Abstract
Bacterial feeding has evolved towards specific evolutionary niches and the sources of energy differ between species and strains. Although bacteria fundamentally compete for nutrients, the excreted products from one strain may be the preferred energy source or a source of essential nutrients for another strain. The large variability in feeding preferences between bacterial strains often provides for complex cross-feeding relationships between bacteria, particularly in complex environments such as the human lower gut, which impacts on the host’s digestion and nutrition. Although a large amount of information is available on cross-feeding between bacterial strains, it is important to consider the evolution of cross-feeding. Adaptation to environmental stimuli is a continuous process, thus understanding the evolution of microbial cross-feeding interactions allows us to determine the resilience of microbial populations to changes to this environment, such as changes in nutrient supply, and how new interactions might emerge in the future. In this review, we provide a framework of terminology dividing bacterial cross-feeding into four forms that can be used for the classification and analysis of cross-feeding dynamics. Under the proposed framework, we discuss the evolutionary origins for the four forms of cross-feeding and factors such as spatial structure that influence their emergence and subsequent persistence. This review draws from both the theoretical and experimental evolutionary literature to provide a cross-disciplinary perspective on the evolution of different types of cross-feeding.
Highlights
All bacteria require an energy source for maintenance of cellular functions, growth, and reproduction, these energy sources may differ between species and between strains
A different, but complementary perspective for the evolution of cross-feeding dependencies is provided by the Black Queen Hypothesis (BQH; Morris et al, 2012)
In a large-scale analysis of metabolic networks and sequenced bacterial genomes, more than 60% of the gut-inhabiting bacteria tested were predicted to be auxotrophic for at least one of the amino acids, nucleosides and vitamins considered, with a median of two auxotrophies per strain (D’Souza et al, 2014). This analysis showed that the majority of the gut strains studied had lost almost all of the genes for the biosynthetic pathway corresponding to their auxotrophy. These results suggest that it is possible that cross-feeding dependencies emerging from gene loss may be widespread in complex communities such as the gut, and that a single gene loss is likely followed by the loss of other genes within the same biosynthetic pathway
Summary
All bacteria require an energy source for maintenance of cellular functions, growth, and reproduction, these energy sources may differ between species and between strains. To examine abstractly how diversification such as that observed in the LTEE may occur, Doebeli (2002) presented a mathematical model for the evolution of cross-feeding on metabolic intermediates In this model, a single-species bacterial population converts an initial molecule to an intermediate, before further converting it to a final end-product. A notable point on which the two models differ is the manner in which new strains are established: the first model involved gradual speciation from a single population over an extended time period, whereas the second considered the occurrence of phenotypically very distinct mutants, which quickly increase in number due to their growth advantage The latter is more readily comparable with the long-term observations of the LTEE, in which the relative proportions of S and L strains vary widely across generations. The answer to this question is likely case-dependent (Pande et al, 2014), and may qualitatively change as a population evolves, due to processes such as adaptive gene loss
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