Table of Contents

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

Sampling
From July 2016 through July 2019, samples were collected from CTD samplers and Niskin bottles during R/V Atlantic Explorer cruises to understand ocean processes and ecological interactions in the open ocean waters near Bermuda.  The BATS program provided monthly collections, while BIOS-SCOPE process cruises provided more detailed information from around-the-clock sampling for the hydrographic variables. Plankton tows were used to assess the temporal and vertical variability of organic and inorganic nutrients, vitamins, metabolites, microbial biomass and production, bacterial and viral DNA, and zooplankton biomass at depths over 1000 meters. In situ sequential filtration pumps collected particles for molecular and isotopic characterization of organic particles that spanned four biologically-relevant size classes over 12 depths. Numerous shipboard experiments were conducted to evaluate zooplankton and microbial respiration, as well as organic matter transformation by bacterioplankton (free living bacteria).

Between February 2017 and September 2018, time series of physical and biogeochemical properties were acquired near the BATS site using three separate Slocum G2 gliders deployed in 10 consecutive missions. Each glider carried a science payload that included a pumped CTD, WetLabs ECOpuck (ChlF and Bp700) and Aanderaa O2 optode, and was programmed to spiral around a 0.5 km box (essentially holding station) and profile between 0 and ~900 meters depth. For five missions the glider was additionally equipped with a Submersible Underwater Nitrate Analyzer (SUNA). Monthly, co-located ship-based CTD and water sample profiles were used to calibrate each of the sensors. These time series demonstrate the relationship between vertical zones, seasons and biogeochemical property distributions.

Analysis
BIOS-SCOPE cruise samples were analyzed at UCSB using the following instruments and methods: 

Flow injection analysis was performed on a Lachat QuikChem 8500 series 2 to obtain concentration data for nitrate, nitrite, NO3 + NO2, ortho-phosphate, ammonium, and silicate. 

Particulate organic carbon (POC) and particulate organic nitrogen (PON) were measured by combustion analysis using a CEC 440HA elemental analyzer.  Additional methodology, calibrations, precision and accuracy, and methodological references are detailed at the UCSB MSI Analytical Lab Website: http://www.msi.ucsb.edu/services/analytical-lab.

Dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) were measured using high temperature catalytic oxidation (HTCO) on a Shimadzu TOC-V system with TNM-1 unit (Carlson et al., 2010). 

Bacterioplankton abundance was obtained using Olympus BX51 epifluorescent microscope (Porter & Feig, 1980).  Heterotrophic bacterial production was analyzed using 3H-leucine uptake (Smith & Azam, 1992). 

Total Dissolved Amino Acids (TDAA) and individual amino acids were measured using HPLC (high performance liquid chromatography) following the methods of Liu et al. (2020). The amino acids include alanine, arginine, aspartic acid, beta-alanine, gamma-aminobutyric acid, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, serine, taurine, threonine, tyrosine, and valine.

Season was derived from the Slocum G2 glider time series data.  The glider data had longer deployment periods marking the seasonal changes, so the CTD sampling dates were lined up with the glider data using date/timestamp.  Each CTD/bottle profile was assigned a season code based on the alignment with the known seasons and dates from the glider data.  Season designations are 1=Mixed, 2=Spring transition, 3=Stratified, 4=Fall transition (for more information, see the Physical Framework document on the Project page)

Slocum G2 glider data. Determined from the glider time series in each year, then each CTD/bottle profile is assigned a season code based on those dates. Season designation. Season = 1 :  Mixed   2: Spring transition  3: Stratified  4: Fall transition  (see Physical Framework document)

Genomic DNA samples were amplified and sequenced using universal primer sets for 16S and 18S with 'general' Illumina overhang adapters at Center for Genome Research and Biocomputing (Oregon State University) Corvallis, OR. These data have been deposited with links to BioProject accession number PRJNA769790 in the NCBI BioProject database.   

