Adaptive Evolution of Geobacter sulfurreducens in Coculture with Pseudomonas aeruginosa

Abstract

Interactions between microorganisms in mixed communities are highly complex, being either syntrophic, neutral, predatory, or competitive. Evolutionary changes can occur in the interaction dynamics between community members as they adapt to coexistence. Here, we report that the syntrophic interaction between Geobacter sulfurreducens and Pseudomonas aeruginosa coculture change in their dynamics over evolutionary time. Specifically, Geobacter sp. dominance increases with adaptation within the cocultures, as determined through quantitative PCR and fluorescence in situ hybridization. This suggests a transition from syntrophy to competition and demonstrates the rapid adaptive capacity of Geobacter spp. to dominate in cocultures with P. aeruginosa. Early in coculture establishment, two single-nucleotide variants in the G. sulfurreducens fabI and tetR genes emerged that were strongly selected for throughout coculture evolution with P. aeruginosa phenazine wild-type and phenazine-deficient mutants. Sequential window acquisition of all theoretical spectra-mass spectrometry (SWATH-MS) proteomics revealed that the tetR variant cooccurred with the upregulation of an adenylate cyclase transporter, CyaE, and a resistance-nodulation-division (RND) efflux pump notably known for antibiotic efflux. To determine whether antibiotic production was driving the increased expression of the multidrug efflux pump, we tested Pseudomonas-derived phenazine-1-carboxylic acid (PHZ-1-CA) for its potential to inhibit Geobacter growth and drive selection of the tetR and fabI genetic variants. Despite its inhibitory properties, PHZ-1-CA did not drive variant selection, indicating that other antibiotics may drive overexpression of the efflux pump and CyaE or that a novel role exists for these proteins in the context of this interaction. IMPORTANCE Geobacter and Pseudomonas spp. cohabit many of the same environments, where Geobacter spp. often dominate. Both bacteria are capable of extracellular electron transfer (EET) and play important roles in biogeochemical cycling. Although they recently in 2017 were demonstrated to undergo direct interspecies electron transfer (DIET) with one another, the genetic evolution of this syntrophic interaction has not been examined. Here, we use whole-genome sequencing of the cocultures before and after adaptive evolution to determine whether genetic selection is occurring. We also probe their interaction on a temporal level and determine whether their interaction dynamics change over the course of adaptive evolution. This study brings to light the multifaceted nature of interactions between just two microorganisms within a controlled environment and will aid in improving metabolic models of microbial communities comprising these two bacteria.

Spatial Engineering of Microbial Consortium for Long‐Lasting, Self‐Sustaining, and High‐Power Generation in a Bacteria‐Powered Biobattery

“…This is in good agreement with other reports and our previous work demonstrating that gases necessary for cyanobacterial maturation and the electron shuttle, phenazine, for the EET process can be produced by P. aeruginosa (PA01). [17,26,27,29,31] Carbon dioxide and nitrogen produced from nitrogen-fixing bacteria such as Pseudomonas sp. can be used to preserve cyanobacterial viability, which consequently exhibit self-sustainable capabilities of the whole artificial microbial consortia.…”

“…[8,[25][26][27][28][29][30] Some other microbial communities were successfully designed to improve their metabolic cooperation through direct interspecies electron transfer (DIET) between cultures. [31] Although microorganisms in nature live in the form of community optimizing and improving their viability and sustainability, and thus the design of the microbial consortia is considered as a valuable approach for biotechnique and bioenergy fields, engineering the microbial communities is in early infancy and faces many technical challenges in predicting their diverse metabolic processes and ecological dependencies. [32][33][34][35][36] Even with homogeneous and controllable laboratory conditions, most attempts to design artificial microbial consortia could not provide desirable functions for long-term operation because of the unbalanced competition among non-spatially structured mixed populations.…”

Cross-protection and cross-feeding between Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence

“…Our knowledge of pathogens largely comes from pure culture laboratory studies, which have been pivotal to understanding single species infections, but have given little information on coinfection dynamics. Given that minority populations of bacterial communities can have significant impacts on the physiology and behaviour of dominant members 2,3 , it is important to understand possible interspecies interactions between coinfecting pathogens and the effects they may have on virulence and antibiotic resistance within polymicrobial infections.…”

Cross-protection and cross-feeding between ESKAPE pathogens Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence

“…Our knowledge of pathogens largely comes from pure culture laboratory studies, which have been pivotal to understanding single species infections, but have given little information on coinfection dynamics. Given that minority populations of bacterial communities can have significant impacts on the physiology and behaviour of dominant members 1,2 , it is important to understand possible interspecies interactions between coinfecting pathogens and the effects they may have on virulence and antibiotic resistance within polymicrobial infections.…”