Press disturbance unveils different community structure, function and assembly of bacterial taxa and functional genes in mesocosm-scale bioreactors

Sustained perturbations, or press disturbances, are of interest in microbial ecology as they can drive systems to alternative stable states. Here, we tested the effect of a sustained doubling of organic carbon loading on structure, assembly and function of bacterial communities. Two sets of replicate 5-liter sequencing batch reactors were operated at two different organic carbon loading levels (323 and 629 mg COD L-1) for a period of 74 days, following 53 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of community taxonomic and functional gene structure were derived from metagenomics and 16S rRNA gene metabarcoding data. Assembly mechanisms were assessed through a mathematical null model on the effective bacterial turnover expressed as a proportion of total bacterial diversity. Disturbed reactors exhibited different community function, structure and assembly compared to the undisturbed reactors. Bacterial taxa and functional genes showed dissimilar alpha-diversity and community assembly patterns. Deterministic assembly mechanisms were generally stronger in disturbed reactors, associated with common taxa. Stochastic assembly was more important for functional genes and was driven by rare genes. We urge caution when assessing microbial community assembly mechanisms, as results can vary depending on the approach.