An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment

Abstract

Microorganisms modify their environment by excreting by-products of metabolism, which can create new ecological niches that can help microbial populations diversify. A striking example comes from experimental evolution of genetically identical Escherichia coli populations that are grown in a homogeneous environment with the single carbon source glucose. In such experiments, stable communities of genetically diverse cross-feeding E. coli cells readily emerge. Some cells that consume the primary carbon source glucose excrete a secondary carbon source, such as acetate, that sustains other community members. Few such cross-feeding polymorphisms are known experimentally, because they are difficult to screen for. We studied the potential of bacterial metabolism to create new ecological niches based on cross-feeding. To do so, we used genome scale models of the metabolism of E. coli and metabolisms of similar complexity, to identify unique pairs of primary and secondary carbon sources in these metabolisms. We then combined dynamic flux balance analysis with analytical calculations to identify which pair of carbon sources can sustain a polymorphic cross-feeding community. We identified almost 10,000 such pairs of carbon sources, each of them corresponding to a unique ecological niche. Bacterial metabolism shows an immense potential for the construction of new ecological niches through cross feeding.

A riboswitch gives rise to multi-generational phenotypic heterogeneity in an auxotrophic bacterium

“…At this stage, we can only speculate what such cooperative benefits might be, but one can imagine that cells might not only differ in methionine uptake, but also in a number of other metabolic traits 21 . If so, this could allow for some form of metabolic division of labor, where subpopulations exchange metabolites in the same way as synthetic bacterial communities can exchange amino acids 8,[68][69][70][71][72] . Exploring these and other potential benefits of the long-term phenotypic heterogeneity in methionine uptake is an exciting topic for future research.…”

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

“…Soil microbial community may also influence the determination of phyllosphere microbial diversity. However, the microbes can construct the niches in the phyllosphere microhabitat wherein it can sustain and establish its population steadily (Agler et al 2016;San Roman and Wagner 2018). Recent studies revealed the special relationships between the bacterial species in the phyllosphere community.…”

Evidence for a multi-level trophic organization of the human gut microbiome

“…The hierarchical trophic organization suggested by our 13 model can help mechanistically establish causal links between the abundances of microbes and 14 metabolites in the human gut. 15 Introduction 16 The human gut microbiome is a complex ecosystem with several hundreds of microbial species 17 [1,2] consuming, producing and exchanging hundreds of metabolites [3,4,5,6,7]. With 18 the advent of high-throughput genomics and metabolomics techniques, it is now possible to 19 simultaneously measure the levels of individual metabolites (the fecal metabolome), as well as 20 the abundances of individual microbial species [8].…”

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