Cobamide-producing microbes as a model for understanding general nutritional interdependencies in soil food webs

TL;DR

Cobamide-producing microbes help maintain soil health by connecting different organisms through nutrient exchange, supporting host development and ecosystem balance.

Contribution

The study introduces a comprehensive database of cobamide-producing microbes and reveals their role in soil food webs and host health.

Findings

Cobamide-producing microbes are phylogenetically diverse and found across various soil environments.

These microbes support host development and gut stability through transkingdom interactions.

They occur at higher trophic levels, indicating a broader role in nutrient transfer across ecosystems.

Abstract

Nutrient crossfeeding critically governs microbiome–host interactions and ecosystem stability. Cobamides, synthesized only by prokaryotes, offer a powerful and tractable model for studying nutrient-mediated interdependencies in soil food webs; however, their ecological role in sustaining soil health remains unclear. Here, we construct the Soil Cobamide Producer database (SCP v.1.0) by integrating over 48,000 metagenomic and genomic datasets from 1,123 sampling sites. This database catalogs phylogenetically diverse prokaryotes (19 phyla, 302 genera) with cobamide biosynthetic potential. Using this resource, we identify host-specific colonization patterns of cobamide-producing microbes in fauna. These microbes also carry diverse functional traits that may contribute to trophic cascades and microbial community stability. In an Enchytraeid model, these colonizers support host development, modulate gene expression, and promote gut stability through transkingdom interactions, with cobamide biosynthesis serving as one representative trait among multiple microbial functions. At macroecological scales, cobamide-producing microbes occur across relatively high trophic levels, reflecting a broader principle of nutrient transfer that may also apply to other essential metabolites. This framework provides a general basis for studying nutritional microbes in soil food webs and advances One Health research.

Soil life relies on microbial nutrient exchange to maintain ecosystem balance. This study shows that cobamide-producing microbes act as essential connectors in soil food webs, supporting host health and highlighting cross-kingdom links central to One Health.

Figures