Biology subjects

Marais, C.

Publications and source records attributed to Marais, C..

4 recordsLinked to original sources

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↗