Table of Contents

• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Parameters
• Instruments
• Deployments
• Project Information
• Program Information
• Funding

This dataset includes original denaturing gradient gel images that resulted in eukaryotic and cyanobacterial DNA sequence data obtained from the upper water column as well as from shallow drifting traps during regular BATS cruises from May 2008-April 2010.  The associated dataset contains a complete list of denaturing gradient gel results and the closest sequence matches from the NCBI database for each excised band (phylotype).

Associated dataset: phytoflux_BATS

Sampling and Analytical Methodology: 
Sampling was conducted monthly from May 2008-April 2010 at the Bermuda Atlantic Time-Series (BATS). Samples were collected for DNA analysis from four depths in the upper water column and from 150 m particle traps. DNA was extracted from these samples and a region of the 18S ribosomal RNA gene for eukaryotes and 16S rRNA gene for cyanobacteria was amplified by PCR using eukaryotic and cyanobacterial primers. Each amplified sample was subjected to Denaturing Gradient Gel Electrophoresis in order to “fingerprint” the community. Individual bands were excised and identified by sequence matching using the NCBI database (http://blast.ncbi.nlm.nih.gov). Quantity One software package was used to determine similarity between samples. The efficiency of recovery was determined by qPCR in order to accurately calculate the DNA present in the water column and DNA flux into particle traps. For further detail please refer to:
Jessica Amacher, Susanne Neuer, Michael Lomas. Accepted. DNA-based molecular fingerprinting of the contribution of eukaryotic protists and cyanobacteria to particle flux at the Bermuda Atlantic Time-Series Study. Deep Sea Research part II.

Data Processing:
Denaturing gradient gels were imaged and analyzed with the BioRad Fluor-S imager. Bands were selected and matched manually for band matrices included in these data.

The overall objective of this proposal is to investigate linkages between the presence of different key groups of phytoplankton in the euphotic zone and their contribution to particle flux at the subtropical North Atlantic time-series station BATS (Bermuda Atlantic Time-series Study) by applying a range of traditional and novel molecular techniques.

The 'biological pump', the photosynthetically mediated transformation of dissolved inorganic carbon into particulate and dissolved organic carbon in surface ocean waters and its subsequent export to deep water, is a significant driver of the atmospheric carbon uptake by the oceans. But this "biologically pumped" production, inasmuch as it depends on the composition and activity of planktonic organisms, is susceptible to long-term climatic changes in surface ocean properties such as increased temperature and changes in nutrient supply, especially in subtropical gyres. The sub-tropical gyres and the transition zones at their boundaries play an important role in the global carbon cycle because of their vast size and generally high per area export production. As evidenced in recent studies, the biological mechanisms driving regional to basin scale variability in carbon export in these biomes is far from understood, thus limiting our ability to mechanistically explain the biological pump and to predict its possible responses in the face of environmental change. In an effort to improve this situation with an accurate assessment of the contribution of different plankton groups to overall fluxes, the investigators will test the following two specific hypotheses: 1. The long held notion that large cells and those with mineral tests are major contributors to downward particle flux needs to be re-evaluated. We hypothesize that pico and nanoplankton (also those without mineral tests) are generally important contributors to downward particle flux at BATS. Consequently, the diversity of taxonomic groups contributing to particle flux is greater than previously expected. 2. The relative contribution of taxonomic groups to downward particle flux is a function of physical forcing. We hypothesize that episodic events (e.g., winter storms and eddies) lead to a reduction in diversity of sedimenting phytoplankton (e.g., dominance by a single group such as diatoms) compared to periods marked by more stable conditions in the water column. The broader impacts include furthering knowledge of the diversity and biology of phytoplankton groups that have a significant impact on the carbon export in subtropical gyres, thereby advancing our understanding of regional to basin scale variability in the biogeochemistry of these biomes. The project provides new opportunities for undergraduate and graduate education, as well as offer research opportunities to local high school students and teachers as part of the "Ask-a-Biologist" initiative. The project also includes an international component through collaboration with a molecular ecology group in Barcelona, Spain.

The Ocean Carbon and Biogeochemistry (OCB) program focuses on the ocean's role as a component of the global Earth system, bringing together research in geochemistry, ocean physics, and ecology that inform on and advance our understanding of ocean biogeochemistry. The overall program goals are to promote, plan, and coordinate collaborative, multidisciplinary research opportunities within the U.S. research community and with international partners. Important OCB-related activities currently include: the Ocean Carbon and Climate Change (OCCC) and the North American Carbon Program (NACP); U.S. contributions to IMBER, SOLAS, CARBOOCEAN; and numerous U.S. single-investigator and medium-size research projects funded by U.S. federal agencies including NASA, NOAA, and NSF.

The scientific mission of OCB is to study the evolving role of the ocean in the global carbon cycle, in the face of environmental variability and change through studies of marine biogeochemical cycles and associated ecosystems.

The overarching OCB science themes include improved understanding and prediction of: 1) oceanic uptake and release of atmospheric CO2 and other greenhouse gases and 2) environmental sensitivities of biogeochemical cycles, marine ecosystems, and interactions between the two.

The OCB Research Priorities (updated January 2012) include: ocean acidification; terrestrial/coastal carbon fluxes and exchanges; climate sensitivities of and change in ecosystem structure and associated impacts on biogeochemical cycles; mesopelagic ecological and biogeochemical interactions; benthic-pelagic feedbacks on biogeochemical cycles; ocean carbon uptake and storage; and expanding low-oxygen conditions in the coastal and open oceans.