DEEPEND: Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples. Cruises DP03 and DP04 from Jan 2016 - December 2016

Sampling

Seawater will be collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. Filters will be 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 will be 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.

Method steps

1. Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/4.1