Antagonism correlates with metabolic similarity in diverse bacteria

Abstract

In the , Charles R. Darwin [Darwin C (1859)] proposed that the struggle for existence must be most intense among closely related species by means of their functional similarity. It has been hypothesized that this similarity, which results in resource competition, is the driver of the evolution of antagonism among bacteria. Consequently, antagonism should mostly be prevalent among phylogenetically and metabolically similar species. We tested the hypothesis by screening for antagonism among all possible pairwise interactions between 67 bacterial species from 8 different environments: 2,211 pairs of species and 4,422 interactions. We found a clear association between antagonism and phylogenetic distance, antagonism being most likely among closely related species. We determined two metabolic distances between our strains: one by scoring their growth on various natural carbon sources and the other by creating metabolic networks of predicted genomes. For both metabolic distances, we found that the probability of antagonism increased the more metabolically similar the strains were. Moreover, our results were not compounded by whether the antagonism was between sympatric or allopatric strains. Intriguingly, for each interaction the antagonizing strain was more likely to have a wider metabolic niche than the antagonized strain: that is, larger metabolic networks and growth on more carbon sources. This indicates an association between an antagonistic and a generalist strategy.

Positive interactions are common among culturable bacteria

“…By measuring interactions across many environments, our study produced many instances in which at least one of the two cocultured strains grew poorly or not at all, a regime in which we found positive interactions were far more likely to occur than previously measured. The study also produced instances where both strains grew well and antagonism was common, a result consistent with previous large-scale studies of bacterial interactions (37,38).…”

Incorporating phylogenetic metrics to microbial co‐occurrence networks based on amplicon sequences to discern community assembly processes

“…In support of this idea, competition by interference among pairs of 148 soil Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes revealed that antagonism increases with phylogenetic proximity (Russel, Roder, Madsen, Burmolle, & Sorensen, 2017).…”

“…Competitive exclusion through niche similarities tends to limit the functional (and phylogenetic) similarity of competing lineages, thus favouring the co‐existence of distantly related taxa (Webb et al, ). In support of this idea, competition by interference among pairs of 148 soil Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes revealed that antagonism increases with phylogenetic proximity (Russel, Roder, Madsen, Burmolle, & Sorensen, ). In contrast, relative fitness differences associated with particular superior clades tend to outcompete entire distant lineages resulting in the co‐existence of closely related taxa (Mayfield & Levine, ).…”

Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids

“…Therefore, plasmids may be more strongly challenged by other intracellular plasmid-like elements which, while not being especially detrimental to the host, may compete directly for common cellular resources 42,43 . The latter argument receives support from the accepted community ecology view that similar entities compete more strongly for overlapping niches and resources 44,45,46 .…”