Sample processing and analyses are detailed in the publications listed below. Briefly, 100ml of seawater was collected onto 25mm dia polycarbonate filters (0.22um pore size), rinsed with Tris-buffered saline, flash frozen in liquid N2, and stored at -80C until extraction. DNA was extracted using a combination of 5min of bead beating and 15min heat lysis at 95C. Extracted DNA was used as template of quantitative PCR reactions using primers specifically designed to target the narB gene from the HLII and LLI clades of Prochlorococcus. Standard curves used for quantitation of field data were derived from DNA extracted from defined cell numbers of cultured representatives of each clade.
Two year time series of the abundance of Prochlorococcus cells containing the nitrate reductase gene (narB) at the HOT and BATS sites in the Pacific and Atlantic Oceans. The goal was to collect long-term, high-resolution data on the temporal and spatial variability of Prochlorococcus narB genotypes belonging to the HLII and LLI clades. The abundance of Prochlorococcus cells containing narB for each of these clades was determined by quantitative PCR at 12 depths every month from October 2005 to December 2007 at two locations: BATS location (5 nautical mile radius around 31 40'N, 64 10'W) and HOT Station ALOHA (5 nautical mile radius around 22 45'N, 158 00' W). These field samples are a subset of those utilized in the \"Prochlorococcus HOT/BATS\" dataset (http://www.bco-dmo.org/dataset/3381).
\nThese data are reported and described in:
\nBerube, P. M., Coe, A., Roggensack, S. E., & Chisholm, S. W. (2015). Temporal dynamics of Prochlorococcuscells with the potential for nitrate assimilation in the subtropical Atlantic and Pacific oceans. Limnology and Oceanography, 61(2), 482\u2013495. doi:10.1002/lno.10226
Estimated abundances that fell below the lowest value of the standard curve were set to the theoretical detection limit of 0.65 cells/mL. Samples were excluded if their melt curves contained multiple peaks or peaks different from those in the DNA standards. Samples were excluded if the coefficient of variation (standard deviation divided by the mean) was greater than 50%. The no data value \"nd\" refers to missing or excluded measurements.
\nRelated files and references:
\nAnalysis and data processing used the same field samples and methods as described in the following publication, but with different primer sets:
\nMalmstrom, R. R., Coe, A., Kettler, G. C., Martiny, A. C., Frias-Lopez, J., Zinser, E. R., & Chisholm, S. W. (2010). Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. The ISME Journal, 4(10), 1252\u20131264. doi:10.1038/ismej.2010.60