Abstract
Microbial communities play a major role in disease, biogeochemical cycling, agriculture, and bioremediation. However, identifying the ecological processes that govern microbial community assembly and disentangling the relative impacts of those processes has proven challenging. Here, we propose that this discord is due to microbial systems being studied at different spatial, temporal, and phylogenetic scales. We argue that different processes dominate at different scales, and that through a more explicit consideration of spatial, temporal, and phylogenetic grains and extents (the two components of scale) a more accurate, clear, and useful understanding of microbial community assembly can be developed. We demonstrate the value of applying ecological concepts of scale to microbiology, specifically examining their application to nestedness, legacy effects, and taxa-area relationships of microbial systems. These proposed considerations of scale will help resolve long-standing debates in microbial ecology regarding the processes determining the assembly of microbial communities, and provide organizing principles around which hypotheses and theories can be developed.
Highlights
Understanding the processes that shape microbial communities holds potential to provide important insights into ecology and evolutionary biology, and can enable forecasting and management of microbial ecosystem services
Thompson et al [27] investigated how nestedness varies with phylogenetic grain, and found that it is strong at coarse grains and weakens with increasingly fine grains, until at the operational taxonomic unit (OTU) level it is almost entirely absent
Concluding Remarks and Future Perspectives Moving forward, we advocate that an explicit consideration of spatial, temporal, and phylogenetic grain and extent would lead to an improved understanding of the mechanisms of community assembly among microbes
Summary
Microbial communities play a major role in disease, biogeochemical cycling, agriculture, and bioremediation. We argue that different processes dominate at different scales, and that through a more explicit consideration of spatial, temporal, and phylogenetic grains and extents (the two components of scale) a more accurate, clear, and useful understanding of microbial community assembly can be developed. In the human microbiome, selection [19], neutral processes [20], dispersal limitation [21], and other mechanisms [22] have been implicated in the assembly of microbial communities. In polluted environments abiotic selection has been implicated [26] These and other examples all point to a heterogeneity of mechanisms of community assembly (selection, neutral processes, dispersal limitation, and mutation) operating across microbial communities. Most ecological patterns vary depending on grain and extent. (The exception being scaling laws and fractal or scale-invariant patterns.) So by necessity, our conceptual models and the mechanisms that we identify as being important will often vary across scales concomitantly
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