Biology subjects

Sarniguet, A.

Publications and source records attributed to Sarniguet, A..

12 recordsLinked to original sources

bioRxiv2026

Seed Microbiota Diversity and Culture Collection of Four Major Crops Covering Different Genotypes and Production Modes

Seed microbiota play a crucial role in plant health and development, yet remain understudied compared to other plant-associated microbial communities. This study aimed to characterize seed microbiota diversity across four major crops (common bean, rapeseed, tomato, and wheat) and establish a comprehensive strain collection of seed-borne microorganisms (bacteria and fungi). We employed a combination of culture-dependent and culture-independent approaches to analyze 68 seed samples representing diverse genotypes and production modes. Our results revealed highly variable seed microbiota, with bacterial colonization ranging from 10 to 100 million bacterial CFUs per gram of seeds, and microbial richness varying from 4 to 351 bacterial and 16 to 138 fungal amplicon sequence variants (ASVs) per sample. Both plant genotype and production mode significantly influenced microbiota composition, with each seed sample produced harboring a distinct microbial assemblage. Interestingly, seeds produced in confined environments exhibited lower bacterial colonization but higher microbial richness compared to field-produced seeds. We observed divergent ecological drivers shaping bacterial and fungal communities. Bacterial assemblages were more host-specific and variable, while fungal communities showed greater stability and a substantial core microbiome shared across plant species. Our culturomics approach yielded a collection of 2,510 bacterial and 837 fungal isolates, representing 10-21% of the seed microbiota diversity detected by metabarcoding and the majority of the prevalent and abundant taxa. Notably, 44-60% of cultured bacterial isolates were not detected by metabarcoding, highlighting the complementary nature of these approaches to detect rare or under amplified taxa in PCR. This study provides insights into the complexity and variability of seed microbiota across different crops and production conditions. Our findings emphasize the importance of combining culturomics and sequencing methods for comprehensive characterization of seed microbiota to uncover the potential of seed-borne microorganisms as bioinoculants for sustainable agriculture.

ecology↗

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↗

bioRxiv2025

Synthetic Community Inoculation on Seeds Revealed its Transient Colonization Capacity but Legacy Effects on Plant Microbiota Assembly

Seed microbiota have the potential to influence the overall plant microbiota assembly. However, to date, studies have mostly focused on early plant development stages. This study aimed to investigate the influence of seed microbiota on plant microbiota assembly throughout an entire life cycle. To achieve this, bacterial synthetic communities (SynComs) were reconstructed and inoculated on common bean seeds to eliminate the natural variability of seed microbiota and provide four different primary inocula for comparison. We then examined bacterial and fungal communities at different developmental stages (seedling, vegetative, flowering, pod-filling, and senescent stages) and in different plant compartments (rhizosphere, root, leaf, seed) of the common bean. SynComs inoculated on seeds significantly contributed to the seedling microbiota, with higher colonization success in the leaves compared to roots and rhizospheres. Strain identity and SynCom composition influenced the strain colonization capacity across the habitats. Also, bacterial SynCom colonization induced composition modification in the seedling root and leaf microbiota. After the seedling stage, SynComs members were not detected in plant compartments but promoted persistent changes in microbial community composition until the next generation of seeds. In conclusion, SynCom inoculated on seeds have a transient colonization that can influence the overall plant microbiota assembly through priority effects.

ecology↗

bioRxiv2025

Lactuchelins: New lipopeptide siderophores from Pseudomonas lactucae inhibit Xanthomonas campestris pv. campestris 8004

Seeds harbor diverse microbial communities, including beneficial microbes that play a vital role in protecting plants from seed-borne pathogens. Despite their critical importance, the molecular mechanisms driving intermicrobial competition within the seed microbiome remain poorly understood, limiting the potential to optimize seed inoculation strategies. In this study, we evaluated the inhibitory potential of 30 seed-borne bacterial strains against the phytopathogen Xanthomonas campestris pv. campestris 8004 (Xcc8004). We identified Pseudomonas lactucae CFBP13502 as a potent inhibitor of Xcc8004, mediated by exometabolites specifically induced in the presence of Lysobacterales (formerly Xanthomonadales). Transcriptomic analysis of CFBP13502 revealed upregulation of a gene cluster involved in the biosynthesis of a lipopeptide siderophore biosynthesis. Gene deletion confirmed that this cluster is essential for the growth inhibition of Xcc8004. Furthermore, iron supplementation abolished this inhibitory effect, providing strong evidence for the role of iron chelation. Through comparative metabolomics, we elucidated the structure of a novel family of lipopeptide siderophores, which we named lactuchelins, produced by CFBP13502. Our findings provide the first molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seed-based biocontrol strategies against seed-borne phytopathogens.

