Dataset contains CTD data collected during R/V Atlantic Explorer cruises in the time period from 2016 up to May 2025. The data are profiles from all CTD casts conducted during the cruises, with the data binned into two decibar profiles from the downcasts. The CTD include primary CTD parameters (pressure, depth, temperature, conductivity, and salinity) plus auxiliary measurements of dissolved oxygen, beam attenuation, relative fluorescence, and photosynthetic active radiation (PAR). Profiles were collected using a standard Sea-Bird SBE-09 plus CTD during the BIOS-SCOPE cruises. Data are processed following the methods of Knap et al., 1997 with the final product being reported as two decibar averages and all profiles for each cruise are reported in a single cruise file. The file also includes derived parameters (mixed layer depths, season, sunrise, sunset, vertical zone) calculated as described in Curry et al. (2026).

Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Curation Notes
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

CTD profiles followed the sampling procedures detailed in the BATS method manual version #4 (Knap et al., 1997). The CTD is operated as per SeaBird's suggested methods with data collection at the full scan rate of 24 hertz (Hz). The CTD is powered up and allowed to stabilize at 12 meters prior to profiling. This stabilization period is important for both the conductivity and dissolved oxygen sensors to warm up prior to making measurements. Once stable (typically 4 minutes) the CTD is brought back to the surface from which point the profile begins with typical descent rates of 0.7 to 1.0 meters per second (m/s), depending on weather conditions. Water samples are collected on the upcast and prior to triggering bottles, the CTD is kept at the desired depth for a minimum of 60 seconds to ensure that entrainment from the following wake has subsided. Once the water sample is taken, the CTD immediately continues with the upcast at an ascent rate of 0.7 to 1.0 m/s.

The basic system used to acquire CTD data is a Sea-Bird SBE 9plus CTD, with an internal Digiquartz pressure sensor, a Sea-Bird SBE-3F temperature sensor, a Sea-Bird SBE-4 conductivity cell and a Sea-Bird SBE-5 pump. Additional sensors include the Sea-Bird SBE-43 dissolved oxygen sensor, the WET Labs C-Star or Chelsea/Seatech Transmissometer, the Chelsea Aqua 3 Fluorometer, and the Biospherical/Licor PAR/Irradiance sensor. Present configuration also includes a secondary temperature sensor, a Sea-Bird SBE-35 temperature sensor, a secondary conductivity sensor and pump, which are connected independently from the primary units. The temperature and conductivity sensors are connected by a standard Sea-Bird TC-duct (clear, low viscous type), which ensures that the same parcel of water is sampled by both sensors, improving the accuracy of the computed salinity. The dissolved oxygen sensor is connected downstream from the conductivity cell and the flow rate through this sensor configuration is maintained at a steady rate by the inertia balanced SBE-5 pump. 

CTD data processing typically follows the procedures outlined in Knap et al., 1997 and can be divided into three major stages: (1) CTD signal conversion and dynamic sensor correction, (2) static drift corrections and empirical field calibrations, (3) calculation of derived variables. Stage 1 is performed using SeaBird's SEASOFT software and some MATLAB scripts; Stage 2 and 3 are performed in the MATLAB environment. 

The basic steps of stage 1 are: preliminary CTD sensor quality check; determination of the dynamic coefficients associated with time alignment and thermal mass problems; application of pressure filter and velocity filter (0.3 m/s); application of digital filters for erroneous signal removal; and finally average to 2 Hz ready for stage 2 processing.

The processing steps in stage 2 include: static drift corrections as determined from the sensor calibration history; empirical field calibration of the conductivity and oxygen sensors; final QC analysis; and bin average downcast data to 2 dbar. Following experience of profiling with the SBE–35RT temperature probes, appropriate routines are being implemented to assess performance of the SBE–03f units against the SBE–35 and implement correction procedures. It should be noted that only downcast data are processed and reported.

The processing in stage 3 includes the calculation of derived parameters (season, sunrise, sunset, vertical zone) calculated as described in Curry et al. (2026). Three calculations are provided for mixed layer depths: MLD_dens125 is based on Suga et al. 2024, MLD_bvfrq is based on Morison et al. (2019) and Graff et al. (2018), MLD_densT2 is based on Sprintall and Tomczak (1992).

See the BIOS-SCOPE data processing pipeline linked in the Related Datasets for more details (Longnecker et al., 2026).

- Loaded CSV file BIOSCCOPE_CTDdataforBCODMO.2026.03.25.csv as table "1000939_v1_bios_scope_ctd"; header row set to row 1; missing value sentinels set to "", "nd", "-999", and "NaN"
- Combined year, month, day columns into a new "date" column formatted as ISO 8601 (YYYY-MM-DD), preserving original year, month, day columns
- Reordered columns so "date" appears immediately after year/month/day, with full column order set as: BATS_id, cruise, cast, date, year, month, day, hour, doy, lat, lon, MLD_dens125, MLD_bvfrq, MLD_densT2, DCM, Season, Sunrise, Sunset, par0, z_par_1pcnt, z_par_halfpcnt, z_par_tenthpcnt, pr, de, te, co, sa, o2, bac, fluor, fluor_filt, par, par_est, th, sig0, rho, bvfrq, vertZone
- Zero-padded Sunrise and Sunset values to 4 digits using string formatting
- Split zero-padded Sunrise and Sunset values into hour and minute component columns via regex, deleting the intermediate padded columns
- Reformatted Sunrise and Sunset as colon-separated HH:MM time strings by combining the hour/minute component columns
- Exported table as 1000939_v1_bios_scope_ctd

** Metadata Update **

- BCO-DMO Data Manager had mistakenly listed BAT_CRUISES as the deployment for this dataset. Data Manager removed that cruise and submitter provided correct cruises to be attached to this dataset. No changes were made to the data file.

Website: http://scope.bios.edu/

Coverage: North Atlantic Subtropical Gyre, Bermuda Atlantic Time Series (BATS) site

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