Processing code for analysis of DNA sequences collected from surface water samples, in bulk sediment traps, and from individual sinking particles as part of the EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) field campaigns. DNA extraction and 18S rRNA gene amplification details can be found in Durkin et al. (2022). Data used in this analysis can be found at: https://seabass.gsfc.nasa.gov/experiment/EXPORTS.
Processing of 18S rRNA gene sequence files was conducted following Durkin et al. (2022) using QIIME2 (Bolyen et al., 2019) and the DADA2 (Callahan et al., 2016) workflow. Taxonomic identities were assigned to amplicon sequence variants (ASVs) based on comparison to the PR2 database (Guillou et al., 2013; v 4.14.0, downloaded September 2022) with a naïve Bayes classifier (Bokulich et al., 2018). Example QIIME code for training a classifier with PR2 v5.0.0 is also included.
Taxa were assigned to photosynthetic or heterotrophic following Supplementary Table 2 in Durkin et al. (2022) and adding photosynthetic taxa found in this dataset that were not found in that dataset (photosynthetic_taxa.csv). If analyzing data processed with PR2 v5.0.0, the photosynthetic taxa in the file "photosynthetic_taxa_v5_0_0.csv" should be used.
Please reference the following work if you use this code to inform your own work:
Kramer, S.J., E.L. Jones, N.L. Paul, M.L. Estapa, T.A. Rynearson, A.E. Santoro, S. Sudek, C.A. Durkin (2024). Ocean carbon export can be predicted from ocean color-based phytoplankton communities. Submitted. https://doi.org/10.1101/2024.09.21.613760
Bokulich, N. A., Kaehler, B. D., Rideout, J. R., Dillon, M., Bolyen, E., Knight, R., et al. (2018). Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome, 6(1), 90. https://doi.org/10.1186/s40168-018-0470-z
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., et al. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8), 852–857. https://doi.org/10.1038/s41587-019-0209-9
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). DADA2: high-resolution sample inference from Illumina amplicon data. Nature Methods, 13(581), 581–583. https://doi.org/10.1038/nMeth.3869
Durkin, C., Cetinić, I., Estapa, M. L., Ljubešić, Z., Mucko, M., Neeley, A., & Omand, M. M. (2022). Tracing the path of carbon export in the ocean though DNA sequencing of individual sinking particles. The ISME Journal, 1–11. https://doi.org/10.1038/s41396-022-01239-2
Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., et al. (2013). The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Research, 41(D1), D597–D604. https://doi.org/10.1093/nar/gks1160