The Seed Core Microbiome as an Ecological Lens

Microbial ecologists are often confronted with overwhelming complexity. High-throughput sequencing reveals thousands of taxa, most of them rare, many of them uncultured, and all embedded in noisy, context-dependent data. In this landscape, one concept has repeatedly emerged as a way to restore ecological meaning: the core microbiome.

In our recent study on the tomato seed microbiome, we used the core microbiome framework to move beyond simple cataloguing of microbial diversity and toward a more ecological interpretation of microbial assembly. Our starting point was a large dataset of 100 different tomato genotypes. Rather than asking which microbes are present, we asked which ones are consistently present across genotypes and locations, and what that consistency tells us about host–microbe relationships.

The seed endosphere represents a particularly informative system for this question as it is spatially constrained, developmentally regulated, and tightly linked to plant fitness. Our analysis revealed that only a small fraction of the total microbial diversity is ubiquitous in tomato seeds, yet this subset accounts for a disproportionately large fraction of total community abundance.

A key next step is to move beyond taxonomic patterns and begin resolving the genomic basis of core membership. If certain microbial lineages consistently persist across hosts and environments, what genetic traits enable this persistence? Are core taxa characterized by shared functional capacities related to seed colonization, stress tolerance, dormancy, or transmission across plant generations?

Addressing these questions will require genome-resolved approaches. The recovery of high-quality whole genomes through cultivation-independent strategies such as long-read sequencing Oxford Nanopore Technologies (ONT) would allow direct comparison between core and non-core members of the seed microbiome. Building pangenomes across these groups could reveal whether core taxa share conserved gene sets associated with persistence and transmission, or whether multiple genomic strategies are involved, toward understanding not only which microbes persist in seeds, but why they do so, and how these associations are maintained across generations.

Keywords: Core microbiome • Seed microbiome • Microbial inheritance • Ecological filtering • Host–microbe interactions • Tomato

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