Quantifying the roles of immigration and chance in shaping prokaryote community structure

Abstract

Naturally occurring populations of bacteria and archaea are vital to life on the earth and are of enormous practical significance in medicine, engineering and agriculture. However, the rules governing the formation of such communities are still poorly understood, and there is a need for a usable mathematical description of this process. Typically, microbial community structure is thought to be shaped mainly by deterministic factors such as competition and niche differentiation. Here we show, for a wide range of prokaryotic communities, that the relative abundance and frequency with which different taxa are observed in samples can be explained by a neutral community model (NCM). The NCM, which is a stochastic, birth-death immigration process, does not explicitly represent the deterministic factors and therefore cannot be a complete or literal description of community assembly. However, its success suggests that chance and immigration are important forces in shaping the patterns seen in prokaryotic communities.

Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale

“…However, the Arctic community diverged with dissimilarity higher than the predicted neutral community, which suggests a major role for environmental stochasticity mediated by niche processes (Dornelas et al, 2006). In the other three cases, dissimilarities converged (that is, lower than expected), which has been proposed to be a signature of niche processes as convergence implies that local communities, with all other conditions being equal and tended to a predictable composition, should depend on the output of nichemediated competition (Tilman, 2004;Etienne, 2007; see also Sloan et al, 2006 for examples on bacterial community). In the remaining cases, data were consistent with the neutral models.…”

“…Neutral theories predict that random patterns in species co-occurrence and environmentally independent spatial autocorrelation (for example, dispersal) should be the main features of community structure if demographic stochasticity and limited dispersal alone were driving population dynamics (Chesson and Huntly, 1989;Engen and Lande, 1996;Bell, 2000;Hubbell, 2001;Whitfield, 2002;McGill, 2003;Volkov et al, 2003Volkov et al, , 2004Chave, 2004;Connell et al, 2004;Maurer and McGill, 2004;Bell et al, 2005;Sloan et al, 2006;Bell, 2010). Conversely, more deterministic processes driven by species interaction and niche partitioning are predicted to produce segregation in terms of species co-occurrence or even aggregation (Chave, 2004;Dornelas et al, 2006;Chase, 2007), if niche partitioning interacts with environmental stochasticity (that is, disturbance regime) or with extreme changes in key abiotic variables such as water availability and temperature.…”

Reproducibility of Vibrionaceae population structure in coastal bacterioplankton

“…However, experimental addition of model organic compounds to marine samples triggered a taxonomically widespread response, which was taken as evidence for dominance of generalist taxa (Mou et al, 2008). Consistent with this observation, some modeling-based studies have de-emphasized niche-based processes (Sloan et al, 2006;Ofiteru et al, 2010). Instead, they explained community assembly by (near) neutral processes, which explain the composition of communities by stochastic birth-death and immigration processes.…”

Mechanisms determining the fate of dispersed bacterial communities in new environments

“…On the other hand, it has been shown that bacterial community assembly is often, to a considerable extent, influenced by regional processes (for example, dispersal) and is conform to predictions made by the neutral model (Sloan et al, 2006;Ö stman et al, 2010). As the main assumption made by the neutral model is the functional equivalence of taxa (Hubbell, 2001), no compositional changes, but rapid functional adaptations of dispersed populations, should occur when they arrive in a new habitat, as functional plasticity is expected to be high.…”