Biology subjects

Barret, M.

Publications and source records attributed to Barret, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Identification of Seed Metabolites and Microbiota members associated with Germination and Emergence in Common Bean

Seed quality is a complex trait shaped by morphological, biochemical and microbiological properties that are rarely characterised simultaneously, limiting our ability to identify robust predictive indicators of germination speed and seedling emergence across varieties. Here, we performed a multi-factor characterisation of eight common bean (Phaseolus vulgaris L.) varieties, combining seed morphometrics, untargeted GC-MS metabolomics on three seed organs, and amplicon sequencing of bacterial and fungal communities, to identify indicators of germination speed and emergence percentage. The eight varieties showed substantial variation in both traits, used as physiological seed quality proxies. Seed weight and size variation between varieties were correlated with germination speed. The intravariety variance of seed weight was independently correlated with emergence performance. Metabolome composition differed strongly across seed organs, with variety as the dominant driver. Individual-seed metabolomic profiles in the plumule and cotyledon were associated with germination speed but not emergence, yielding 16 plumule and three cotyledon candidate metabolite markers. Fungal community composition was associated with both germination speed and emergence, while bacterial communities were associated with emergence only. Nine fungal and four bacterial taxa were identified as candidate indicators. Inter-kingdom co-occurrence network analysis revealed that fungi with similar germination speed associations tend to cluster in the same modules, suggesting that community-level modules rather than individual taxa may constitute more robust microbial indicators. These results demonstrate that germination speed and emergence capacity are governed by distinct seed properties, and provide morphological, metabolic and microbial candidate indicators for integration into targeted seed quality assessment frameworks for common bean.

plant biology↗

bioRxiv2026

The efficiency of different transmission routes of Xanthomonas citri pv. fuscans and other seed-borne bacteria to bean seeds.

Seed transmission is a critical pathway for the dispersal of phytopathogenic bacteria. This transmission can occur through three main routes: floral, internal, and external. Yet the relative contribution of individual transmission routes remains poorly characterized. Using a pathosystem based on Xanthomonas citri pv. fuscans (Xcf) and common bean (Phaseolus vulgaris cv. Flavert), we quantified the efficiency of each route. Under our experimental conditions, the vascular route was the most efficient with 25% of contaminated seeds and population sizes averaging 107 CFU per contaminated seed. Deploying this experimental framework to ten seed-borne bacterial strains isolated from bean revealed that almost none transmitted to seeds through any route, or at best at low efficiency. However, most of the strains were capable of surviving and disseminating within the vascular system. A major bottleneck for seed transmission was identified for pod vascular organs colonization and the similar behavior of an Xcf mutant, deficient in the T3SS, suggested that plant immunity could be involved at this step. Co-inoculation of a consortium composed of the seed-borne strains with Xcf reduced the number of seeds contaminated by Xcf at the highest inoculum concentration, although other consortia members were never recovered from seeds. This suggests that the strains are recognized by the plant and trigger defense responses. These findings also raise questions about the mechanisms used by seed-associated bacteria to colonize seeds in situ.

microbiology↗

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↗

bioRxiv2026

Comparing DNA Extraction Protocols for Freshwater Prokaryotic Communities: Impacts on Yield and Microbial Profiling

DNA extraction from aquatic samples is a critical process that influences the quantity and purity of the DNA obtained. This can have profound effects on the accuracy of the community depiction. In this study, DNA extraction workflows of seven commercial kits (Qiagen: DNeasy PowerLyzer PowerSoil, DNeasy PowerSoil Pro, DNeasy PowerSoil, DNeasy PowerMax Soil; Macherey-Nagel: NucleoSpin Soil; Zymo: ZymoBIOMICS DNA; MP Biomedicals: FastDNA SPIN), along with several modifications of manufacturer's protocols focusing on the lysis and elution steps, were tested, accounting for a total of 18 different protocols. For each protocol, DNA yield (quantity, replicability and quality), richness and compositional reproducibility based on 16S rRNA gene sequencing, as well as processing time and cost were assessed. The standard protocols recommended by the manufacturer showed comparable DNA yield results. Shared ASVs between all protocols accounted for >90% of the reads and were mostly abundant ASVs, indicating consistent detection of dominant taxa across all protocols. Adding supplementary lysis and elution steps to the manufacturer's protocols yielded up to ~4x more DNA. However, total read counts and ASV richness were lower as total DNA increased. Manufacturer's protocols therefore showed higher values than their modified versions, although these effects were not significant on community composition. We conclude that the choice of a protocol is the balance between recovering sufficient DNA of good quality versus potential effects on downstream sequencing output (reads and ASVs).

