Genome-Resolved Metabolic Potential of Colony-Associated Bacteria Selectively Enriched from Microcystis aeruginosa Blooms in a Chilean Urban Wetland

Cyanobacterial blooms are a widespread concern in freshwater ecosystems worldwide because of their impacts on water quality, ecosystem functioning, and human health. Bloom-forming cyanobacteria such as Microcystis coexist with diverse bacterial assemblages whose metabolic capabilities may contribute to the organization of the bloom-associated microbial environment, yet these traits remain comparatively understudied at genome resolution, particularly in South American freshwater systems. Here, we characterized a microbial community recovered after laboratory enrichment of Microcystis-dominated cyanobacterial biomass recovered from the El Loto urban wetland in southern Chile, using high-throughput DNA sequencing, co-assembly, and genome-resolved metabolic reconstruction. Five independent enrichments yielded 40 metagenome-assembled genomes (MAGs) across seven bacterial phyla, of which 19 (>90% completeness, <5% contamination) were retained for metabolic reconstruction. Pathway predictions were evaluated against pathway-specific diagnostic genes. Central carbon and respiratory functions were broadly represented, whereas carbon fixation, phototrophy, and nutrient-related traits showed more restricted, lineage-associated distributions. The Calvin–Benson–Bassham cycle was supported in four MAGs, while alternative carbon-fixation pathways lacked diagnostic-gene support. Oxygenic photosynthetic machinery was restricted to the two Cyanobacteriota MAGs, whereas seven Pseudomonadota encoded syntenic gene clusters consistent with anoxygenic phototrophic potential. Nitrogen fixation and canonical ammonia oxidation were not represented among the retained MAGs, although associated genes were detected in the community gene catalogue. Phosphonate-related traits were also unevenly distributed, with phnJ and the associated C–P lyase system detected in five Pseudomonadota MAGs, while phosphonate transport-related genes occurred more broadly. Taken together, these results reveal a broadly shared core metabolic repertoire alongside a more restricted, lineage-associated distribution of other metabolic traits within the enrichment-derived microbial community.