Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input.

Genomic and metagenomic explorations of the oceans have identified well-structured microbial assemblages showing endemic genomic adaptations with increasing depth. However, deep water column surveys have been limited, especially of the Gulf of Mexico (GoM) basin, despite its importance for human activities. To fill this gap, we report on 19 deeply sequenced (~5 Gbp/sample) shotgun metagenomes collected along a vertical gradient, from the surface to about 2,000 m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station. However, a community-level pangenome style gene content analysis revealed ~54% of predicted gene sequences to be station-specific within our GoM samples. Of the 154 medium-to-high-quality MAGs recovered, 145 represent novel species compared with the NCBI genomes and Tara Oceans MAGs databases. Two of these MAGs were relatively abundant at both surface and deep samples, revealing remarkable versatility across the water column. A few MAGs of freshwater origin (~6% of total detected) were relatively abundant at 600 m deep and 270 miles from the coast at one station, revealing that the effects of freshwater input in the GoM can sometimes be far-reaching and long-lasting. Notably, 1,447/16,068 of the total COGs detected were positively (Pearson's r ≥ 0.5) or negatively (Pearson's r ≤ -0.5) correlated with depth, including beta-lactamases, dehydrogenases, and CoA-associated oxidoreductases. Taken together, our results reveal substantial novel genome and gene diversity across the GoM's water column, and testable hypotheses for some of the diversity patterns observed.IMPORTANCETo what extent microbial communities are similar between different ocean basins at similar depths, and what the impact of freshwater input by major rivers may be on these communities, remain poorly understood issues with potentially important implications for modeling and managing marine biodiversity. In this study, we performed metagenomic sequencing and recovered 154 medium-to-high-quality metagenome-assembled genomes (MAGs) from three stations in the Gulf of Mexico (GoM) and from various depths up to about 2,000 m. Comparison to MAGs recovered from other ocean basins highlighted the unique diversity harbored by the GoM, which could be driven by more substantial input from the Mississippi River and by human activities, including offshore oil drilling. The data and results provided by this study should be useful for future comparative analysis of marine biodiversity and contribute to its more complete characterization.