Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

Abstract

In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology.

Keywords: ecological theory; ecosystem function; functional traits; microbial diversity; study designs.

Figure 1

Temporal variations in (top) the number of publications on Biodiversity-Ecosystem Functioning, BEF, relationships in a broad sense for microorganisms as compared to plants, and (bottom) the percentage of publications on microbial BEF or plant BEF where biodiversity was directly manipulated. The search terms used are provided in Supplementary Material 1. At each step of the search profile development, we checked on subsamples that the search hits corresponded to the targeted type of studies. We also checked that a selection of key experiments/papers we knew about were found.

Figure 2

Reflection of microbial traits on the Competitor-Ruderal-Stress tolerator life strategy framework as was proposed for plants (Grime, 1977). The scheme has been adapted for Ho et al. (2013) who used this framework for assigning life-strategies to methane-oxidizing bacteria. The scheme groups subsets of microbial traits which collectively would be of most importance for the respective strategy. The traits collectively accommodate exploring and exploiting habitats, competing with other organisms, tolerating or avoiding surviving stress, and deprivation. This classification is purely qualitative but, for some traits, life-history strategies have been proposed in earlier studies (Fierer et al., ; Portillo et al., 2013).