Biology subjects

Devers-Lamrani, M.

Publications and source records attributed to Devers-Lamrani, M..

5 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↗

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↗

bioRxiv2022

The central role of the interspecific interactions in the evolution of microbial communities

The interspecific interactions play an important role in the establishment of a community phenotype. Furthermore, the evolution of a community can not only occur through an evolution of the species composing the community but also of the interactions among them. In this study, we investigated how widespread was the evolution of interspecific interactions in the evolutionary response of eight two-bacterial species communities regarding productivity. We found evidence for an evolution of the interactions in half of the studied communities which gave rise to a mean change of 15% in community productivity as compared to what was expected from the individual responses. Even when the interactions did not evolve themselves, they influenced the evolutionary responses of the bacterial strains within the communities which further affected community response. We found that the evolution within a community often promoted an adaptation of the bacterial strains to the abiotic environment, especially for the dominant strain in a community. Overall, this study suggested that the evolution of the interspecific interactions was frequent and that it could increase community response to evolution. We propose that the existence of an evolution of the interspecific interactions can justify the consideration of the community as a unit of selection.

evolutionary biology↗