Abstract:

This dataset contains genomes assembled from metagenomes (novel methanotrophs) and oceanographic measurements from samples obtained aboard the R/V Pelican, PE13-NNBT, in the Gulf of Mexico hypoxic zone on 2013-07-23. Samples were collected on the R/V Pelican during the annual study of the dead zone on 23 July of 2013 in order to investigate the microbial community of this dynamic environment. Starting at the Mississippi River and ending at the Louisiana-Texas border, transects were made in order to collect samples from both oxic and hypoxic locations. Up to 5 L of water was collected at each station using a peristaltic pump. Nutrient analysis was performed and methane concentrations and oxidation rates were determined. Samples were filtered through 2.7 um pre-filter the onto 0.22 um Stervix filters, which were preserved in RNAlater. DNA and RNA were extracted and 16S rRNA genes were amplified and sequenced. Metagenomes and metatranscriptomes from the five sites were also sequenced to provide a snapshot of the identity and activity of the microbial community. Metagenome-assembled genomes (MAGs) were obtained and annotated revealing six novel MAGs (nGOM MAGs) with at least one gene copy of methane monooxygenase (pmoA), the enzyme required for the first step of aerobic methane oxidation. The metagenomes and metatrscriptomes of the five dead zone sites were mapped to the genomes of the nGOM MAGs, plus other MAGs from publicly available datasets, including MAGs assembled from TARA Oceans samples to determine activity of global methanotrophs in the 2013 nGOM dead zone. This dataset includes the chemical and nutrient information from the dead zone sample locations. Sequence read data are available at the NCBI SRA repository under the BioSample accession numbers SAMN05791315 to SAMN05791320 (DNA) and SAMN05791321 to SAMN05791326 (RNA). The dataset contains the date, latitudes and longitudes of the sampling locations. The cruise documentation was provided for the R/V Pelican (PE13-NNBT). The cruise was led by chief scientist Dr. Nancy Rabalais.

Suggested Citation:

Mason, Olivia. 2021. Genomes assembled from metagenomes (novel methanotrophs) and oceanographic measurements (nutrients, temperature, salinity, oxidation rates etc.) from samples obtained aboard the R/V Pelican research cruise PE13-NNBT in the Gulf of Mexico hypoxic zone on 2013-07-23. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/D7MJVFX0

Purpose:

Determine microbial composition and activity of the 2013 northern Gulf of Mexico dead zone.

Data Parameters and Units:

Site Name, Date sampled (mm/dd/yyyy), Lat (N), Lon (E), Depth (m), Depth Env (Bottom), Temperature (C), Salinity (ppt), DO (mg/L), Oxygen Env (oxic/hypoxic), Chlorophylla (ug/L), PO4 (uM), NO3 (uM), NO2 (uM), Combined NO3_NO2, NH4 (uM), Sequence Date (mm/dd/yyyy), DNA Biosample Accession, RNA Biosample Accession, O2 Range (mg/L), CH4 average (nM), CH4 stdev(nM), MOX average (pmol /L/d), MOX stdev (pmol /L/d), Number of sites sampled, and Number of sites sampled

Methods:

CTD, water filtration, chemical and nutrient analysis, DNA and RNA sequencing

Individual Files: