The probe and hybridization protocol for members of the SAR11 clade are described in Morris et al. (2002).
\nStudy site and sample collection:
\nSamples were collected aboard the\u00a0RV Weatherbird II\u00a0or the\u00a0RV Atlantic Explorer\u00a0at the BATS site (31\u00b0 40\u2032 N, 64\u00b010\u2032 W). All cruises were conducted as part of the larger BATS program and sampled at least monthly with biweekly sampling between February and April. This sampling strategy has been successful in revealing the major temporal microbial and biogeochemical patterns at this site (Carlson and Ducklow, 1996;\u00a0Steinberg et al., 2001;\u00a0Morris et al., 2005;\u00a0Carlson et al., 2009;\u00a0Treusch et al., 2009;\u00a0Lomas et al., 2010). A broader assessment of the BATS biogeochemical data is presented in\u00a0Deep Sea Research II\u00a0in 1996 (volume 43, issues 2\u20133) and 2001 (volume 48, issues 8\u20139).
Samples for virioplankton (0, 20, 40, 60, 80, 100, 140, 160, 200, 250 and 300\u2009m) and bacterioplankton (0, 10, 20, 40, 60, 80, 100, 120, 140, 160, 200, 250 and 300\u2009m) were collected at the BATS site from January 2000 to December 2009 via conductivity, temperature, depth profiling rosette equipped with 12\u2009l Niskin bottles. The 120\u2009m virioplankton sample was added after October 2007. Throughout the entire time-series, all virioplankton samples were fixed with 0.02\u2009\u03bcm filtered formalin (1% final concentration), placed in 5\u2009ml cryovials and flash frozen in liquid nitrogen (Wen et al., 2004) until processing (within 12 weeks of collection). Samples for bacterioplankton abundance were fixed with 0.2\u2009\u03bcm filtered gluteraldehyde (1% final concentration) and stored at either 4\u2009\u00b0C for 72\u2009h or flash frozen and subsequently stored at \u221280\u2009\u00b0C for up to 6 months until processing as described in\u00a0Steinberg et al (2001). Storage tests demonstrated no appreciable loss of virioplankton or bacterioplankton abundance when stored in liquid nitrogen for periods up to 6 months (unpublished data). Picophytoplankton samples were collected at the same depths through 250\u2009m from October 2001 to December 2009 (Casey et al., 2007). Samples for fluorescence\u00a0in situ\u00a0hybridization (FISH) of specific heterotrophic bacterioplankton lineages were collected from the upper 300\u2009m from January 2003 to December 2005 (Carlson et al., 2009).
\nBiogeochemical and physical data collected at the BATS site are available at\u00a0http://bats.bios.edu. The MLD was determined as the depth where potential density (sigma-t) of the water was equal to sea surface sigma-t\u00a0plus the equivalent in sigma-t\u00a0to a 0.2\u2009\u00b0C decrease in temperature (Sprintall and Tomczak, 1992). Contour plots were created in Ocean Data View (R Schlitzer,\u00a0http://odv.awi.de/) with VG Gridding and linear mapping adjusted to the median of each data set. Statistics (Pearson's correlation and two-tailed Student's\u00a0t-test for unequal variances), ratios and percent contributions were determined using Microsoft Excel.
\nFluorescence\u00a0in situ\u00a0hybridization:
\nFISH was used to quantify the abundance of members of the SAR11 and\u00a0Rhodobacteraceae\u00a0clades. The probe and hybridization protocol for members of the SAR11 clade are described in\u00a0Morris et al. (2002). The probe for\u00a0Rhodobacteraceae\u00a0(5\u2032-CAACGCTAACCCCCTCCG-3\u2032) was used at a final concentration of 2\u2009ng\u2009\u03bcl\u22121\u00a0in hybridization buffer (0.9\u2009mol\u2009l\u22121\u00a0NaCl, 35% formamide, 20\u2009mmol\u2009l\u22121\u00a0Tris-HCl (pH 7.4) and 0.01% (w/v) sodium dodecyl sulfate). The hybridization wash temperature was 52\u2009\u00b0C. Washes were conducted in buffer containing 20\u2009mmol\u2009l\u22121\u00a0Tris-HCl (pH 7.4), 70\u2009mmol\u2009l\u22121\u00a0NaCl, 5\u2009mmol\u2009l\u22121\u00a0EDTA and 0.01% sodium dodecyl sulfate. Filters were mounted with 20\u2009\u03bcl of 1.67\u2009\u03bcg\u2009ml\u22121\u00a0DAPI (SIGMA-Aldrich) in citiflour solution (Ted Pella Inc., Redding, CA, USA) and sealed with nail polish. Image analysis was performed using Cy3 and DAPI filter sets as described by\u00a0Carlson et al (2009).
Virioplankton abundances were measured from samples collected from January 2000 to December 2011 as part of the larger BATS program aboard the R/V Weatherbird II or the R/V Atlantic Explorer. Supporting data provided by the BATS time-series program and are available at (http://bats.bios.edu/). This dataset reports abundances quantified using FISH (Fluorescence in situ hybridization).
BCO-DMO Processing:
\n- added conventional header with dataset name, PI name, version date, reference information
\n- renamed parameters to BCO-DMO standard
\n- converted longitudes to negative values to represent degrees West