Abstract:

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. 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 regions were generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Raw paired-end sequences were joined and quality filtered in the bioinformatics program, QIIME. Vertical baseline characterizations will track alpha and beta diversity at different depths ranging from 0 – 1500 m, assess seasonal variation, and examine variation related to nektonic vertical migration. Microbiome analyses will also consider environmental variables unique to the GOM, such as Mississippi river green water inputs, mesoscale features, or microbiomes of associated GOM marine fauna as part of community ecology profiles. When possible, correlations will be made to other environmental factors such as nutrient concentrations.

Suggested Citation:

Cole G. Easson, Lindsey Freed. 2018. Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples, cruises DP03 and DP04 from April - August 2016. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7833QCP

Publications:

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

Purpose:

The purpose of these data were to assess natural variability in bacterioplankton communities associated with a wide variety of forces. These data will be linked with higher taxon and environmental data to assess connections between bacterioplankton and higher trophic levels.

Data Parameters and Units:

Profiles and measurement of genetic variability in 16S and 18S (eukaryotic) small subunit rRNA genes, variability of expressed genes, metagenomes or other useful taxonomic markers. sample_name = NCBI Biosample Accession; sample_id = the Sample_ID that appears in the fastq file in NCBI; sample_title = internal sample name; organism = NCBI organism category; isolation_source = matrix from which metagenomes were isolated (seawater); collection date = date of sample collection (D-Mon-YY), geo_location = place name samples collected (USA); lat_lon = latitude longitude (decimal degrees); collected by = name of person who collected sample; Cruise = cruise ID, depth_meters = depth of sample collection (meters); station = station ID, replicate = replicate number; samp_collection_device = device used to collect samples (Niskin bottles); samp_mat_process = sample material processing method (DNA_isolation_Illumina_sequencing); Tax ID; Bioproject = NCBI Bioproject accession (PRJNA429259) The naming convention is as follows: CTD#.SampleCollectionDepth.NiskinBottle#.Replicate# . CTD # is an internal DEEPEND standardization and likely has no meaning outside of that. Sample collection depth is in the unit 'meters'. Surface collections are sometimes indicated as 'S' and if a seawater sample was collected from the ship's seawater system it is labeled 'SWSYS'. Niskin Bottle # ranges from 1-12, but is not always present in the sample label. If only one number appears after the depth, it indicates the replicate number.

Instruments:

Illumina MiSeq sequencer

Individual Files: