A fundamental question in biology is why some species tend to occur together in the same locations, while others are never observed coexisting. This question becomes particularly relevant for microorganisms thriving in the highly diluted waters of high mountain lakes, where biotic interactions might be required to make the most of an extreme environment. We studied a high-throughput gene data set of alpine lakes (>220 Pyrenean lakes) with cooccurrence network analysis to infer potential biotic interactions, using the combination of a probabilistic method for determining significant cooccurrences and coexclusions between pairs of species and a conceptual framework for classifying the nature of the observed cooccurrences and coexclusions. This computational approach (i) determined and quantified the importance of environmental variables and spatial distribution and (ii) defined potential interacting microbial assemblages. We determined the properties and relationships between these assemblages by examining node properties at the taxonomic level, indicating associations with their potential habitat sources (i.e., aquatic versus terrestrial) and their functional strategies (i.e., parasitic versus mixotrophic). Environmental variables explained fewer pairs in bacteria than in microbial eukaryotes for the alpine data set, with pH alone explaining the highest proportion of bacterial pairs. Nutrient composition was also relevant for explaining association pairs, particularly in microeukaryotes. We identified a reduced subset of pairs with the highest probability of species interactions ("interacting guilds") that significantly reached higher occupancies and lower mean relative abundances in agreement with the carrying capacity hypothesis. The interacting bacterial guilds could be more related to habitat and microdispersal processes (i.e., aquatic versus soil microbes), whereas for microeukaryotes trophic roles (osmotrophs, mixotrophs, and parasitics) could potentially play a major role. Overall, our approach may add helpful information to guide further efforts for a mechanistic understanding of microbial interactions in situ. IMPORTANCE A fundamental question in biology is why some species tend to occur together in the same locations, while others are never observed to coexist. This question becomes particularly relevant for microorganisms thriving in the highly diluted waters of high mountain lakes, in which biotic interactions might be required to make the most of an extreme environment. Microbial metacommunities are too often only studied in terms of their environmental niches and geographic barriers since they show inherent difficulties to quantify biological interactions and their role as drivers of ecosystem functioning. Our study highlights that telling apart potential interactions from both environmental and geographic niches may help for the initial characterization of organisms with similar ecologies in a large scope of ecosystems, even when information about actual interactions is partial and limited. The multilayered statistical approach carried out here offers the possibility of going beyond taxonomy to understand microbiological behavior in situ.
Keywords: cell-cell interaction; microbes; networks.