DNA sampling in the Gulf of America/Mexico (GOM) on GOMECC-4

This repository has QIIME 2 compatible files, metadata, R Markdown files, and all other input files needed for analysis and figure generation for the following manuscript:

Microbial community dynamics over large spatial and environmental gradients in a subtropical ocean basin
Sean R. Anderson, Katherine Silliman, Leticia Barbero, Fabian A. Gomez, Beth A. Stauffer, Astrid Schnetzer, Christopher R. Kelble, and Luke R. Thompson, (2025)

• Preprint

1. Summary

Microbes form the foundation of ocean food webs, and are sensitive to changes in their surrounding environment. However, the effects of changing abiotic factors on diverse marine microbes remains unclear, in large part due to a lack of spatial sampling of microbes and environmental variables in many ocean basins, including the GOM. In this study, we collected DNA samples at the basin scale in the GOM as part of the fourth Gulf of Mexico and East Coast Carbon (GOMECC-4) cruise that sailed in the summer-fall of 2021. DNA samples were collected at 51 sites along 16 inshore-offshore transects and up to three depths per site that reflected the surface, deep chlorophyll maximum, and near bottom (481 total filters). DNA metabarcoding captured prokaryotes (16S V4-V5) and protists (18S V9) at previously unresolved spatial scales. Generalized additive models were used to reveal the effects of carbonate chemistry parameters, temperature, oxygen, salinity, and nutrients on group-specific log abundance in the photic zone. Model results for SAR11 and SAR86 indicated a positive association with temperaure and dissolved inorganic carbon, while models for major cyanobacterial genera (Prochlorococcus and Synechococcus) were differently influenced by nutrients, salinity, and pH that often were in line with expected ecological niches. Elsewhere, enigmatic protist parasites (Syndiniales) and grazers (Sagenista) exhibited non-linear associations with salinity, oxygen, nutrients, and temperature. At the sequence level, picoeukaryotes like Ostreococcus sp. and Gephyrocapsa huxleyi were found to be indicator taxa of less buffered waters in the GOM at this time. These results set the stage for future omics data collection in the GOM, with sustained sampling efforts being important to accurately predict microbial responses to ocean change.

2. Bioinformatics

Code for 16S and 18S datasets are available in the code folder.

• 16S and 18S amplicons processed separately
• Remove primers with Cutadapt
• Process reads with Tourmaline
• Tourmaline uses a Snakemake workflow and wraps QIIME 2 and DADA2 to infer amplicon sequence variants (ASVs)
• Taxonomy assigned for 16S using SILVA (Version 138.1) and 18S with the PR2 database (Version 5.0.1)
• All Tourmaline output files and taxonomic reference databases for this project have been archived on Zenodo

3. R data analysis and visualization

Code is available as markdown files for 16S and 18S datasets. Raw markdown files are also in the code folder.

• QIIME 2 files uploaded to R using qiime2R
• Hierarchical clustering of microbial composition to resolve spatial patterns
• Population dynamics observed in each cluster with stacked bar plots, PCoA plots, and diversity plots (richness and Shannon index)
• Generalized additive models (GAMs) constructed for major microbial groups (class level 18S; order level 16S) using log abundances and non-collinear variables
• Models focused on the photic zone to mitigate collinearity
• GAMs applied to all GOMECC-4 sites to expand microbial distributions at the surface; plots made in Ocean Data View
• ODV plots in the odv-plots folder.
• Indicator analysis performed to reveal ASVs indicative of less buffered surface waters (via TA:DIC ratio) using indicspecies
• All other input files necessary for analyses are in the data-input folder.

4. Links to associated data

• Raw sequence data for this project are available in NCBI SRA under Bioproject PRJNA887898
• Species observation data (counts) has been published on the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF)
• Biological data has also been submitted to the National Centers for Environmental Information (NCEI)
• Environmental measurements from the Niskin bottles and CTD profiles are also available at NCEI via Accession numbers 0294320 and 0284051
• The GOMECC-4 cruise report is also available and details all sampling and processing on the cruise

This work was funded in part through the NOAA Ocean Acidification Program (OAP) ROR #02bfn4816 under project numbers 21392 (Thompson) and 20708 (Barbero) and by awards NA16OAR4320199 and NA21OAR4320190 to the Northern Gulf Institute from NOAA’s Office of Oceanic and Atmospheric Research, U.S. Department of Commerce. This research was carried out in part under the auspices of the Cooperative Institute for Marine and Atmospheric Studies (CIMAS) and NOAA, cooperative agreement NA20OAR4320472.

Disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an 'as is' basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.