microbiology↗

bioRxiv2024

T6SS-mediated competition by Stenotrophomonas rhizophila shapes seed-borne bacterial communities and seed-to-seedling transmission dynamics

Seeds harbor diverse microbial communities important for plant growth and health. During germination, seed exudation triggers intense microbial competition, shaping the communities transmitted to seedlings. This study explores the role of the bacterial type VI secretion system (T6SS)-mediated interference competition in seed microbiota transmission to seedlings. The analysis of T6SS distribution within 180 genome sequences of seed-borne bacterial strains enabled the construction of synthetic communities (SynCom) with different levels of phylogenetic diversity and T6SS richness. These SynComs were inoculated with Stenotrophomonas rhizophila CFBP13503, a bacterial strain possessing an active T6SS in vitro and in planta. The impact of T6SS on SynCom composition was assessed in vitro by comparing CFBP13503 wild-type strain or its isogenic T6SS-deficient mutant co-inoculation. Additionally, the effects of T6SS on bacterial community dynamics during seed-to-seedling transmission were examined following seed-inoculation. The T6SS of S. rhizophila CFBP13503 targets a broad range of bacteria belonging to 5 different orders. The susceptibility of competing bacteria was partly explained by their phylogenetic proximity and metabolic overlap with CFBP13503. Furthermore, the T6SS modulates the relative abundance of specific bacterial taxa during seed-to-seedling transmission, depending on the initial seed inoculum and plant developmental stage. Depending on the sensitivity of the co-inoculated competitors, the T6SS can provide a competitive advantage to CFBP13503, resulting in an increase in population size. ImportanceThe high prevalence of T6SS in seed-borne bacteria supports the importance of T6SS-mediated competition for seed microbiota assembly. In vitro, S. rhizophila CFBP13503 T6SS exerts a strong impact on bacterial community dynamics. The susceptibility to T6SS increases with the phylogenetic and metabolic proximity of bacteria to CFBP13503, suggesting an influence of interspecies trophic patterns in T6SS-mediated competitions. In planta and in soil, CFBP13503 T6SS influences specific bacterial taxa, leading to shifts in bacterial interactions and distinct community dynamics. T6SS-mediated competition plays a pivotal role in shaping seed bacterial communities and the dynamics of seed-to-seedling transitions.

microbiology↗

bioRxiv2023

Seedling microbiota engineering using bacterial synthetic community inoculation on seeds

Synthetic Communities (SynComs) are being developed and tested to manipulate plant microbiota and improve plant health. To date, only few studies proposed the use of SynCom on seed despite its potential for plant microbiota engineering. We developed and presented a simple, reproducible and effective seedling microbiota engineering method using SynCom inoculation on seeds. The method was successful using a wide diversity of SynCom compositions and bacterial strains that are representative of the common bean seed microbiota. First, this method enables the modulation of seed microbiota composition and community size. Then, SynComs strongly outcompeted native seed and potting soil microbiota and contributed on average to 80% of the seedling microbiota. We showed that strain abundance on seed was a main driver of an effective seedling microbiota colonization. Also, selection was partly involved in seed and seedling colonization capacities since strains affiliated to Enterobacteriaceae and Erwiniaceae were good colonizers while Bacillaceae and Microbacteriaceae were poor colonizers. Additionally, the engineered seed microbiota modified the recruitment and assembly of seedling and rhizosphere microbiota through priority effects. This study shows that SynCom inoculation on seeds represents a promising approach to study plant microbiota assembly and its consequence on plant fitness.

ecology↗

bioRxiv2023

The Type VI secretion system of Stenotrophomonas rhizophila CFBP13503 limits the transmission of Xanthomonas campestris pv. campestris 8004 from radish seeds to seedlings

