Table of Contents

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

Methodology:

To obtain samples, a 1 m Multiple Opening/Closing Net and Environmental Sensing System  (MOCNESS; Wiebe et al., 1985) equipped with 150 m nets was deployed during the mid-day and mid-night on cruises carried out in the vicinity of the Bermuda Atlantic Time-series Study site (BATS) in July of 2016, 2017, and 2018 as well as October 2018 (eight casts in total, 63 discrete nets; Table 1). The net sampling plan used adaptive profiling, modifying the depth of closure to capture eight distinct ecological zones from surface to 1000 m depth: e.g. the thermocline, deep chl-a maximum (DCM), above the O2 minimum, within the O2 minimum core, and below the O2 minimum (Maas et al., 2014, Steinberg et al., 2008a). The actual tow depths were set on a cruise-by-cruise basis, using CTD profiles to determine the depths of each ecological zone. Upon retrieval, the catch from each of the eight discrete nets were divided into splits. Half were preserved in 95% undenatured ethanol and the remainder preserved in buffered 4% formalin in seawater.

A representative subsample of the zooplankton community from each net were imaged from the formalin-preserved samples, then measured, using a ZooSCAN ver. 3 at 4,800 dpi (following the methods in: Gorsky et al., 2010, Vandromme et al., 2012). In order to better represent all size classes in the images, the original sample was divided into three size categories. All individuals larger than 2 cm were selected by eye and scanned separately from all the others. The remainder of the sample was sieved through a 1-mm mesh sieve, and both size fractions were individually scanned. From these smaller size fractions, at least 1500 particles were scanned after subsampling using a Motoda splitter (Motoda, 1959), requiring generation of two separate scans for both size classes. This resulted in a total of five images per net. Raw images were then processed in ZooProcess (Gorsky et al., 2010, Vandromme et al., 2012), and the resulting vignettes, along with a measurement and metadata file, were uploaded to EcoTaxa (https://ecotaxa.obs-vlfr.fr/; Picheral et al., 2017) for machine-assisted identification, using a training set developed by the authors. The taxonomy of one paired set of tows was completely validated (July 2017). For the remaining tows taxonomy is based on the Ecotaxa prediction using this 2017 training set.

Object_id and imagenames:

BCO-DMO data manager processing notes:
* File DATASET_M3_to_M13_BATS_v3Nov21.txt imported into the BCO-DMO data system.
* zero padding time for cases when single digit hour (e.g. 35000-> 035000 meaning 03:50:00).
*  local dates and time converted to ISO 8601 formats (yyyy-mm-dd and HH:MM:SS)
* Added timestamp in ISO 8601 format yyyy-mm-ddTHH:MM:SSZ

NSF Award Abstract:
The daily vertical migration (DMV) of zooplankton and fish across hundreds of meters between shallow and deep waters is a predominant pattern in pelagic ecosystems. This migration has consequences for biogeochemical cycling as it moves a substantial portion of fixed carbon and nitrogen (an estimated 15 to 40 % of the total global organic export) from the surface directly to depth where it feeds the midwater food chain and sequesters nutrients away from atmospheric mixing. Estimates and predictions of these fluxes are, however, poorly understood at present. New observations have shown that one source of uncertainty is due to the assumption that metabolic rates and processes do not vary over the course of the day, except based on changes in temperature and oxygen availability. Rates are, however, also driven by differences in feeding, swimming behavior, and underlying circadian cycles. The objective of this project is to improve the ability of scientists to understand and predict zooplankton contributions to the movement of carbon and nitrogen in the ocean by detailing daily changes in physiological processes of these organisms. By producing a set of respiration and excretion measurements over a daily time series, paired with simultaneously collected gene and protein expression patterns for an abundant vertically migratory species, the investigators will provide unprecedented and predictive insight into how changes in the environment affect the contribution of zooplankton to biogeochemical fluxes. The sampling design of the project will advance discovery and understanding by providing hands-on training opportunities to at least two undergraduate researchers. The project will broaden dissemination of the research via development of an educational module, focusing on rhythms in the ocean. The module will initially be piloted with the Bermuda Institute of Ocean Sciences (BIOS) summer camp students and then disseminated through the BIOS Explorer program, the Teacher Resources Page on the BIOS website, and published in a peer-reviewed educational journal.

