Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments

Abstract

A major open question in microbiome research is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by this challenge, here we ask whether communities assembled in a mixed nutrient environment can be predicted from those assembled in every single nutrient in isolation. To that end, we first formulate a quantitative null model of community assembly in a mixture of nutrients that recruit species independently. We then test the model predictions by assembling replicate communities in synthetic environments that contain either a pair of nutrients, or each nutrient in isolation. We find that the null, naturally additive model generally predicts well the family-level community composition. However, we also identify systematic deviations from the additive predictions that reflect generic patterns of nutrient dominance at the family-level of taxonomy. Pairs of more-similar nutrients (e.g. two sugars) are on average more additive than pairs of more dissimilar nutrients (e.g. one sugar and one organic acid). A simple dominance rule emerges, where we find that sugars generally dominate organic acids. This simple dominance rule extends to most families and most sugar-organic acid pairs in our experiment. Our results suggest that regularities in the ways nutrients interact may help us predict how microbial communities respond to changes in nutrient composition.

Spatially explicit depiction of a floral epiphytic bacterial community reveals role for environmental filtering within petals

“…Interestingly, in our petal community members of the Pseudomonadaceae and Enterobacteriaceae are common ( Figure A3), and recent studies have shown that these same two families tend to dominate communities assembled in minimal media with carbon as the main limiting resource (Goldford et al, 2018). In these artificial communities, as in our functional tests, Enterobacteriaceae tend to grow better on sugars, and Pseudomonadaceae in organic acids (Estrela et al, 2020). An extreme case of this potential specialization was the Rosenbergiella species, which are known nectar inhabitants.…”

“…Results of the carbon use assay indicate that most of the cultured strains differentiated along a sugar-organic acid axis, corroborating known familial proclivities (Estrela et al, 2020), with most Enterobacteriaceae specializing on sugars and most Pseudomonadaceae specializing on organic acids ( Figure A4A).…”

Exploring the interaction network of a synthetic gut bacterial community

“…Differences between the behavior of strains in pairwise versus complex communities point at higher-order ecological interactions that emerge in the community context. As previously shown in other studies, the underlying mechanisms may involve metabolic flexibility or mixed substrate utilization of the strains in the presence of competitors (41), metabolite cross-feeding and lack of waste-product inhibition and overall change in pH (11) or an excess of provided substrates in the medium.…”

Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology

“…Enrichment communities are an ideal system to test this hypothesis. In recent work, we have reported that increasing the number of supplied resources from 1 to 2 or 3 had a very small effect in the total biodiversity and did not lead to an appreciable increase in species richness (Estrela et al, 2020a; Figure 2). Consumerresource models with cross-feeding recapitulated this observation, and found that the identity of the nutrients in mixed-nutrient environments (i.e., whether they were two sugars or one sugar and one organic acid) had a larger effect on biodiversity than the number of those nutrients one adds.…”