*Related dataset with NCBI sequence information and links is (BCO-DMO dataset number TBD)*

Quality Flags:
0=good
1=unknown/below detection limit
4=questionable/high error
8=bad quality/outlier

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Mixed Layer Depth (MLD):

Overview in de Boyer Montegut (2004).  The CTD, bottle, and glider profiles are labeled with three definitions of MLD which reflect processes that affect stratification on different time scales: 

ML_dens125 
   - ML_dens125 is defined as the depth where sigma-theta is greater than the surface density by 0.125 kg m-3
   - ML_dens125 reflects deepest reach of seasonal convective mixing
   - ML_dens125 exhibits LOWEST frequency variability
   - ML_dens125 is DEEPEST of three MLD   
   -  refer to Suga et al (2004)     

ML_densT2
   - ML_densT2 is defined as the depth where sigma-theta exceeds the surface density +0.2*alpha
              (where alpha is the thermal expansion coefficient)
   -  ML_densT2 marks intermediate episodes of convective mixing;
   - ML_desnsT2 marks intermediate episodes of convective mixing; 
   - ML_densT2 exhibits MEDIUM variability
   - ML_densT2 has depths between the other two definitions.   
   - refer to Sprintall & Tomczak (1992)

ML_bvfrq 
   - ML_bvfrq is defined as the depth where the buoyancy frequency (N2) first exceeds the standard deviation of N2.
   - ML_bvfrq responds to diurnal scales of restratification/mixing (and has been adopted by the NAAMES program).   
   - ML_bvfrq exhibits HIGHEST frequencies
   - ML_bvfrq has SHALLOWEST depth
   - refer to Mojica & Gaube (in review)

See PhysicalFramework.pdf on Project page for plots comparing these parameters.

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BCO-DMO Processing:

- converted latitude and longitude to decimal degrees (south and west are negative)
- combined date and time columns into a single ISO 8601 formatted datetime
- modified parameter (column) names to conform with BCO-DMO naming conventions
- added conventional header with dataset name, PI name, version date
- missing data identifier "-999" in the original source file was replaced with BCO-DMO default missing data identifier, which varies depending on the type of file that is downloaded from the BCO-DMO data system.  For example, missing data will be shown as blank (null) values in the csv files. In MATLAB .mat files it will be displayed as NaN. When viewing data at BCO-DMO the missing value will be shown as "nd" meaning "no data."
 

The aim of BIOS-SCOPE is to expand knowledge about the BATS ecosystem and achieve a better understanding of ocean food web sources, sinks and transformations of DOM. Advances in knowledge and technology now poise us to investigate the specific mechanisms of DOM incorporation, oxidation and transformation by zooplankton and the distinct microbial plankton communities that have been discovered at BATS.

The overarching goal of the BIOS-SCOPE is to form and foster collaborations of cross disciplinary science that utilize a broad suite of genomic, chemical, ecological, and biogeochemical approaches to evaluate microbial process, structure and function on various scales. These scales will range from organism-compound and organism-organism interactions to large biogeochemical patterns on the ecosystem scale. For this purpose we have assembled a cross-disciplinary team including microbial oceanographers (Carlson and Giovannoni), a chemical oceanographer (Kujawinski), biological oceanographer / zooplankton ecologists (Maas and Blanco-Bercial) and microbial bioinformatician (Temperton) with the expertise and technical acuity that are needed to study complex interactions between food web processes, microbes and DOM quantity and quality in the oligotrophic ocean. This scientific team has a vision of harnessing this potential to produce new discoveries that provide a mechanistic understanding of the carbon cycle and explain the many emergent phenomenon that have yet to be understood.

For additional details:

• BIOS-SCOPE Narrative: 
  https://datadocs.bco-dmo.org/docs/302/BIOSSCOPE/data_docs/BIOS-SCOPE_Narrative_FINAL.pdf
• Physical Framework:
  https://datadocs.bco-dmo.org/docs/302/BIOSSCOPE/data_docs/Physical_Framework.pdf

BIOSSCOPE I: November 1st, 2015 through October 31st, 2020
Current: November 1st, 2020 to October 31st, 2025