Label-Free Proteomics of a Defined, Binary Co-culture Reveals Diversity of Competitive Responses Between Members of a Model Soil Microbial System

Abstract

Interactions among members of microbial consortia drive the complex dynamics in soil, gut, and biotechnology microbiomes. Proteomic analysis of defined co-cultures of well-characterized species provides valuable information about microbial interactions. We used a label-free approach to quantify the responses to co-culture of two model bacterial species relevant to soil and rhizosphere ecology, Bacillus atrophaeus and Pseudomonas putida. Experiments determined the ratio of species in co-culture that would result in the greatest number of high-confidence protein identifications for both species. The 281 and 256 proteins with significant shifts in abundance for B. atrophaeus and P. putida, respectively, indicated responses to co-culture in overall metabolism, cell motility, and response to antagonistic compounds. Proteins associated with a virulent phenotype during surface-associated growth were significantly more abundant for P. putida in co-culture. Co-culture on agar plates triggered a filamentous phenotype in P. putida and avoidance of P. putida by B. atrophaeus colonies, corroborating antagonistic interactions between these species. Additional experiments showing increased relative abundance of P. putida under conditions of iron or zinc limitation and increased relative abundance of B. atrophaeus under magnesium limitation were consistent with patterns of changes in abundance of metal-binding proteins during co-culture. These results provide details on the nature of interactions between two species with antagonistic capabilities. Significant challenges remaining for the development of proteomics as a tool in microbial ecology include accurate quantification of low-abundance peptides, especially from rare species present at low relative abundance in a consortium.

Enhancement of antibiotic production by co-cultivation of two antibiotic producing marine Vibrionaceae strains

“…co-cultivations are common but are often, at least partly, the result of exploitative competition(Hibbing et al 2010) in which one of the strains grows significantly faster than the other(Chignell et al 2018;Khan et al 2018;Sathe and Kuemmerli 2020), and that was not the case in this study. Sampling at multiple time points showed decreasing abundance of V. coralliilyticus cells in the stationary phase, indicating interference competition.…”

Plant-beneficial functions and interactions of Bacillus subtilis SL-44 and Enterobacter cloacae Rs-2 in co-culture by transcriptomics analysis

“…For example, Bacillus sp. and Pseudomonas sp., which are common in soil, have a slight inhibition between each other (Chignell et al 2017). Inhibition also occurs in mixed systems with certain functions, such as lactic acid bacteria and yeasts, which are the main microorganisms of fermentation (Leroi and Pidoux 2008).…”

Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfei

“…This process enables acquisition of tandem mass spectra across the peptide's elution period, yielding fragment ion chromatograms from which abundance is determined, allowing for a highly specific and selective MS approach for targeted peptide quantitation (Peterson et al, 2012). One of the key challenges in quantitatively comparing proteins from microbial consortia is that the relative distribution of organisms comprising the population (e.g., co-versus mono-culture) influences peptide abundance measurements (Chignell et al, 2018). To overcome this limitation, unmodified peptides from the respective acylated proteins were used as internal standards to normalize acylated peptide levels.…”