Biology subjects

Jacquiod, S.

Publications and source records attributed to Jacquiod, S..

7 recordsLinked to original sources

bioRxiv2026

Bacterial Strain Identity and Community Composition Drive the Seed-to-Seedling Microbiota Assembly

The seed-to-seedling transition is a key step of plant microbiota assembly, where the seed microbiota meets the soil microbiota. Seed germination triggers profound physiological changes, including exudate release and oxidative bursts, which generate selective pressures shaping microbial survival and interactions. Here, we investigated how host selection and community composition influence bacterial colonization during this transition using a Synthetic Community (SynCom) approach on common bean (Phaseolus vulgaris) seeds. Specifically, we tested the importance of microbial interactions by applying 30 bacterial SynComs spawning a phylogenetic diversity gradient. Seedling colonization success was primarily determined by strain identity but was strongly modulated by the SynCom context. Strains that were highly effective colonizers when inoculated alone often exhibited reduced transmission within SynComs, indicating that microbial interactions can either inhibit or facilitate colonization. Random forest models confirmed that colonization outcomes could not be predicted from single-strain performance alone. Instead, both phylogenetic relatedness and metabolic similarity among SynCom members emerged as key predictors of strain success, supporting the competition-relatedness hypothesis and highlighting the importance of community-dependent effects in shaping colonization success. Genomic analyses identified microbial traits linked to efficient seedling colonization, notably amino acid transport and metabolism, stress tolerance, ROS detoxification, and biofilm formation, highlighting the strong selective pressures acting during the seed-to-seedling transition. Besides key adaptative traits, our findings underscore the importance of microbial interactions to survive and colonize seedlings, bringing a novel perspective for the successful engineering of seed and seedling microbiota.

ecology↗

bioRxiv2021

Changes in wheat rhizosphere microbiota in response to chemical inputs, plant genotype and phenotypic plasticity

Since modern wheat varieties are grown with chemical inputs, we ignore if changes observed in rhizosphere microorganisms between ancient and modern varieties are due to i) breeding-induced changes in plant genotype, ii) modifications of the environment via synthetic chemical inputs, or (iii) phenotypic plasticity, defined as the interaction between the genotype and the environment. In the field, we evaluated the effects of various wheat varieties (modern and ancient) grown with or without chemical inputs (N-fertilizer, fungicide and herbicide together) in a crossed factorial design. We analysed rhizosphere bacteria and fungi by amplicons sequencing and mycorrhizal association by microscopic observations. When considered independently of plant genotype, chemical inputs were responsible for an increase in dominance for bacteria and decrease in evenness for bacteria and fungi. Independently of inputs, modern varieties had richer and more even bacterial communities compared to ancient varieties. Phenotypic plasticity had a significant effect: bacterial and fungal diversity decreased when inputs were applied in ancient varieties but not in modern ones. Mycorrhiza were more abundant in modern than ancient varieties, and less abundant when using chemical inputs. Although neglected, phenotypic plasticity is important to understand the evolution of plant-microbiota associations and a relevant target in breeding programs.

microbiology↗

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↗

bioRxiv2021

Comparative genomics analysis of Chryseobacterium sp. KMC2 reveals metabolic pathways involved in keratinous utilization and natural product biosynthesis

Several efforts have been made to valorize keratinous materials, an abundant and renewable resource. Despite these attempts to valorize products generated from keratin hydrolysate, either via chemical or microbial conversion, they generally remain with an overall low value. In this study, a promising keratinolytic strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against publicly available reference genomes to reveal the metabolic potential for biosynthesis of valuable secondary metabolites. Genome and metabolic features of four species were compared, shows different gene numbers but similar functional categories. We successfully mined eleven different secondary metabolite gene clusters of interest from the four genomes, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, all showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from Chryseobacterium sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic Chryseobacterium spp. and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, providing alternatives to valorize keratinous materials into high-value natural products. ImportanceKeratin is an abundant and renewable resource from slaughterhouses or the poultry industry. Low-value products such as animal feed and fertilizer were generated from these feedstocks based on conventional processing like chemical conversion. In fact, microorganisms possess the potential to synthesize valuable natural products. In this work, we explored the metabolic potential of Chryseobacterium sp. KMC2, which was isolated with efficient keratinolytic capacity from a previous study. Comparative genomics analysis displayed similar functional categories against three publicly available reference genomes of keratin-degrading Chryseobacterium spp.. Eleven different secondary metabolite gene clusters of interest were mined among four genomes, including five common and unique ones. Furthermore, we provide a more comprehensive understanding of metabolic pathways on keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid assimilation and sulfate reduction. These findings contribute to expanding the application of Chryseobacterium sp. KMC2 on the valorization of keratinous materials.

