Function and functional redundancy in microbial systems

Abstract

Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.

Multi‐trophic β‐diversity mediates the effect of environmental gradients on the turnover of multiple ecosystem functions

“…Unlike total β‐diversity (Figure ), total α‐diversity (Figure S8) appeared to be a weak predictor of ecosystem functioning, suggesting that a number of species perform similar functions in soil communities, that is they are functionally redundant. Also, vertical β‐diversity did not cause turnover of ecosystem functions (Figure ), indicating that whatever their richness, trophic groups cluster particularly functionally redundant species (Louca et al, ; Setälä et al, ). Nevertheless, intra‐group functional redundancy level may depend on the studied trophic group.…”

“…Surprisingly, only the turnover of soil but not climatic properties contributed significantly to the direct pathway. Due to varying limitations in soil organic matter and water availability, decomposition rates and nutrient retention times changed across the gradient, with direct consequences on N‐cycling, productivity and N‐leaching (Gavazov, ; Louca et al, ). In contrast to our findings, a large body of literature on size reduction of alpine plants with increasing elevation led us expect that differences in temperature‐related variables (e.g.…”

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

“…Lastly, the data we have collected, 16S rRNA gene sequencing and relative abundance of bacterial taxa, can be thought of as the first pass of data for understanding the microbiome of a host species or clade. Taxonomic composition is more variable than functional capability in many microbial systems (Burke, Steinberg, Rusch, Kjelleberg, & Thomas, ; Human Microbiome Project Consortium, ), including avian microbiomes (Oakley et al, ), which is probably due to functional redundancy (Louca et al, ). Additionally, sequencing a single gene and assessing the relative abundance of the data is compositional by definition and limited in its ability to describe and compare communities because changes in relative abundance cannot be used to infer changes in absolute abundance (Gloor, Macklaim, Pawlowsky‐Glahn, & Egozcue, ).…”

Introduction: The host‐associated microbiome: Pattern, process and function

“…This finding necessitated a change in our understanding of host/microbe relationships and the factors that determine microbiome assembly. It has also been replicated across systems (Louca et al., ), again pointing towards next steps for systems like the aforementioned marine nematodes. In this issue, Roth‐Schulze and colleagues expand on this body of work in Ulva , targeting closely related species from Spain and Australia with metagenomics (Roth‐Schulze et al., ).…”

“…Morella and colleagues use manipulation to gain insight into a hard‐to‐study fraction of earth's microbiome, bacteriophage and their effects on host‐associated bacterial communities. Phage is hypothesized to underlie bacterial community dynamics, particularly in systems with high functional redundancy (Louca et al., ). Such effects can, in turn, impact the eukaryotic hosts of these bacteria (Manrique et al., ).…”