Nutrient disturbance in a shallow aquaculture pond impacts Microcystis gene expression but does not impact bacterial community function during bloom conditions

Cyanobacterial harmful algal blooms (cHABs) are worldwide issues. Reduced nitrogen forms (ammonium and urea) have recently been measured in freshwater systems at concentrations not previously recorded. These reduced nitrogen forms have been shown to favor the proliferation of harmful cyanobacteria. These blooms are comprised of a diverse community of microbes that contribute to nutrient cycling and other ecosystem functions. To measure the response of the Microcystis bloom microbiome, a field experiment was conducted to examine the transcriptional responses of Microcystis , a common bloom‐forming cyanobacterium, as well as the co‐occurring bacteria associated with the bloom. Limnocorrals were fertilized with either nitrate, ammonium, or urea, and samples were collected across a 24‐h time series after nutrient additions to track changes in Microcystis gene expression along with bacterial function and composition using metatranscriptomics. Microcystis spp. dominated experimental enclosures throughout the experiment (>70% of total bacterial reads). This stability was also reflected in the community structure and function of the co‐occurring bacteria, which had no substantial changes over the 24‐h after nutrient additions. Nutrient additions drove immediate differential expression responses for Microcystis , and the response was nitrogen form dependent. Key gene groups including core metabolite‐related genes and carbon acquisition genes had pronounced differences among treatments, while toxin‐related gene expression ( mcy ABCDEFGHIJ) was not impacted by nitrogen treatments. Results support previous lab and field‐based experiments that have suggested that reduced nitrogen forms impact cHAB molecular physiology, even during peak bloom and elevated nutrient conditions in shallow systems frequently impacted by agricultural runoff and/or aquacultural input.