Incorporating phylogenetic metrics to microbial co‐occurrence networks based on amplicon sequences to discern community assembly processes

Abstract

Co‐occurrence network analysis based on amplicon sequences is increasingly used to study microbial communities. Patterns of co‐existence or mutual exclusion between pairs of taxa are often interpreted as reflecting positive or negative biological interactions. However, other assembly processes can underlie these patterns, including species failure to reach distant areas (dispersal limitation) and tolerate local environmental conditions (habitat filtering). We provide a tool to quantify the relative contribution of community assembly processes to microbial co‐occurrence patterns, which we applied to explore soil bacterial communities in two dry ecosystems. First, we sequenced a bacterial phylogenetic marker in soils collected across multiple plots. Second, we inferred co‐occurrence networks to identify pairs of significantly associated taxa, either co‐existing more (aggregated) or less often (segregated) than expected at random. Third, we assigned assembly processes to each pair: patterns explained based on spatial or environmental distance were ascribed to dispersal limitation (2%–4%) or habitat filtering (55%–77%), and the remaining to biological interactions. Finally, we calculated the phylogenetic distance between taxon pairs to test theoretical expectations on the linkages between phylogenetic patterns and assembly processes. Aggregated pairs were more closely related than segregated pairs. Furthermore, habitat‐filtered aggregated pairs were closer relatives than those assigned to positive interactions, consistent with phylogenetic niche conservatism and cooperativism among distantly related taxa. Negative interactions resulted in equivocal phylogenetic signatures, probably because different competitive processes leave opposing signals. We show that microbial co‐occurrence networks mainly reflect environmental tolerances and propose that incorporating measures of phylogenetic relatedness to networks might help elucidate ecologically meaningful patterns.

Phylogenetic relatedness drives protist assembly in marine and terrestrial environments

“…By taking advantage of the modular structure of the co‐occurrence networks, microbial occurrences have also been linked to habitat preference, which can be interpreted as the signal for environmental filtering (de Menezes et al., 2015; Lentendu et al., 2014; Milici et al., 2016; Morriën et al., 2017). However, studies have yet to integrate phylogenetic relatedness as an explanatory parameter for network structure, which has been introduced recently for soil bacteria (Goberna et al., 2019).…”

nir gene‐based co‐occurrence patterns reveal assembly mechanisms of soil denitrifiers in response to fire

“…This observation, although not being a direct evidence, might indicate environmental filtering due to local abiotic conditions (Soininen et al ., 2018). Our results add up to previous studies suggesting that abiotic filtering is the prevailing assembly mechanism of bacterial communities (Pascual‐García et al ., 2014; Goberna et al ., 2019).…”

“…A signal for potential positive interactions is the fact that pairs of taxa sharing co‐presence links doubled those of mutually excluding taxa. This pattern is commonly found in networks built for different organisms and has been attributed to the easiness to detect physical co‐aggregation (Pascual‐García et al ., 2014; Freilich et al ., 2018; Goberna et al ., 2019). Organisms that co‐aggregate, e.g.…”

“…Organisms that co‐aggregate, e.g. in biofilms, might leave more detectable signals because they greatly increase cell density and expand the niche for other species (Nadell et al ., 2016; Freilich et al ., 2018; Goberna et al ., 2019). Under prefire conditions, we detected a prevalence of nirS ‐ nirS links between bacteria whose nirS was most closely related to that in Magnetospirillum .…”

“…Patterns of co‐presence (positive associations) and mutual exclusion (negative associations) can be interpreted in terms of either niche preferences or ecological interactions (Faust and Raes, 2012; Barberán et al ., 2012; Pascual‐García et al ., 2014; Jones and Hallin, 2019). We have previously shown that the phylogenetic analysis of bacteria that co‐occur or mutually exclude each other based on 16S rRNA gene networks allows discerning among assembly processes that shape soil bacterial communities (Pérez‐Valera et al ., 2017; Goberna et al ., 2019). In nir gene‐based co‐occurrence networks (hereinafter ‘ nir ‐based networks’), the co‐presence of microorganisms bearing the same nir variant (i.e.…”