformatics.

microbiology↗

bioRxiv2024

Engineering multi-degrading bacterial communities to bioremediate soils contaminated with pesticides residues

Parallel to the important use of pesticides in conventional agriculture there is a growing interest for green technologies to clear contaminated soil from pesticides and their degradation products. One specific technique, the inoculation of degrading micro-organisms in polluted soil, known as bioaugmentation, is a promising method still in needs of further developments. Specifically, improvements in the understanding of how degrading microorganisms must overcome abiotic filters and interact with the autochthonous microbial communities are needed in order to efficiently design bioremediation strategies. Here we designed a protocol aiming at studying the degradation of two herbicides, glyphosate (GLY) and isoproturon (IPU), via experimental modifications of two source bacterial communities. We used statistical methods stemming from genomic prediction to link community composition to herbicides degradation potentials. Our approach proved to be efficient with correlation estimates over 0.8 - between model predictions and measured pesticide degradation values. OTUs significantly associated with the degradation ability, and therefore identified as relevant by the models were confronted to the literature. Next, multi-degrading bacterial communities were obtained by coalescing bacterial communities with high GLY or IPU degradation ability based on their community-level properties. Finally, we evaluated the efficiency of constructed multi-degrading communities to remove pesticide contamination in a different soil. While results are less clear in the case of GLY, we showed an efficient transfer of degrading capacities towards the receiving soil even at relatively low inoculation levels in the case of IPU. Altogether, we developed an innovative protocol for building multi-degrading simplified bacterial communities with the help of genomic prediction tools and coalescence, and proved their efficiency in a contaminated soil.

microbiology↗

bioRxiv2023

Evidence that common arbuscular mycorrhizal network alleviates phosphate shortage in interconnected walnut sapling and maize plants

Under agroforestry practices, inter-specific facilitation between tree rows and cultivated alleys occurs when plants increase the growth of their neighbours especially under nutrient limitation. Due to a coarse roots architecture limiting soil inorganic phosphate (Pi) uptake, walnut trees (Juglans spp.) exhibit dependency on soil-borne symbiotic arbuscular mycorrhizal fungi that extend extra-radical hyphae beyond the root Pi depletion zone. To investigate the benefits of mycorrhizal walnuts in alley cropping, we experimentally simulated an agroforestry system in which walnut rootstocks RX1 (J. regia x J. microcarpa) were connected or not by a common mycelial network (CMN) to maize plants grown under two contrasting Pi levels. Mycorrhizal colonization parameters showed that the inoculum reservoir formed by inoculated walnut donor saplings allowed the mycorrhization of maize recipient roots. Relative to non-mycorrhizal plants and whatever the Pi supply, CMN enabled walnut saplings to access maize Pi fertilization residues according to significant increases in biomass, stem diameter and expression of JrPHT1;1 and JrPHT1;2, two mycorrhiza-inducible phosphate transporter candidates here identified by phylogenic inference of orthologs. In the lowest Pi supply, stem height, leaf Pi concentration and biomass of RX1 were significantly higher than in non-mycorrhizal controls, showing that mycorrhizal connections between walnut and maize roots alleviated Pi deficiency in the mycorrhizal RX1 donor plant. Under Pi limitation, maize recipient plants also benefited from mycorrhization relative to controls, as inferred from larger stem diameter and height, biomass, leaf number, N content and Pi concentration. Mycorrhization-induced Pi uptake generated a higher carbon cost for donor walnut plants than for maize plants by increasing walnut plant photosynthesis to provide the AM fungus with carbon assimilate. Here we show for the first time that CMN alleviates Pi deficiency in co-cultivated walnut and maize plants, and may therefore contribute to limit the use of chemical P fertilizers in agroforestry systems.

plant biology↗

bioRxiv2019

Labour sharing promotes coexistence in atrazine degrading bacterial communities

Microbial communities exert a pivotal role in the biodegradation of xenobiotics including pesticides1. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species2,3,4,5, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQH) formalized theoretically the conditions leading to the evolution of dependency between species6: members of the community called helpers provide publicly common goods obtained from the costly degradation of a compound, while others called beneficiaries take advantage of the public goods, but lose access to the primary resource through adaptive degrading gene loss. Here, we test whether liquid media supplemented with the herbicide atrazine could support coexistence of bacterial species through BQH mechanisms. We observed the establishment of dependencies between species through atrazine degrading gene loss. Labour sharing between members of the consortium led to coexistence of multiple species on a single resource and improved atrazine degradation potential. Until now, pesticide degradation has not been approached from an evolutionary perspective under the BQH framework. We provide here an evolutionary explanation that might invite researchers to consider microbial consortia, rather than single isolated species, as an optimal strategy for isolation of xenobiotics degraders. Also, we anticipate that future research should focus on the bioaugmentation with stabilized and tightly structured microbial degrading consortia as an effective solution for in situ bioremediation of sites polluted with recalcitrant compounds.

evolutionary biology↗