supporting data for journal paper "Optimizing sampling methods for assessing microbial communities in biofilms from intertidal rocky shores"

Intertidal rocky shores are harsh extremophilic environments characterized by tidal submersion/emersion cycles that cause extreme fluctuations of most abiotic factors. Such conditions are spatially heterogenous and can subject surface-associated microorganism to environmental stress gradients that modulate species richness and diversity along vertical clines. The accuracy in the assessment of these communities and the influence of environmental stress is highly conditioned by the sampling approach used. This study assessed the consistency, effectiveness and potential trade-offs of three commonly applied sampling methods for rocky shore biofilms. Compared to adhesive sheets and hammer disruption of the rocks, samples collected by swabs had higher performance in DNA concentration and PCR products. Additionally, the adhesive sheet method produced unreal amplicon sequencing results due to low DNA concentration resulting in an overrepresentation of rare taxa and underrepresentation of dominant taxa. Finally, we further assessed and discussed the potential influence of other factors such as primer selection and DNA extraction methods on the reliability of the sequencing results and the overall rocky shore microbial community characterization.