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 2,000m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station, even when including previously determined samples from other ocean basins. 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 high-quality MAGs recovered, 145 represent novel species compared to NCBI genomes and TARA 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 600m 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, dehydrogenase, 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.