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

Abstract

Unlocking the secrets of microbial interactions through genomics is pivotal for advancing microbial ecology. In most ecosystems, the scarcity of iron makes iron-mediated interactions a central theme in shaping microbial communities. Bacteria have evolved diverse strategies, including the production of siderophores—diverse secondary metabolites—to scavenge iron from their surroundings. Here, we use bioinformatic tools to predict siderophore iron-interaction networks among 1928Pseudomonasstrains from sequence data. Our approach uses coevolution analysis to group siderophore synthetase clusters and receptors used for uptake into key-lock pairs. Through a mix of computational analyses and experimental validation, we reconstructPseudomonasiron-interaction networks across a spectrum of habitats, from soil to water, plants, and human-related environments and reveal substantial differences in network structure and connectivity across habitats. Altogether, our sequence-to-interaction mapping tool empowers researchers to decode bacterial ecology in complex microbiomes, setting the stage for novel interventions to engineer microbiome functionality.

From sequence to molecules: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

“…While experimental work is often restricted to a low number of strains, we propose that our bioinformatic pipeline can be used to predict pyoverdine-mediated interaction networks across thousands of strains and across different habitats. We have addressed this point in a complementary study 61 .…”