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

Abstract

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.

Bacterial Endophytes Contribute to Rice Seedling Establishment Under Submergence

“…The bacteria microbiota composition of Arborio (long coleoptile) and Lamone (short coleoptile) varieties identified the prevalence of Bacteroidetes , Firmicutes and Proteobacteria ( Figure 1C ) that are well represented endophytic phyla detected in seeds of various plants ( Truyens et al, 2015 ; Simonin et al, 2022 ). Seed microbiota generated by analysing several Oryza spp accessions has identified the prevalence of the phylum Proteobacteria and the abundance of Bacteroidetes and Firmicutes ( Kim et al, 2020 ).…”

Seed pathway for pest dissemination: The ISTA Reference Pest List, a bibliographic resource in non‐vegetable crops

“…In addition, treatments might also have harmful effects on desirable, non‐target microorganisms (i.e. seed microbiome), whose importance in crop health is becoming better understood (Berendsen et al, 2012; Berg & Raaijmakers, 2018; Lamichhane et al, 2020; Simonin et al, 2021). Seed testing will face many challenges in the near future.…”

Metadata harmonization–Standards are the key for a better usage of omics data for integrative microbiome analysis

“…In plant microbiome research, microbial communities inside seeds came recently into the spotlight due to their implications for host health and fitness, as well as their potential for biotechnological applications (Berg & Raaijmakers, 2019). Simonin et al [ 50 ] have conducted the first meta-analysis of seed microbiome datasets by retrieving data from 63 studies that encompassed 50 different plant species. They re-analyzed raw data from a number of metabarcoding studies, which were obtained from public databases and used 16S rRNA gene fragments, gyrB , and the fungal ITS region s genetic markers for microbial community profiling.…”

“…Such microorganisms likely have an intrinsic, evolutionary conserved association with plant hosts that would have remained undiscovered without this study. The ongoing exploitation of this meta-analysis resulted in the identification of bacterial and fungal core taxa, such as Pantoea agglomerans , Pseudomonas viridiflava, P. fluorescens , Cladosporium perangustum and Alternaria sp., [ 50 ]. Another study, based on short-read metagenomics, addressed environmental resistomes in bog ecosystems.…”