Species sorting and neutral processes are both important during the initial assembly of bacterial communities

Abstract

Many studies have shown that species sorting, that is, the selection by local environmental conditions is important for the composition and assembly of bacterial communities. On the other hand, there are other studies that could show that bacterial communities are neutrally assembled. In this study, we implemented a microcosm experiment with the aim to determine, at the same time, the importance of species sorting and neutral processes for bacterial community assembly during the colonisation of new, that is, sterile, habitats, by atmospheric bacteria. For this we used outdoor microcosms, which contained sterile medium from three different rock pools representing different environmental conditions, which were seeded by rainwater bacteria. We found some evidence for neutral assembly processes, as almost every 4th taxon growing in the microcosms was also detectable in the rainwater sample irrespective of the medium. Most of these taxa belonged to widespread families with opportunistic growth strategies, such as the Pseudomonadaceae and Comamonadaceae, indicating that neutrally assembled taxa may primarily be generalists. On the other hand, we also found evidence for species sorting, as one out of three media selected a differently composed bacterial community. Species sorting effects were relatively weak and established themselves via differences in relative abundance of generalists among the different media, as well as media-specific occurrences of a few specific taxa. In summary, our results suggest that neutral and species sorting processes interact during the assembly of bacterial communities and that their importance may differ depending on how many generalists and specialists are present in a community.

Mechanisms determining the fate of dispersed bacterial communities in new environments

“…On the other hand, the effect of the incubation environment conflicts with predictions made by the 'adjustment scenario' or neutral model (Hubbell, 2001;Comte and del Giorgio, 2011). Thus, our study shows that several mechanisms determine community composition and functioning at the same time, and is in congruence with previous studies showing that species sorting and neutral processes have simultaneous roles during community assembly (Ofiteru et al, 2010;Langenheder and Székely, 2011). Moreover, environmental changes are prone to increase the abundance of generalists (Clavel et al, 2011), and also the adjustment scenario (Comte and del Giorgio, 2011) predicts a conversion towards generalists upon exposure to new environmental conditions.…”

“…The amplicons for 454-pyrosequencing were prepared, sequenced and the sequences were processed (quality checked, aligned, clustered, identified and normalized) as described before (Langenheder and Székely, 2011). Accordingly, singletons and operational taxonomic units (OTUs) with low abundance (o0.24% of total abundance) were not considered.…”

Community history affects the predictability of microbial ecosystem development

“…Some studies suggest that for a given set of environmental conditions, microbial community development is convergent: common environmental selection recruits the same or similar species from diverse starting species sets to produce similar final community structures (Figure 1; left panel). This view is supported by studies of sulphate-reducing bacteria (SRB) in replicate sediment slurry microcosms (Kurtz et al, 1998), lab-scale activated sludge bioreactors inoculated with wastewater treatment plant communities (Ayarza and Erijman, 2011), soil community transplantation experiments (Lazzaro et al, 2011), microcosm colonization by rainwater bacteria from different sites (Langenheder and Székely, 2011) and analysis of the predictability of seasonal changes in microbial community composition in the Pacific Ocean . In contrast, other studies suggest that microbial community development is divergent: that is, inoculation of identical replicate environments with the same initial microbial community results in different final community structures ( Figure 1, right panel).…”

“…This need is especially acute for microbial communities, which are key drivers of the Earth's biogeochemical cycles (Whitman et al, 1998), industrial processes including wastewater treatment, and human gut health (Palmer et al, 2007) and are the subject of ever increasing data sets generated by modern DNA-based community analysis methods Prosser, 2012). Predictable factors such as environmental selection and interspecies interactions, as well as unpredictable factors such as random dispersal, stochastic population dynamics and priority effects (Chase, 2003(Chase, , 2007, are all believed to affect microbial community structure and function Langenheder and Székely, 2011). However, the relative importance of these factors remains unclear.…”

“…Microcosms provide a powerful tool for microbial ecology (Jessup et al, 2004), as they make it possible to perform replicate laboratory experiments under manipulable conditions. Many important advances have been made using 'simple' microcosm communities with relatively few species (Weatherby et al, 1998;Langenheder and Székely, 2011;Hekstra and Leibler, 2012). In contrast, in this study we aim to preserve the key features of natural microbial ecosystems-high microbial diversity, nutrient cycling, community-environment feedbacks, strong interspecies interactions and spatial structure.…”