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

Chesneau, Guillaume; Laroche, Béatrice; Préveaux, Anne; Marais, Coralie; Briand, Martial; Marolleau, Brice; Simonin, Marie; Barret, Matthieu

doi:10.1101/2021.05.31.446402

Cited by 10 publications

(4 citation statements)

References 58 publications

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“…This variability in the assembly of seed microbiota has been reported by different studies and can be observed even at the single‐seed level (e.g. 2–28 bacterial ASVs per oak seed or 1–45 bacterial ASVs per bean seed) (Abdelfattah et al ., 2021; Chesneau et al ., 2021). However, the variability observed in this meta‐analysis also could be partly methodological because of the variable number of seeds used in different samples to characterize seed microbiota (from one to 1000 seeds).…”

Section: Discussionmentioning

confidence: 99%

“…Additionally, this meta‐analysis included mainly seed microbiota characterization from multiple seeds (> 3 seeds in sample) with > 1000 reads. More work is needed at the single‐seed level (Abdelfattah et al ., 2021; Bintarti et al ., 2021; Chesneau et al ., 2021) to assess seed‐to‐seed variation and the proportion of seeds that do not have detectable microbiota (i.e. sterile seeds) (Newcombe et al ., 2018; Ridout et al ., 2019).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2022

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Seed microbiota constitutes a primary inoculum for plants that is gaining attention owing 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.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

et al. 2022

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“…Additionally, this meta-analysis included mainly seed microbiota characterization from multiple seeds (>3 seeds in sample) with more than 1000 reads. More work is needed at the single seed level 37,59,60 to assess seed-to-seed variation and the proportion of seeds that do not have detectable microbiota (i.e. sterile seeds) 9,61 .…”

Section: Discussionmentioning

confidence: 99%

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

Simonin

Briand

Chesneau

et al. 2021

Preprint

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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.

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“…The functional elucidations would warrant concerted efforts by different research groups. The recent report that the individual seeds of bean and radish were associated with a dominant bacterial taxon which in turn was highly variable between plants and within seeds of the same plant is worth noting ( Chesneau et al, 2021 ). The embryo-associated bacteria have the advantage of being able to establish and spread to different parts of seedlings at germination before the externally associated microorganisms make their way inside seedlings.…”

Section: Discussionmentioning

confidence: 99%

Vertical Transmission of Diverse Cultivation-Recalcitrant Endophytic Bacteria Elucidated Using Watermelon Seed Embryos

Thomas

Sahu

2021

Front. Microbiol.

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Seed transmission of endophytic microorganisms is a growing research area in plant biology and microbiology. We employed cultivation versus cultivation-independent approaches on excised embryos from watermelon seeds (6–12 months in storage) and on embryo-derived in vitro seedlings (EIVS) to assess the vertical transmission of endophytic bacteria. Surface-disinfected watermelon seeds bore abundant residual bacteria in the testa and perisperm tissues, predominantly Bacillus spp. propounding the essentiality of excluding all non-embryonic tissues for vertical transmission studies. Tissue homogenates from re-disinfected seed embryos displayed no cultivable bacteria during the 1-week monitoring. Bright-field live microscopy revealed abundant bacteria in tissue homogenates and in embryo sections as intracellular motile particles. Confocal imaging on embryo sections after SYTO-9 staining and eubacterial fluorescent in situ hybridization (FISH) endorsed enormous bacterial colonization. Quantitative Insights Into Microbial Ecology (QIIME)-based 16S rRNA V3–V4 taxonomic profiling excluding the preponderant chloroplast and mitochondrial sequences revealed a high bacterial diversity in watermelon seed embryos mainly Firmicutes barring spore formers followed by Proteobacteria, Bacteroidetes, and Actinobacteria, and other minor phyla. Embryo-base (comprising the radicle plus plumule parts) and embryo-cotyledon parts differed in bacterial profiles with the abundance of Firmicutes in the former and Proteobacteria dominance in the latter. EIVS displayed a higher bacterial diversity over seed embryos indicating the activation from the dormant stage of more organisms in seedlings or their better amenability to DNA techniques. It also indicated embryo-to-seedling bacterial transmission, varying taxonomic abundances for seed embryos and seedlings, and differing phylogenic profiles for root, hypocotyl, and cotyledon/shoot-tip tissues. Investigations on different watermelon cultivars confirmed the embryo transmission of diverse cultivation recalcitrant endophytic bacteria. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes formed the core phyla across different cultivars with 80–90% similarity at genus to phylum levels. Conversely, freshly harvested seeds displayed a dominance of Proteobacteria. The findings revealed that dicot seeds such as in different watermelon cultivars come packaged with abundant and diverse vertical and seedling-transmissible cultivation recalcitrant endophytic bacteria with significant implications for plant biology.

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

Cited by 10 publications

References 58 publications

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

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

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

Vertical Transmission of Diverse Cultivation-Recalcitrant Endophytic Bacteria Elucidated Using Watermelon Seed Embryos

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