Deciphering the electric code of Geobacter sulfurreducens in cocultures with Pseudomonas aeruginosa via SWATH-MS proteomics

Semenec, Lucie; Laloo, Andrew Elohim; Schulz, Benjamin L.; Vergara, Ismael A.; Bond, Philip L.; Franks, Ashley E.

doi:10.1016/j.bioelechem.2017.09.013

Cited by 25 publications

(13 citation statements)

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“…became more metabolically flexible with coculture adaptation. We also found that the abundance of Geobacter proteins was greater than that of Pseudomonas proteins in extracted coculture proteomes (39). To determine whether the increase in Geobacter metabolic flexibility changed coculture population dynamics over time, we directly quantified the abundance of each microbe in the population by performing qPCR on all cocultures (PAO1 ϩ DL-1, PA14 ϩ DL-1, and phz mutant ϩ DL-1) for both initial (subculture 0 [s0]) and adapted (subculture 13 [s13]) cocultures.…”

Section: Resultsmentioning

confidence: 66%

“…The results described here show the propensity of G. sulfurreducens to undergo rapid adaptive evolutionary changes that may play a role in protection against competition with stresses created by P. aeruginosa, as Geobacter spp. become more metabolically versatile during coculture adaptation (39). Strong and rapid selection driven by a limited number of mutations has been observed in other work, where a single-nucleotide mutation of a regulatory gene confers rapid adaptive resilience to stress (23,67,68).…”

Section: Discussionmentioning

confidence: 78%

“…became the most abundant community members by S13. This corresponds with its enhanced metabolic flexibility as it adapts (39), and hence its diminished reliance on Pseudomonas spp. for providing electron donors through DIET.…”

Section: Resultsmentioning

confidence: 99%

“…TetR is situated upstream of a predicted operon composed of genes GSU0950 and GSU0949, which putatively encode an outer membrane adenylate cyclase transporter (CyaE) and an RND efflux pump, respectively, and predicted ABC transporter genes, GSU0948 and GSU0947 (40). As TetR is predicted to negatively regulate this operon, we looked at the protein abundances of these gene products within our proteomics data previously obtained by sequential window acquisition of all theoretical spectra-mass spectrometry (SWATH-MS) (39). Both GSU0950 (herein referred to as CyaE) and GSU0949 (RND family efflux pump) were found in significantly higher abundances in cocultures than in G. sulfurreducens pure cultures.…”

Section: Resultsmentioning

confidence: 99%

“…Their potential for interaction, however, has only recently been investigated. Our recent adaptive evolution study on cocultures of G. sulfurreducens and P. aeruginosa found that several electron transfer processes were possible with the evolution of serially transferred cocultures, which progressively increased in fitness (39). Initially, DIET was the predominant form of syntrophic interaction.…”

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confidence: 99%

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Adaptive Evolution of Geobacter sulfurreducens in Coculture with Pseudomonas aeruginosa

Semenec

Vergara

Laloo

et al. 2020

mBio

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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.

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Section: Resultsmentioning

confidence: 66%