microbiology↗

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

Contribution of floral transmission to the assembly and health impact of bacterial communities in watermelon seeds

Flower-sourced assembly of seed microbiota remains an understudied ecological process. Here, we investigated the floral transmission pathway for bacterial acquisition by developing seeds of watermelon (Citrullus lanatus). Comparison of stigma- and seed-associated bacterial communities from field-grown C. lanatus revealed significant overlap: up to 40% of the bacterial diversity that was detected in seed was also found on stigmas. In a field pollinator exclusion experiment, honeybee visitation to flower stigmas had no significant effect on bacterial community composition in seeds. Among a collection of bacterial isolates from stigmas and seeds in the field, more than half (57%) were able to transmit to seeds after inoculation onto stigmas under laboratory conditions. Interestingly, for most bacterial strains, fruit set rates increased after floral inoculation, and in some cases even in the absence of transmission to the seed. We also found that bacterial isolates from watermelon stigmas and seeds had variable (i.e. positive or negative) effects on seed germination and seedling emergence. Our findings highlight the contribution of floral transmission to seed microbiota assembly and its consequences for plant fitness.

ecology↗

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↗

bioRxiv2024

Stable, multigenerational transmission of the bean seed microbiome despite abiotic stress

Seed microbiomes initiate plant microbiome assembly, but the consequences of environmental conditions of the parent plant for seed microbiome assembly and transmission are unknown. We tracked endophytic seed bacterial communities of common bean lines exposed to drought or excess nutrients, and discovered stable transmission of 22 bacterial members regardless of parental plant treatment. This study provides insights into the maintenance of plant microbiomes across generations, even under challenging environmental stress.

microbiology↗

bioRxiv2023

A novel "ceasefire" model to explain efficient seed transmission of Xanthomonas citri pv. fuscans to common bean.

O_LIAlthough seed represents an important means of plant pathogen dispersion, the seed-pathogen dialogue remains largely unexplored. C_LIO_LIA multi-omic approach (i.e. dual RNAseq, plant small RNAs and methylome) was performed at different seed developmental stages of common bean (Phaseolus vulgaris L.) during asymptomatic colonization by Xanthomonas citri pv. fuscans (Xcf). C_LIO_LIIn this condition, Xcf did not produce disease symptoms, neither affect seed development. Although, an intense molecular dialogue, via important transcriptional changes, was observed at the early seed developmental stages with down-regulation of plant defense signal transduction, via action of plant miR, and upregulation of the bacterial Type 3 Secretion System. At later seed maturation stages, molecular dialogue between host and pathogen was reduced to few transcriptome changes, but marked by changes in DNA methylation of plant defense and germination genes, in response to Xcf colonization, potentially acting as defense priming to prepare the host for the post-germination battle. This distinct response of infected seeds during maturation, with a more active role at early stages refutes the widely diffused assumption considering seeds as passive carriers of microbes. C_LIO_LIFinally, our data support a novel plant-pathogen interaction model, specific to the seed tissues, which differs from others by the existence of distinct phases during seed-pathogen interaction with seeds first actively interacting with colonizing pathogens, then both belligerents switch to more passive mode at later stages. We contextualized this observed scenario in a novel hypothetical model that we called "ceasefire", where both the pathogen and the host benefit from temporarily laying down their weapons until the moment of germination. C_LI

plant biology↗

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↗

bioRxiv2022

Honey bees change the microbiota of pollen

Pollen, as all other plant tissues, harbors different microorganisms. As honey bees (Apis mellifera) collect and pack pollen they add regurgitated nectar to moisten and glue the pollen grains, possibly changing the microbial composition. In this study, we compared the microbiota of clean Brassica napus pollen with that of bee-worked corbicular pollen. We found that by working pollen, bees increase the bacterial diversity of pollen, by adding honey bee symbionts such as Bombella, Frischella, Gilliamella and Snodgrassella, bee pathogens as Spiroplasma and nectar dwelling Lactobacillus to the new pollen microbiota. The bee gut is an important source of inoculum of the corbicular pollen microbiota. We discuss the implications of these findings and propose future research avenues.

