Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

Abstract

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North–South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species.

Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease

“…The network diameter is defined as the longest of the pairwise shortest path lengths. This method is commonly applied in microbial 49 50 51 and ecological 52 53 co-occurrence networks to assess the dependence of global network structure on particular species. While co-occurrence networks do not allow for direct prediction of the impact of network perturbation in an individual, they do provide insight to population-level ramifications of species removal.…”

Diversity and potential activity of methanotrophs in high methane-emitting permafrost thaw ponds

“…We note that previous studies on the bacterial communities in these permafrost thaw ponds based on 16S rRNA genes and 16S rRNA failed to detect members of the NC10 phylum and only one OTU of Crenothrix , in low abundance, has been recorded. For the Verrucomicrobia that account for 1 to 6% of the reads of the total bacterial community in the KWK and SAS valleys [ 34 , 82 ], the presence of any methanotrophic taxa in this group would need to be verified with alternative primers.…”

Landscape‐scale spatial abundance distributions discriminate core from random components of boreal lake bacterioplankton

“…Most spatial studies of bacterial communities to date have focused on differences in bacterial communities among similar types of ecosystems, or on the variation in dominant taxa or specific bacterial groups along environmental gradients. These studies have revealed recurrent biogeographic patterns at different phylogenetic levels (Newton et al 2011;Jones et al 2012), taxon-specific differences in the environmental range of preferences (Lennon et al 2012;Evans & Wallenstein 2013) and clusters of taxa showing similar associations with environmental conditions (Steele et al 2011;Williams et al 2014;Comte et al 2016). These approaches, however, have been insufficient to elucidate the patterns or significance of rarity in bacterial communities.…”