Patterns and processes of microbial community assembly

Abstract

Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183-206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.

Fig 1

Typical rank-abundance plot, where each point represents the abundance of one organism within the community (data from reference 120). A common feature of many biological communities is that few organisms are present in high abundances, while the majority of taxa are found in low abundances.

Fig 2

Variogram showing how phylogenetic distance between soil rotifer communities (community dissimilarity) varies with the log of geographic distance between communities. Weighted UniFrac values (a measure of phylogenetic distance between communities [51, 52]) close to 1 indicate very different communities, and values close to 0 indicate almost identical communities. The red vertical line is an estimate of the autocorrelation range (∼60 m), beyond which communities show very little autocorrelation. Replotted from data reported by Robeson et al. (143).

Fig 3

Contrasting hypotheses of community assembly. Numbers represent hypothetical species, arrows represent species immigration, letters represent different immigration histories, and roman numerals represent variations in habitat conditions. (Top) Local communities converge in species composition under the same environmental conditions regardless of immigration history. (Bottom) Local communities diverge in species composition when immigration history is variable, even under the same environmental conditions (i.e., priority effects). (Adapted from references [p. 45] and with permission.)

Fig 4

Conceptual model outlining the relationship between edaphic factors, soil microbial community composition, and ecosystem processes for deterministic and stochastic assembly mechanisms.