Biology subjects

Spor, A.

Publications and source records attributed to Spor, A..

11 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↗

bioRxiv2024

Evaluating the Effects of Environmental Disturbances and Pesticide Mixtures on Soil Microbial Endpoints

Pesticides are widely used in conventional agriculture, either applied separately or in combination during the culture cycle. Due to their occurrence and persistence in soils, pesticide residues may have an impact on soil microbial communities and on supported ecosystem services. In this regard, the EFSA (European Food Safety Authority) recently published a scientific opinion inciting to change pesticide risk assessment to better protect soil microbe-mediated processes. Climate change is another major concern for all living organisms including soil microbial community stability. Extreme climatic events, such as heat waves or heavy rainfalls, are becoming more and more frequent and their impact on soil microbial diversity and functions have already been demonstrated. The objectives of this study were to evaluate the effects of temperature and humidity disturbances and pesticide active ingredients exposure on soil microbial community structure and functions. To this end, 250 soil microcosms were exposed to either a heat disturbance, a high humidity to mimic heavy rain, or no environmental disturbance. After three days of recovery, soil microcosms were treated with different active ingredients: clopyralid (herbicide), cypermethrin (insecticide) and pyraclostrobin (fungicide). The treatments were applied alone or in combination at 1x or 10x of the agronomical dose. We then evaluated the effects of the disturbances and the active ingredients on various microbial endpoints related to the diversity and the structure of soil microbial communities, and with a specific focus on microbial guilds involved in nitrification. Overall, we demonstrated that the impact of environmental disturbances applied to soil microcosms, especially heat, on microbial endpoints was stronger than that of the active ingredients applied alone or in combinations. Compounded effects of environmental disturbances and active ingredients were detected, but sparsely and were of small scale for the chosen pesticides and applied doses.

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↗

bioRxiv2021

Community diversity determines the evolution of synthetic bacterial communities under artificial selection

Artificial selection can be conducted at the community level in the laboratory through a differential propagation of the communities according to their level of expression of a targeted function (i.e. community phenotype). Working with communities instead of individuals as selection units brings in additional sources of variation in the considered phenotype that can arise through changes in community structure and influence the outcome of the artificial selection. These sources of variation could even be increased by manipulating species diversity. In this study, we wanted to assess the effect of manipulating initial community richness on artificial selection efficiency, defined as the change in the targeted function over time as compared to a control treatment without artificial selection. We applied artificial selection for a high productivity on synthetic bacterial communities varying for their initial richness level (from one to 16 strains). Our results showed that, overall, the communities that were artificially selected were 16% more productive than the control communities. Community richness positively influenced community productivity and metabolic capacities and was a strong determinant of the dynamics of community evolution. Our results suggested that community richness could influence artificial selection efficiency but a convergence of the community composition might have limited the effect of diversity on artificial selection efficiency. We propose that applying artificial selection on communities varying for their diversity could allow to find communities differing for their level of expression of a function but also for their responsiveness to artificial selection, provided that their initial composition is different enough.

evolutionary biology↗

bioRxiv2021

Artificial selection of stable rhizosphere microbiota leads to heritable plant phenotype changes

Research on artificial selection of microbial community has become popular due to perspectives in improving plant and animal health1-4. However, reported results still lack consistency5-8. We hypothesized that artificial selection may provide desired outcomes provided that microbial community structure has stabilized along the selection process. In a ten-generation artificial selection experiment involving 1,800 plants, we selected rhizosphere microbiota of Brachypodium distachyon that were associated with high or low levels of leaf greenness, a proxy for plant health9. Monitoring of the rhizosphere microbiota dynamics showed strong oscillations in community structure during an initial transitory phase of five generations, with no heritability in the selected property. In the last five generations, the structure of microbial communities displayed signs of stabilization, concomitantly to the appearance of heritability in leaf greenness. Selection pressure, initially ineffective, became successful in changing the greenness index in the intended direction, especially toward high greenness values. We showed a remarkable congruence between plant traits and selected microbial community structures, highlighting two phylogenetically distinct microbial sub-communities correlating with leaf greenness, whose abundance was significantly steered by directional artificial selection. Understanding microbial community structure stabilization can thus help improve the reliability of artificial microbiota selection. Short SentenceStable microbiota selection enables trait heritability

evolutionary 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↗

bioRxiv2019

A core microbiota of the plant-earthworm interaction conserved across soils

Microorganisms participate in most crucial soil functions and services benefiting human activities, such as biogeochemical cycles, bioremediation and food production. Their activity happens essentially in hotspots created by major soil macroorganisms, like rhizosphere and cast shaped by plants and earthworms respectively1. While effects of individual macroorganism on soil microbes are documented, no studies attempted to decipher how the mosaic of microhabitats built by multiple macroorganisms and their interaction determine the structure of microbial communities. Here we show a joint shaping of soil bacterial communities by these two macroorganisms, with a prevalent role of plants over earthworms. In a controlled microcosm experiment with three contrasted soils and meticulous microhabitat sampling, we found that the simultaneous presence of barley and endogeic earthworms resulted in non-additive effects on cast and rhizosphere bacterial communities. Using a source-sink approach derived from the meta-community theory2,3, we found specific cast and rhizosphere core microbiota4,5 of the plant-eartworm interaction, detected in all soils only when both macroorganisms are present. We also evidenced a core network of the plant-earthworm interaction, with cosmopolitan OTUs correlated both in cast and rhizosphere of all soils. Our study provides a new framework to explore aboveground-belowground interactions through the prism of microbial communities. This multiple-macroorganisms shaping of bacterial communities also affects fungi and archaea, while being strongly influenced by soil type. Further functional investigations are needed to understand how these core microbiota and core network contribute to the modulation of plant adaptive response to local abiotic and biotic conditions.

ecology↗