Siderophore synthetase-receptor gene coevolution reveals habitat and pathogen-specific bacterial iron interaction networks

Bacterial social interactions play crucial roles in various ecological,
medical, and biotechnological contexts. However, predicting these
interactions from genome sequences is notoriously difficult. Here, we
developed bioinformatic tools to predict whether secreted iron-scavenging
siderophores stimulate or inhibit the growth of community members.
Siderophores are chemically diverse and can be stimulatory or inhibitory
depending on whether bacteria possess or lack corresponding uptake
receptors. We focused on 1928 representative Pseudomonas genomes and
developed an experimentally validated co-evolution algorithm to match
encoded siderophore synthetases to corresponding receptor groups. We
derived community-level iron interaction networks to show that
siderophore-mediated interactions differ across habitats and lifestyles.
Specifically, dense networks of siderophore sharing and competition were
observed among environmental and non-pathogenic species, while small,
fragmented networks occurred among human-associated and pathogenic
species. Altogether, our sequence-to-ecology approach empowers the
analyses of social interactions among thousands of bacterial strains and
offers opportunities for targeted intervention to microbial communities.