Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during two planned DEEPEND cruise expeditions to the GOM. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable region was generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Bioinformatics analyses in QIIME and R was used to quality filter and assess microbial community diversity and taxonomic composition. These baseline characterizations track alpha and beta diversity at different depths ranging from 0 – 1500 m, across the spatial extent of the northern GOM, and over time. Microbiome analyses also considered environmental variables unique to the GOM, including the Mississippi river inputs, mesoscale cyclonic and anticyclonic eddies, and in relation to measured environmental parameters at collection time using the CTD.