Functional genomics study of Pseudomonas putida to determine traits associated with avoidance of a myxobacterial predator

Shukria Akbar,D Cole Stevens

doi:10.1038/s41598-021-96046-8

Abstract

Predation contributes to the structure and diversity of microbial communities. Predatory myxobacteria are ubiquitous to a variety of microbial habitats and capably consume a broad diversity of microbial prey. Predator–prey experiments utilizing myxobacteria have provided details into predatory mechanisms and features that facilitate consumption of prey. However, prey resistance to myxobacterial predation remains underexplored, and prey resistances have been observed exclusively from predator–prey experiments that included the model myxobacterium Myxococcus xanthus. Utilizing a predator–prey pairing that instead included the myxobacterium, Cystobacter ferrugineus, with Pseudomonas putida as prey, we observed surviving phenotypes capable of eluding predation. Comparative transcriptomics between P. putida unexposed to C. ferrugineus and the survivor phenotype suggested that increased expression of efflux pumps, genes associated with mucoid conversion, and various membrane features contribute to predator avoidance. Unique features observed from the survivor phenotype when compared to the parent P. putida include small colony variation, efflux-mediated antibiotic resistance, phenazine-1-carboxylic acid production, and increased mucoid conversion. These results demonstrate the utility of myxobacterial predator–prey models and provide insight into prey resistances in response to predatory stress that might contribute to the phenotypic diversity and structure of bacterial communities.

Highlights

Predation contributes to the structure and diversity of microbial communities
P. putida has exhibited resistance to the predation by protozoan grazers[14]. To identify any such predation avoidance of P. putida when interacting with a bacterial predator, we chose to utilize a culture-based predation assay on solid agar media and investigated the predatory interaction between a predatory myxobacterium C. ferrugineus and P. putida prey
Utilizing predation assays where an inoculum of C. ferrugineus was introduced to the edge of an established spot of P. putida[24], we considered swarming overtaking the P. putida spot with no visible prey biomass remaining to be an endpoint of predation

Summary

Introduction

Predation contributes to the structure and diversity of microbial communities. Predatory myxobacteria are ubiquitous to a variety of microbial habitats and capably consume a broad diversity of microbial prey. Unique features observed from the survivor phenotype when compared to the parent P. putida include small colony variation, efflux-mediated antibiotic resistance, phenazine-1-carboxylic acid production, and increased mucoid conversion These results demonstrate the utility of myxobacterial predator–prey models and provide insight into prey resistances in response to predatory stress that might contribute to the phenotypic diversity and structure of bacterial communities. Examples of prey responses correlated with resistance to myxobacterial predation include Escherichia coli biofilm formation[17], Bacillus subtilis sporulation and production of bacillaene[18,19], Bacillus licheniformus glycosylation of the predation-associated metabolite myxovirescin A 20, galactoglucan exopolysaccharide production and increased melanin production by Sinorhizobium meliloti[21,22], and formaldehyde secretion by Pseudomonas aeruginosa[11] All of these features were discovered from predator–prey experiments utilizing the model myxobacterium M. xanthus. We report the generation and predator avoidance of a P. putida phenotype resistant to myxobacterial predation using standard predator–prey experiments, differential gene expression data comparing the survivor phenotype with predator-unexposed P. putida, and traits observed to potentially contribute to predator avoidance

Methods

Results

Conclusion