Stenotrophomonas rhizophila CFBP13503 is a seed-borne commensal bacterial strain, which is efficiently transmitted to seedlings and can outcompete the phytopathogenic bacteria Xanthomonas campestris pv. campestris (Xcc8004). The type VI Secretion System (T6SS), an interference contact-dependent mechanism, is a critical component of interbacterial competition. The involvement of the T6SS of S. rhizophila CFBP13503 in the inhibition of Xcc8004 growth and seed-to-seedling transmission was assessed. The T6SS cluster of S. rhizophila CFBP13503 and nine putative effectors were identified. Deletion of two T6SS structural genes, hcp and tssB, abolished the competitive advantage of S. rhizophila against Xcc8004 in vitro. The population sizes of these two bacterial species were monitored in seedlings after inoculation of radish seeds with mixtures of Xcc8004 and either S. rhizophila wild type (wt) strain or isogenic hcp mutant. A significant decrease in the population size of Xcc8004 was observed during confrontation with the S. rhizophila wt in comparison to T6SS- deletion mutants in germinated seeds and seedlings. We found that the T6SS distribution among 835 genomes of the Stenotrophomonas genus is scarce. In contrast, in all available S. rhizophila genomes, T6SS clusters are widespread and mainly belong to the T6SS group i4. In conclusion, the T6SS of S. rhizophila CFBP13503 is involved in the antibiosis against Xcc8004 and reduces seedling transmission of Xcc8004 in radish. The distribution of this T6SS cluster in the S. rhizophila complex could make it possible to exploit these strains as biocontrol agents against X. campestris pv. campestris.

microbiology↗

bioRxiv2023

Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype

Seed-borne microorganisms can be pioneer taxa during germination and seedling emergence. Still, the identity and phenotypic effects of these taxa that constitute a primary inoculum of plant microbiota is mostly unknown. Here, we studied the transmission of bacteria from radish seeds to seedlings using the inoculation of individual seed-borne strains and synthetic communities (SynComs) under in vitro conditions. The SynComs were composed of highly abundant and prevalent, sub-dominant or rare bacterial seed taxa. We monitored the transmission of each strain alone or in communities using gyrB gene amplicon sequencing and assessed their impacts on germination and seedling phenotype. All strains and SynComs successfully colonized seedlings and we were able to reconstruct a richness gradient (6, 8 and 12 strains) on both seeds and seedlings. Stenotrophomonas rhizophila became dominant on seedlings of the three SynComs but most strains had variable transmission success (i.e increasing, stable or decreasing during seed to seedling transition) that also depended on the SynCom richness. Most individual strains had no effect on seedling phenotypes, at the exception of Pseudomonas viridiflava and Paenibacillus sp. that had detrimental effects on germination and seedling development. Abnormal seedling morphologies were also observed with SynComs but their proportions decreased at the highest richness level. Interestingly, some bacterial strains previously identified as core taxa of radish seeds (Pseudomonas viridiflava, Erwinia persicina) were associated with detrimental effects on seedling phenotypes either in isolation or in SynComs. These results confirm that the plant core microbiome includes pathogenic and not only commensal or mutualistic taxa. Altogether, these results show that SynCom inoculation can effectively manipulate seed and seedling microbiota diversity and thus represents a promising tool to better understand the early stages of plant microbiota assembly. This study also highlights strong differences between native seed-borne taxa in the colonization and survival on plant habitats.

microbiology↗

bioRxiv2021

Seed microbiota revealed by a large-scale meta-analysis including 50 plant species

Seed microbiota constitutes a primary inoculum for plants that is gaining attention due to its role for plant health and productivity. Here, we performed a meta-analysis on 63 seed microbiota studies covering 50 plant species to synthesize knowledge on the diversity of this habitat. Seed microbiota are diverse and extremely variable, with taxa richness varying from one to thousands of taxa. Hence, seed microbiota presents a variable (i.e flexible) microbial fraction but we also identified a stable (i.e. core) fraction across samples. Around 30 bacterial and fungal taxa are present in most plant species and in samples from all over the world. Core taxa, such as Pantoea agglomerans, Pseudomonas viridiflava, P. fluorescens, Cladosporium perangustum and Alternaria sp., are dominant seed taxa. The characterization of the core and flexible seed microbiota provided here will help uncover seed microbiota roles for plant health and design effective microbiome engineering.

microbiology↗

bioRxiv2020

Asymmetric outcome of community coalescence of seed and soil microbiota during early seedling growth

Seed microbial community constitutes a primary inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. Here, we characterized the interchange event or coalescence of seed and soil microbiota and how it structured seedling bacterial and fungal communities. We performed eight contrasted coalescence events to identify drivers influencing seedling microbiota assembly: four seed lots of two Brassica napus genotypes were sown in two soils of contrasted diversity. We found that seedling root and stem microbiota were influenced by soil diversity but not by initial seed microbiota composition. A strong selection on the two-source communities occurred during microbiota assembly, with only 8-32% of soil taxa and 0.8-1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35-72% of diversity) and not from seeds (0.3-15%). The outcome of seed and soil microbiota coalescence is therefore strongly asymmetrical with a dominance of soil taxa. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil or unknown origin) and sub-dominant soil taxa. Our results suggest that plant microbiome engineering success based on native seed or soil microbiota will rely on rare and sub-dominant taxa in source communities.

