Determinants of microbial community structure in aquatic environments remain poorly understood. In rocky shore environments, microbes might be influenced by both local abiotic and biotic factors, as well as larger-scale physical drivers. Using spatially and temporally broad field surveys, we identified microbial community identity and structure present in rocky intertidal benthic biofilm. We addressed three questions: 1) Within a site (<100m), do benthic surfaces of tidepools and emergent rock host distinct microbial communities? 2) Do intertidal microbial communities vary on a regional (>25km), between-site scale? 3) Are microbial communities temporally stable? We cultured microbial communities in situ on replicated artificial surfaces deployed May-August in 2013 and 2014 at four southwest-facing sites in the San Juan Islands, WA, USA on both emergent rock and in permanent tidepools. Microbial DNA was extracted and sequenced following EMP (Earth Microbiome Project) protocols, and 16S rRNA sequences from microbial assemblages were analyzed in the open source bioinformatics pipeline QIIME (Quantitative Insights Into Microbial Ecology). Simultaneous with microbial community sampling, we quantified neighboring macrobiota and local environmental variables. This nested approach allowed us to consider how regional variation, substrate, macroscopic community, and physical conditions contributed to microbial community structure and stability.
Results/Conclusions
Our multi-scale study showed strong local control of microbial community composition. Microbial communities were highly differentiated between habitat types (tidepools, emergent rock). In PCoA ordination, benthic samples clustered into distinct groups reflecting habitat type using both weighted and unweighted distance metrics, suggesting both similar abundance of shared taxa among samples cultured within a habitat type, as well as similar presence/absence of unique taxa within each habitat type. Several phototrophic cyanobacteria were tightly associated with emergent substrate, suggesting that temperature, desiccation, and light are strong drivers of community variability. A supervised learning protocol was highly effective at determining source habitat for these samples, though this tool could not correctly classify samples by site. Sites, despite variation in macroscopic community composition, hosted only weakly differentially structured microbial communities. Taken together, these results indicate intersite (>25km) homogeneity of intertidal microbial communities present in biofilm, with overwhelming intrasite (<100m) heterogeneity. We observed significant community turnover on a coarse annual scale (August 2013 to August 2014), with maintenance of source habitat identity. Although distribution of microbial taxa was broadly regional, microbial community structure in this NE Pacific rocky intertidal system was strongly environmentally selected.