Analysis of bacterioplankton genes in an impaired Great Lakes harbour reveals seasonal metabolic shifts and a previously undetected cyanobacterium

Hamilton Harbour is an impaired embayment of Lake Ontario that experiences seasonal algal blooms despite decades of remedial efforts. To study the harbour's cyanobacterial and heterotrophic bacterial communities, we extracted and sequenced community DNA from surface water samples collected biweekly from different sites during summer and fall. Assembled con-tigs were annotated at the phylum level, and Cyanobacteria were further characterized at order and species levels. Actinobac-teria were most abundant in early summer, while Cyanobacteria were dominant in mid-summer. Microcystis aeruginosa and Limnoraphis robusta were most abundant throughout the sampling period, expanding the documented diversity of Cyanobacte-ria in Hamilton Harbour. Functional annotations were performed using the MG-RAST pipeline and SEED database, revealing that genes for photosynthesis, nitrogen metabolism, and aromatic compound metabolism varied in relative abundances over the season, while phosphorus metabolism was consistent, suggesting that these genes remained essential despite fluctuating environmental conditions and community succession. We observed seasonal shifts from anoxygenic to oxygenic phototrophy, and from ammonia assimilation to nitrogen fixation, coupled with decreasing heterotrophic bacteria and increasing Cyanobac-teria relative abundances. Our data contribute important insights into bacterial taxa and functional potentials in Hamilton Harbour, revealing seasonal and spatial dynamics that can be used to inform ongoing remediation efforts.

Automated summary

Despite remedial efforts, Hamilton Harbour in Lake Ontario still experiences seasonal algal blooms. Community DNA from surface water samples was extracted and sequenced to study its cyanobacterial and heterotrophic bacterial communities. The results showed a shift in dominant bacteria from Actinobacteria to Cyanobacteria during the sampling period. Functional annotations revealed variations in gene abundances for photosynthesis, nitrogen metabolism, and aromatic compound metabolism, while phosphorus metabolism remained consistent. The study also observed seasonal and spatial dynamics in bacterial taxa and functional potentials, providing insights for ongoing remediation efforts.