microbiology↗

bioRxiv2020

Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes

The contribution of surrounding plant microbiota to disease development has led to the postulation of the pathobiome concept, which represents the interaction between the pathogen, the host-plant, and the associated biotic microbial community, resulting or not in plant disease. The structure, composition and assembly of different plant-associated microbial communities (soil, rhizosphere, leaf, root) are more and more described, both in healthy and infected plants. A major goal is now to shift from descriptive to functional studies of the interaction, in order to gain a mechanistic understanding of how microbes act on plant growth and defense, and/or on pathogen development and pathogenicity. The aim herein is to understand how the soil microbial environment may influence the functions of a pathogen and its pathogenesis, as well as the molecular response of the plant to the infection, with a dual-RNAseq transcriptomics approach. We address this question using Brassica napus and Plasmodiophora brassicae, the pathogen responsible for clubroot. A time-course experiment was conducted to study interactions between P. brassicae, two B. napus genotypes, and three soils harboring High (H), Medium (M) or Low (L) microbiota diversities and displaying different levels of richness and diversity. The soil microbial diversity levels had an impact on disease development (symptom levels and pathogen quantity). The P. brassicae and B. napus transcriptional patterns were modulated by these microbial diversities, and the modulations were dependent of the host genotype plant and the kinetic time. The functional analysis of gene expressions allowed the identification of pathogen and plant-host functions potentially involved in the change of plant disease level, such as pathogenicity-related genes (NUDIX effector) in P. brassicae and plant defense-related genes (glucosinolate metabolism) in B. napus. Author summaryThe untapped soil microbiota diversity can influence plant tolerance and resistance to several pests. A better understanding of the mechanisms underlying the plant / pests / microbiota interaction is required to contribute to the improvement of new plant protection methods taking into account sustainability, respect for the environment, and low input utilization. Our work showed that in the Plasmodiophora brassicae / Brassica napus pathosystem, the soil microbiota diversity modulated the disease symptom level and the pathogen development. We discovered that soil microbial composition modulated both the pathogen and the plant expression genes profiles. On one hand, the pathogen transcriptome was mainly modulated by the microbial communities at the end of infection, when the pathogen infects a susceptible plant genotype, and the expression of genes potentially involved in growth and pathogenicity was affected. On the other hand, the plant transcriptome was more modulated by the microbial communities at the early step of infection, in the most resistant genotype and the expression of genes potentially involved in defense was affected. This study provides new insights into the molecular basis of soil microbiota-mediated modulation of plant pest diseases.

pathology↗

bioRxiv2018

Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae

The temporal dynamics of rhizosphere and root microbiota composition was compared between healthy and infected Chinese cabbage plants by the pathogen Plasmodiophora brassicae. When inoculated with P. brassicae, disease was measured at five sampling dates from early root hair infection to late gall development. The first symptoms of clubroot disease appeared 14 days after inoculation (DAI) and increased drastically between 14 and 35 DAI. The structure of microbial communities associated to rhizosphere soil and root from healthy and inoculated plants was characterized through high-throughput DNA sequencing of bacterial (16S) and fungal (18S) molecular markers and compared at each sampling date. In healthy plants, Proteobacteria and Bacteroidetes bacterial phyla dominated the rhizosphere and root microbiota of Chinese cabbage. Rhizosphere bacterial communities contained higher abundances of Actinobacteria and Firmicutes compared to the roots. Moreover, a drastic shift of fungal communities of healthy plants occurred between the two last sampling dates, especially in plant roots, where most of Ascomycota fungi dominated until they were replaced by a fungus assigned to the Chytridiomycota phylum. Parasitic invasion by P. brassicae disrupted the rhizosphere and root-associated community assembly at a late step during the root secondary cortical infection stage of clubroot disease. At this stage, Flavisolibacter and Streptomyces in the rhizosphere, and Bacillus in the roots, were drastically less abundant upon parasite invasion. Rhizosphere of plants colonized by P. brassicae was significantly more invaded by the Chytridiomycota fungus, which could reflect a mutualistic relationship in this compartment between these two microorganisms.

ecology↗