Interplay between stochastic and deterministic processes in the maintenance of alternative community states in Verrucomicrobia-dominated shallow lakes

Abstract

We analyzed the interplay between neutral and deterministic processes in maintaining contrasting alternative bacterioplankton communities through time in highly productive shallow lakes and evaluated the relevance of these processes when a regime shift from a clear to a turbid state occurred. We observed that local assembly is ruled primary deterministically, via local habitat filtering, with a secondary role of stochastic processes. We also found a hierarchy in the environmental sorting: while an unusual Verrucomicrobia dominance characterizes the three systems, local conditions limit within-bacterial community membership to closely phylogenetically related and ecologically similar taxa. These results indicate that bacterial abilities to establish in these lakes are strongly determined by their traits, and point toward special physiological adaptations to persist when these systems undergo a regime shift. Altogether, these results hint to a divergence in function among these alternative communities, mediated by major shifts in bacterial community trait structure, particularly regarding carbon use.

Diversity of photosynthetic picoeukaryotes in eutrophic shallow lakes as assessed by combining flow cytometry cell-sorting and high throughput sequencing

“…This high variation between lakes community compositions cannot be explained by the low connectivity among lakes, since very close lakes, like LI, CH and VI, harbour very different PPE composition. Moreover, CH and VI are directly connected by a short stream, suggesting that local forces would be important drivers of the community structure of PPE, as it was already determined for heterotrophic bacteria in three lakes from the same area (Llames et al 2017).…”

The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time

“…The prevalence of this phylum during winter seems to be typical for temperate and boreal lakes (Tran, Ramachandran, & Khawasik, 2018). Nevertheless, the detection of Verrucomicrobia in freshwaters has been compromised by methodological issues (e.g., primers bias (McCarthy, Chiang, Schmidt, & Denef, 2015)), and therefore, there are contrasting reports regarding its numerical importance or dominance (Chiang et al., 2018; Llames, Huber, Metz, & Unrein, 2017; Newton, Jones, Eiler, McMahon, & Bertilsson, 2011). Our results additionally suggest that differences in the relative abundance of this phylum lie in its seasonality and in the trophic state of the lake considered.…”

Gut microbiome is more stable in males than in females during the development of colorectal cancer

“…Although these two ecological processes have been widely used in soil and water systems (Llames et al . 2017; Feng et al . 2018), they have not been applied to explain the variation in microbial communities with the development of CRC in males and females.…”