Microbial composition and function are nested and shaped by food web topologies

TL;DR

This study shows that bacteria in food webs are nested and follow the structure of the food web, with their composition and function influenced by host trophic position.

Contribution

The study introduces the concept of microbial composition and function being nested within food web topologies.

Findings

Bacterial taxonomy and function are compositionally nested and mirror the pyramid-shaped food web structure.

Most bacterial taxa and genes associated with hosts are found in host-independent environmental samples.

Bacterial taxa correlate with host location and trophic position, but functional genes do not show spatial structure.

Abstract

Food webs govern interactions among organisms and drive energy fluxes within ecosystems. With an increasing appreciation for the role of symbiotic microbes in host metabolism and development, it is imperative to understand the extent to which microbes conform to, and potentially influence, canonical food web efficiencies and structures. Here, we investigate whether bacteria and their taxa and functional genes are compositionally nested within a simple model food web hierarchy, and the extent to which this is predicted by the trophic position of the host. Using shotgun and amplicon sequencing of discrete food web compartments within replicate tank bromeliads, we find that both taxonomy and function are compositionally nested and largely mirror the pyramid-shaped distribution of food webs. Further, nearly the entirety of bacterial taxa and functional genes associated with hosts are contained within host-independent environmental samples. Community composition of bacterial taxa did not significantly correlate with that of functional genes, indicating a high likelihood of functional redundancy. Whereas bacterial taxa were shaped by both location and trophic position of their host, functional genes were not spatially structured. Our work illustrates the advantages of applying food web ecology to predict patterns of overlapping microbiome composition among unrelated hosts and distinct habitats. Because bacterial symbionts are critical components of host metabolic potential, this result raises important questions about whether bacterial consortia are shaped by the same energetic constraints as hosts, and whether they play an active role in food web efficiency.

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