Abstract:

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.

Suggested Citation:

Cole Easson, Jose Lopez. 2017. Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples, Cruises DP01 and DP02 from May 2015 - August 2015. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7P55KWX

Publications:

Easson, C. G., & Lopez, J. V. (2019). Depth-Dependent Environmental Drivers of Microbial Plankton Community Structure in the Northern Gulf of Mexico. Frontiers in Microbiology, 9. doi:10.3389/fmicb.2018.03175

Freed, L. L., Easson, C., Baker, L. J., Fenolio, D., Sutton, T. T., Khan, Y., … Lopez, J. V. (2019). Characterization of the microbiome and bioluminescent symbionts across life stages of ceratioid anglerfishes of the gulf of mexico. FEMS Microbiology Ecology. doi:10.1093/femsec/fiz146

Baker, L. J., Freed, L. L., Easson, C. G., Lopez, J. V., Fenolio, D., Sutton, T. T., … Hendry, T. A. (2019). Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment. eLife, 8. doi:10.7554/elife.47606

Purpose:

The dataset was generated to characterize the composition and dynamics of pelagic microbial communities in the northern Gulf of Mexico.

Data Parameters and Units:

SampleID_in_OTU_table – sample label corresponding to OTU table columns and Sequence labels Original Tube label – Label on original sample New Tube label - sample label corresponding to OTU table columns and Sequence labels Cruise number – Sequential cruise number Sample_depth – depth in meters from which sample was collected Site - Site name from which the sample was collected. LAT – Latitude of collection site in decimal degrees LONG – Longitude of collection site in decimal degrees Pelagic_zone – Pelagic depth zone in which the sample was collected Identifier – Unique sample identifier SampleID-Long – Complete SampleID Feature – Depth feature from which sample was taken

Individual Files: