Spatio-Temporal Resolution of Microbial Functions and Taxa Associated With Cyanobacterial Harmful Algae Blooms Along a 500-Km Aquatic Continuum in the Lake Erie Watershed

Biogeochemical processes rendered by the aquatic microbiome could influence the development of cyanobacterial harmful algal blooms (cHABs), but those biotic factors are poorly understood and rarely considered. We focused on the link between microbial functions, community composition and environmental gradients along the Thames River-Lake St. Clair-Detroit River-Lake Erie corridor across different seasons. We measured the abundance and expression (transcripts) of genes involved in nutrient cycling and microcystin toxin production with qPCR and determined microbial community composition with high-throughput sequencing of the 16S rRNA gene. Throughout the year, genes and transcripts involved in P acquisition, denitrification and N fixation were in higher abundance upstream in the Thames River and Lake St. Clair. Gene abundance, rather than expression, correlated with environmental variables, but functional changes were linked to changes in the aquatic microbiome and did not respond directly to larger environmental gradients. Network analysis revealed tighter connections between gene expression and biotic variables than gene presence, with ubiquitous and streamlined-genomes microbes associated with the dominant bloom-causing cyanobacteria, highlighting the cooperative dynamic of these associations. Overall, the results highlight the link between the changing microbiome, microbial processes and the watershed influence in the presence of cHABs.