Competitive interactions between culturable bacteria are highly non-additive

Abstract

Microorganisms are found in diverse communities whose structure and function are determined by interspecific interactions. Just as single species seldom exist in isolation, communities as a whole are also constantly challenged and affected by external species. Though much work has been done on characterizing how individual species affect each other through pairwise interactions, the joint effects of multiple species on a single (focal) species, remain under explored. As such, it is still unclear how single species effects combine to a community-level effect on a species of interest. To explore this relationship, we assayed thousands of communities of two, three, and four bacterial species, measuring the effect of single, pairs of, and trios of 61 affecting species on six different focal species. We found that when multiple species each have a negative effect on a focal species, their joint effect is typically not given by the sum of the effects of individual affecting species. Rather, they are dominated by the strongest individual-species effect. Therefore, while joint effects of multiple species are often non-additive, they can still be derived from the effects of individual species, making it plausible to map complex interaction networks based on pairwise measurements. This finding is important for understanding the fate of species introduced into an occupied environment, and is relevant for applications in medicine and agriculture, such as probiotics and biocontrol agents, as well as for ecological questions surrounding migrating and invasive species.

Environmental modulators of algae-bacteria interactions at scale

“…In this study, we used droplet-based microfluidic chip (“kChip” with k=2) to rapidly assay the phototroph-heterotroph interactions in hundreds of environmental conditions in parallel. The kChip platform has previously been utilized for drug discovery, pathogen detection, and the study of bacterial interactions [9, 31–33]. Briefly, the experiment proceeds by first generating a library of environmental conditions that vary in the initial pH, buffering capacity, concentration of phosphorus, and concentration of carbon of a chemically defined minimal medium (Fig.…”

“…The kChip platform has previously been utilized for drug discovery, pathogen detection, and the study of bacterial interactions [9,[31][32][33]. Briefly, the experiment proceeds by first gen-erating a library of environmental conditions that vary in the initial pH, buffering capacity, concentration of phosphorus, and concentration of carbon of a chemically defined minimal medium (Fig.…”

Microbiome diversity protects against pathogens by nutrient blocking

“…That is, whereas either E. coli alone or the rest of the community without E. coli has little impact on pathogen growth, together they have a strong effect on pathogen growth. Such higher-order effects are considered important in ecology because they imply context dependence, which can make a system difficult to understand and predict (22,(29)(30)(31)(32). Another way to illustrate the effect of diversity on colonization resistance is to compare our data with a simple null…”

Environmental selection overrides host selection in a horizontally acquired microbiota

“…The copyright holder for this preprint this version posted March 24, 2023. ; https://doi.org/10.1101/2023.03.22.533819 doi: bioRxiv preprint complexity of most microbiotas makes it difficult to assess the relative influence of host and environmental selection as biotic interactions between microbiota members influence fitness, yet become non-linear with increasing community complexity 11 .…”

“…However, it is unclear how strategies of co-existing microbes affect an evolving community. Experimentally, the complexity of most microbiotas makes it difficult to assess the relative influence of host and environmental selection as biotic interactions between microbiota members influence fitness, yet become non-linear with increasing community complexity 11 .…”