microbiology↗

bioRxiv2019

Construction of simplified microbial consortia to degrade recalcitrant materials based on enrichment and dilution-to-extinction cultures

The capacity of microbes degrading recalcitrant materials has been extensively explored from environmental remediation to industrial applications. Although significant achievements were obtained with single strains, focus is now going toward the use of microbial consortia because of advantages in terms of functional stability and efficiency. While consortia assembly attempts were made from several known single strains, another approach consists in obtaining consortia from complex environmental microbial communities in search for novel microbial species, genes and functions. However, assembling efficient microbial consortia from complex environmental communities is far from trivial due to large diversity and biotic interactions at play. Here we propose a strategy containing enrichment and dilution-to-extinction cultures to construct simplified microbial consortia (SMC) for keratinous waste management, from complex environmental communities. Gradual dilutions were performed from a keratinolytic microbial consortium, and dilution 10-9 was selected to construct a SMC library. Further compositional analysis and keratinolytic activity assays demonstrated that microbial consortia were successfully simplified, without impacting their biodegradation capabilities. These SMC possess promising potential for efficient keratinous valorization. More importantly, this reasoning and methodology could be transferred to other topics involving screening for simplified communities for biodegradation, thus considerably broadening its application scope.\n\nImportanceMicrobial consortia have got more and more attention and extensive applications due to their potential advantages. However, a high diversity of microbes is likely to hide uncontrollable risks in practice specific to novel strains and complicated interaction networks. Exploring a convenient and efficient way to construct simplified microbial consortia is able to broaden the applied scope of microbes. This study presents the approach based on enrichment and dilution-to-extinction cultures, which gain abundance microbial consortia including some without losing efficiency from the enriched functional microbial community. The microbial interactions at the strain level were evaluated by using compositional identification and correlation analysis, which contribute to revealing the roles of microbes in the degradation process of recalcitrant materials. Our findings provide a systematic scheme to achieve optimizing microbial consortia for biodegradation from an environmental sample, could be readily applied to a range of recalcitrant materials management from environmental remediation to industrial applications.

microbiology↗

bioRxiv2019

Transcriptomic responses to warming and cooling of an Arctic tundra soil microbiome

BackgroundArctic surface soils experience pronounced seasonal changes in temperature and chemistry. However, it is unclear how these changes affect microbial degradation of organic matter, nitrogen cycling and microbial stress responses. We combined measurements of microbiome transcriptional activity, CO2 production, and pools of carbon and nitrogen to investigate the microbial response to warming in the laboratory, from -10 {degrees}C to 2 {degrees}C, and subsequent cooling, from 2 {degrees}C to -10 {degrees}C, of a high Arctic tundra soil from Svalbard, Norway.\n\nResultsGene expression was unaffected by warming from -10 {degrees}C to -2 {degrees}C and by cooling from -2 {degrees}C to -10 {degrees}C, while upon freezing (2 {degrees}C to -2 {degrees}C) a defense response against oxidative stress was observed. Following modest transcriptional changes one day after soil thaw, a more pronounced response was observed after 17 days, involving numerous functions dominated by an upregulation of genes involved in transcription, translation and chaperone activity. Transcripts related to carbohydrate metabolism and degradation of complex polymers (e.g. cellulose, hemicellulose and chitin) were also enhanced following 17 days of soil thaw, which was accompanied by a four-fold increase in CO2 production. In addition, anaerobic ammonium oxidation and turnover of organic nitrogen were upregulated. In contrast, nitrification, denitrification and assimilatory nitrate reduction were downregulated leading to an increase in the concentration of soil inorganic nitrogen.\n\nConclusionthe microorganisms showed negligible response to changes in sub-zero temperatures and a delayed response to thaw, which after 17 days led to upregulation of soil organic matter degradation and enhanced CO2 production, as well as downregulation of key pathways in nitrogen cycling and a concomitant accumulation of inorganic nitrogen available for plants.

microbiology↗

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↗