Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

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).

The probe and hybridization protocol for members of the SAR11 clade are described in Morris et al. (2002).

Study site and sample collection:
Samples were collected aboard the RV Weatherbird II or the RV Atlantic Explorer at the BATS site (31° 40′ N, 64°10′ 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; Steinberg et al., 2001; Morris et al., 2005; Carlson et al., 2009; Treusch et al., 2009; Lomas et al., 2010). A broader assessment of the BATS biogeochemical data is presented in Deep Sea Research II in 1996 (volume 43, issues 2–3) and 2001 (volume 48, issues 8–9).

Samples for virioplankton (0, 20, 40, 60, 80, 100, 140, 160, 200, 250 and 300 m) and bacterioplankton (0, 10, 20, 40, 60, 80, 100, 120, 140, 160, 200, 250 and 300 m) were collected at the BATS site from January 2000 to December 2009 via conductivity, temperature, depth profiling rosette equipped with 12 l Niskin bottles. The 120 m virioplankton sample was added after October 2007. Throughout the entire time-series, all virioplankton samples were fixed with 0.02 μm filtered formalin (1% final concentration), placed in 5 ml 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 μm filtered gluteraldehyde (1% final concentration) and stored at either 4 °C for 72 h or flash frozen and subsequently stored at −80 °C for up to 6 months until processing as described in Steinberg 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loss of virioplankton or bacterioplankton abundance when stored in liquid nitrogen for periods up to 6 months (unpublished data).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 m from October 2001 to December 2009 (Casey et al., 2007). Samples for fluorescence in situ hybridization (FISH) of specific heterotrophic bacterioplankton lineages were collected from the upper 300 m from January 2003 to December 2005 (Carlson et al., 2009).

Biogeochemical and physical data collected at the BATS site are available at http://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 plus the equivalent in sigma-t to a 0.2 °C decrease in temperature (Sprintall and Tomczak, 1992). Contour plots were created in Ocean Data View (R Schlitzer, http://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 t-test for unequal variances), ratios and percent contributions were determined using Microsoft Excel.

Fluorescence in situ hybridization:
FISH was used to quantify the abundance of members of the SAR11 and Rhodobacteraceae clades. The probe and hybridization protocol for members of the SAR11 clade are described in Morris et al. (2002). The probe for Rhodobacteraceae (5′-CAACGCTAACCCCCTCCG-3′) was used at a final concentration of 2 ng μl−1 in hybridization buffer (0.9 mol l−1 NaCl, 35% formamide, 20 mmol l−1 Tris-HCl (pH 7.4) and 0.01% (w/v) sodium dodecyl sulfate). The hybridization wash temperature was 52 °C. Washes were conducted in buffer containing 20 mmol l−1 Tris-HCl (pH 7.4), 70 mmol l−1 NaCl, 5 mmol l−1 EDTA and 0.01% sodium dodecyl sulfate. Filters were mounted with 20 μl of 1.67 μg ml−1 DAPI (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 Carlson et al (2009).

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date, reference information
- renamed parameters to BCO-DMO standard
- converted longitudes to negative values to represent degrees West

(Adapted from the NSF award abstract)

The premise of this project is that stratified bacterioplankton clades engage in specialized biogeochemical activities that can be identified by integrated oceanographic and microbiological approaches. Specifically, the objective of this project is to assess if the mesopelagic microbial community rely on diagenetically altered organic matter and subcellular fragments that are produced by microbial processes in the euphotic zone and delivered into the upper mesopelagic by sinking or mixing. In past efforts this microbial observatory had greater success cultivating members of the euphotic zone microbial community, and revealed an unanticipated growth requirement for reduced sulfur compounds in alphaproteobacteria of the SAR11 clade. Genomic information showed that intense competition for substrates imposes trade-offs on bacterioplankton - there are regions of N dimensional nutrient space where specialists win. We postulate that specific growth requirements may explain some the regular spatial and temporal patterns that have been observed in upper mesopelagic bacterioplankton communities, and the difficulties of culturing some of these organisms.

The specific objectives of this project are: 1) to produce 13C and 15N labeled subcellular (e.g., soluble, cell wall, and membrane) and DOM fractions from photosynthetic plankton cultures and use stable isotope probing to identify specific clades in the surface and upper mesopelagic microbial community that assimilate fractions of varying composition and lability. 2) to use fluorescence in situ hybridization approaches to monitor temporal and spatial variability of specific microbial populations identified from the SIP and HTC experiments. To increase resolution we will use CARD-FISH protocols. 3) to measure the proteomes of bacterioplankton communities to identify highly translated genes in the surface layer and upper mesopelagic, and community responses to seasonal nutrient limitation. 4) and, to cultivate these organisms via high throughput culturing (HTC) by pursuing the hypothesis that they require specific nutrient factors and/or diagenetically altered organic substrates. Complete genome sequences from key organisms will be sought and used as queries to study patterns of natural variation in genes and populations that have been associated with biogeochemically important functions.