Surface colonization byFlavobacterium johnsoniaepromotes its survival in a model microbial community

Abstract

Flavobacterium johnsoniaeis a ubiquitous soil and rhizosphere bacterium, but despite its abundance, the factors contributing to its success in communities are poorly understood. Using a model microbial community,TheHitchhikersOf the Rhizosphere (THOR), we determined the effects of colonization on fitness ofF. johnsoniaein the community. Insertion sequencing (INSeq), a massively parallel transposon mutant screen, on sterile sand identified 25 genes likely to be important for surface colonization. We constructed in-frame deletions of nine candidate genes predicted to be involved in cell membrane biogenesis, motility, signal transduction, and transport of amino acids and lipids. All mutants poorly colonized sand, glass, and polystyrene and produced less biofilm than the wild type, indicating the importance of the targeted genes in surface colonization. Eight of the nine colonization-defective mutants were also unable to form motile biofilms, or zorbs, thereby suggesting that the affected genes play a role in group movement and linking stationary and motile biofilm formation genetically. Furthermore, we showed that deletion of colonization genes inF. johnsoniaeaffected its behavior and survival in THOR on surfaces, suggesting that the same traits are required for success in a multispecies microbial community. Our results provide insight into the mechanisms of surface colonization byF. johnsoniaeand form the basis for further understanding its ecology in the rhizosphere.IMPORTANCEMicrobial communities direct key environmental processes through multispecies interactions. Understanding these interactions is vital for manipulating microbiomes to promote health in human, environmental, and agricultural systems. However, microbiome complexity can hinder our understanding of the underlying mechanisms in microbial community interactions. As a first step towards unraveling these interactions, we explored the role of surface colonization in microbial community interactions using THOR, a genetically tractable model community of three bacterial species,Flavobacterium johnsoniae,Pseudomonas koreensis,andBacillus cereus.We identifiedF. johnsoniaegenes important for surface colonization in solitary conditions and in the THOR community. Understanding the mechanisms that promote success of bacteria in microbial communities brings us closer to targeted manipulations to achieve outcomes that benefit agriculture, the environment, and human health.