This project will characterize the metabolic consequences of daily physiological rhythms and DVM for a model zooplankton species, the abundant subtropical copepod Pleuromamma xiphias. Flux processes (oxygen consumption, carbon dioxide production, production of ammonium and fecal pellet production) will be interrogated using directed experiments testing the effects of temperature, feeding and circadian cycle. Circadian cycling will further be examined using transcriptomic and proteomic profiling. These experiments will be related to field samples taken at 6-h intervals over the course of the diel migration using an integrated suite of molecular and organismal metrics. Combined organismal, transcriptomic and proteomic profiles will provide an understanding of which metabolic pathways and associated flux products vary in relation to particular environmental variables (food, light cycle, temperature). Diel variation in metabolic rates will also be assessed across seasons and species using other important migratory groups (pteropod, euphausiid, and another copepod). The metabolic data will then be contextualized with abundance estimates from archived depth-stratified tows to allow scaling to community-level patterns and will be used to improve calculations of zooplankton contribution to particulate organic carbon, nitrogen and respiratory active flux. The results of this study will both improve our flux estimates and provide predictive insight into how various environmental variables influence the underlying physiological pathways generating carbon and nitrogen flux.

Cruise reports are available from the completed cruises:
SD031019
AE1910
AE1918

NSF Award Abstract: 

Processes in the midwater region below 200 m depth, also known as the twilight zone, represent a major unknown for the biology and chemistry of the ocean. Studies of animals drifting in the oceans, known as zooplankton, are scarce due to the difficulty and associated time and costs of sampling deep waters. The advent of automated image analysis and genetic tools is leading to a rapid increase in our knowledge of the diversity, abundances and size distribution of communities in shallow waters. However, our understanding of the deeper layers of the ocean is still in its infancy, and there are few studies that combine these three facets of the ecology of the zooplankton. The objective of this project is to leverage existing samples, obtained from previously NSF-funded research in the North Pacific and North Atlantic, to study how the abundances, diversity, and size distribution of zooplankton in the midwater vary with latitude and environmental factors. Automated image analyses provide information on abundance and size, and genetic analyses give unprecedented data on the diversity of the midwater community for the North Atlantic and the North Pacific, from subtropical to subarctic environments. This project provides high quality hands-on training opportunities for at least two undergraduate researchers and generates material for undergraduate and graduate courses. Two workshops train educators on the classroom use of the NSF-funded Biological and Chemical Oceanography Data Management Office (BCO-DMO) open access oceanographic data.

Recent advances in image analysis and metabarcoding of zooplankton communities via new data tools are an opportunity to generate quantitative and predictive relationships between environmental drivers and zooplankton diversity, abundances and size distribution. While this information is available for plankton in epipelagic regions, the focus of this study is on midwater communities, which remain poorly characterized. Obtaining these data is the first step towards a quantitative analysis that assesses the impact of the midwater community on biogeochemical cycles. The project uses archived samples from two cruises conducted in the N. Atlantic and N. Pacific to test hypotheses about how temperature, midwater hypoxia, primary productivity and biogeographic province shape the size class structure, biodiversity and behavior (diurnal vertical migration) of zooplankton communities. These newly-generated image and metabarcoding datasets of the mesozooplankton community from 0-1000 m are cross-comparable with other ocean regions. These data describe how migratory and midwater resident zooplankton communities are structured by environmental variables and demonstrate how this influences their biogeochemical contributions (specifically active flux and midwater attenuation of flux). Data tools generated for the image analysis in combination with metabarcoding has broad application in plankton ecology and allows metanalysis of other datasets. The project is complementary to ongoing national and international projects that seek to describe the function and structure of the midwater. In contrast to existing modeling and process projects, this project covers a moderately large geographic area and thus provides a strong comparative foundation for broader community-wide assessment of the function of zooplankton in the twilight zone.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

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