ecology↗

bioRxiv2021

Temperature increase affects acetate-derived methane production in Alaskan lake sediments and wetland soils

Under climate change framework, methanogens activity is expected to be strongly affected, eventually resulting in positive feedback on global climate, with higher greenhouse gas (GHG) emissions in the Arctic. This work aimed to evaluate the effect of increasing temperature on methane production rate and archaeal community of lake sediments and wetland soils from Denali to Toolik regions in Alaska (USA). For that, anaerobic acetate-amended microcosms were incubated at 5, 10, 15 and 20 {degrees}C. The acetate-derived methanogenic rate was determined and the methanogenic communities were analyzed by qPCR and 16S rRNA sequencing. Warmer temperatures yielded 4-6 times higher methane production rates and organic matter content (OM) showed significant positive correlation to methane production. Different patterns were observed in the archaeal communities after incubation at higher temperatures, with an increase in Methanosarcina abundance for most of the samples and Methanosaeta in one of the lakes tested, showing the adaptation of key acetoclastic groups among different temperatures. Our results demonstrate the impact of increasing temperature on methane production, bringing insights on key drivers involved in the process of acetoclastic methanogenic potential occurring in these ecosystems in Alaska.

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↗

bioRxiv2021

Single seed microbiota: assembly and transmission from parent plant to seedling

Gaining basic understanding of processes involved in seed microbiota assembly is a prerequisite for improving crop establishment. Investigation of microbiota structure during seed development revealed that individual seeds of bean and radish were associated with a dominant bacterial taxon representing more than 75% of all reads. The identity of this taxon was highly variable between plants and within seeds of the same plant. Succession of dominant taxa occurred during seed filling and maturation through Selection. In a second step, we evaluated seed to seedling transmission of these dominant seed-borne taxa. We showed that initial bacterial abundance on seeds was not a good predictor of seedling transmission and that the identity of seed-borne taxa can impact seedling phenotype. Altogether this work unveiled that seeds are colonized by few bacterial taxa of highly variable identity, which appears to be important for the early stages of plant development.

microbiology↗

bioRxiv2021

Synergy of culture-dependent molecular identification and whole-community metabarcode sequencing for characterizing the microbiota of arable crop residues

This study is the first to compare culture-dependent (strain isolation plus molecular identification) and culture-independent (whole-community metabarcode sequencing) approaches for characterizing the microbiota of crop residues. We investigated the diversity of fungal and bacterial communities in wheat and oilseed rape residues, using two different culture-dependent strategies to cover the maximum diversity for each kingdom: broad substrate sampling coupled with low-throughput isolation and diversity analysis for fungi, and reduced substrate sampling coupled with high-throughput isolation and diversity analysis for bacteria. The proportion of cultivable microorganisms was neither as low as the 1% paradigm long associated with the rhizosphere microflora, nor as high as the 50% sometimes reported for the phyllosphere microflora. It was, thus, intermediate between the values for soil and plants. This finding is consistent with residues being considered to constitute an ecotone, at the interface between soil and phyllosphere. Isolation and metabarcoding provided consistent complementary information: they revealed close community profiles, leading to the identification of several common and specific amplicon sequence variants (ASVs). The power of the culture-independent approach was thus confirmed. By contrast the culture-dependent approach was less weak than anticipated. Firstly, it provided complementary information about microbial diversity, with several ASVs not retrieved by metabarcoding being identified after isolation in the community-based culture collection. Secondly, this approach made it possible to preserve and test different taxa either individually or after the creation of synthetic communities, for deciphering the ecological functions of communities beyond merely descriptive aspects.

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↗