Mesopelagic Mesozooplankton and Micronekton Database

This work builds upon the research of McIvor²¹, who during his MSc project compiled zooplankton distribution data from various sources to create vertical distribution profiles for organisms in the epi- and mesopelagic layers of nine Longhurst’s²² pelagic ecological provinces. McIvor’s database included 71 articles and 220 study locations and allowed for inter-area comparisons during the summer period. This work expands on previous efforts by attempting to gather as comprehensively as possible available literature on abundance and biomass of mesopelagic zooplankton and micronekton during various seasons.

To expand the intial database, a literature search was conducted via the keywords: ‘mesopelagic,’ ‘vertical distribution,’ ‘mesopelagic zooplankton,’ ‘mesopelagic micronekton,’ ‘twilight zone,’ and ‘deepwater plankton’ through the Web of Science and Google Scholar search engines. Any paper containing data on mesopelagic mesozooplankton biomass or abundance were selected. Additional sources included unpublished data from Dr. A. Yamaguchi (Hokkaido University, Japan) on copepod data from the North Pacific²³ and Dr. Evgeny Pakhomov’s (University of British Columbia, Canada) unpublished data from the Southern Ocean (Figure S3a). From each article, raw density data for zooplankton taxa were collated on the basis of biomass and/or density at discrete depth ranges within the mesopelagic layers (200–1,000 m). In addition to density data, vertical distributions and geographical locations, information related to the date of collection, sampling location, net mesh size (or sieve mesh size for bottle data) and taxa was also recorded. Samples from epipelagic and/or bathypelagic zones were also included in the database if the sampling is performed beyond the mesopelagic zone. Out of many entries collected for the mesopelagic, only data that had quantitative measurements of biomass and abundance were included in the database. Original columns of depth ranges and abundance/biomass estimates are preserved in the database.

In addition, we extracted relevant biomass and abundance data from the PANGAEA Data Publisher²⁴ for records with available geolocation and depths greater than 200 m, specifically targeting zooplankton and micronekton. This process resulted in 38,017 entries sourced from 25 studies.

We also downloaded abundance, biomass, and composition data from the COPEPOD global plankton database⁸ (downloaded on 2019/01/07). To make comparisons easier, the data were then filtered on the basis of depth (only entries between 200–1,000 m) and taxa (zooplankton only), and only quantitative records of biomass and abundance were included. After applying these filters, the dataset contained 89,308 entries. However, the filtered dataset did not include any records from the North Atlantic Ocean basin, despite significant sampling efforts in this area (Figure S3b).

The BioTIME database¹⁰ (downloaded on 2018/09/03) is a comprehensive collection of biodiversity time series comprising records of abundances and biomass for a range of marine and nonmarine species. The marine realm alone contains approximately 5,664,196 records, represented by 152 studies across six categories (benthic, fish, marine birds, marine invertebrates, marine mammals, and marine plants). However, extracting data on the basis of depth or elevation is challenging, as no depth information was available in the downloaded file. To address this, a file with depth information was obtained through personal communication with the authors and linked with the main query using the STUDY_ID as a common field. The resulting data were filtered for a depth range between 200 and 1,000 meters. However, some studies in the database lack depth information, resulting in significant data reduction. In addition, only two taxa (fish and marine invertebrates) were included in the current study, resulting in only 6,720 entries from three studies. Fish records (n = 719) were collected with 1.3 cm mesh and could not be classified as mesozooplankton or micronekton and were removed from the analysis, leaving 5,990 records for zooplankton (Figure S3b). Unfortunately, information on mesh size or net type was not available for these studies.

The Jellyfish Initiative (JeDI) Database²⁵ is a comprehensive global database dedicated to gelatinous zooplankton (Cnidaria, Ctenophora and Thaliacea), aimed at defining a global baseline of gelatinous zooplankton populations²⁶. The database consists of 476,000 quantitative, categorical, presence-absence, and presence-only records spanning three centuries (1790–2011), gathered from various published and unpublished sources. These records were collected globally, with the greatest concentration of data in the mid-latitudes of the Northern Hemisphere. After filtering for depths greater than 200 m and removing two density columns (density and density_integrated) due to a lack of identified units, the data were further filtered for nonzero quantitative density or biomass values (Figure S3b). This approach resulted in 8,413 entries remaining for analysis. Additionally, errors in units for mesh sizes reported in millimeters versus micrometers were corrected.

All data sources were compiled together in a single database for further standardization and cleanup. Depending on the date of collection/entry to the database, some taxonomic names can be entered as abbreviated names (e.g., S. gazellae), outdated names (e.g., Phyllopus helgae is unaccepted name for Nullosetigera helgae), or misspelled names (e.g., Conchoecinae instead of Conchoeciinae). To standardize the naming of different taxa, names were checked with the World Register of Marine Species⁷ (WoRMS), an authoritative classification and catalog of marine names. We used the worrms package to match the species names to their accepted WoRMS names²⁷. The original names were retained, and the standardized values were put into the taxa_standardized column along with AphiaID (aphia_id column). In addition, for each organism, taxonomic rank was specified. The exceptions were paraphyletic terms such as Gammaridea or Natantia, where precise taxonomic classification was not available, or when several taxa were listed together (e.g., copepods, chaetognaths or gelatinous zooplankton). In these cases, the rank ‘Group’ was assigned to taxa_standardized and rank columns. In cases where the community of organisms was given (e.g., Mesozooplankton and/or Micronekton), standardized name was assigned to ‘Zooplankton/ Micronekton.’ When organisms were recorded as “unidentified” or “other,” the standardized name were assigned to ‘Other taxa.” Records of terrestrial taxa (e.g., the genus Mesoniscus) were removed from the database.

Standardization for net types involved consolidating various net names, abbreviations, and descriptions into consistent categories. Similar or synonymous terms for the same net type, such as “Bongo,” “BN,” and “Bongo Net,” were grouped under a single standard name. Acronyms and abbreviations were aligned to their full forms where possible, and different variations of net descriptions were unified. For example, “IKMT” was standardized across variations like “Isaac-Kidd Midwater Trawl” and “Isaacs-Kidd midwater trawl.” Nets with the same function but different local variations were also combined, and generic terms like “Plankton Net” were clarified when possible. This process ensured consistency across different data sources and improved clarity for analysis. In addition, volumetric abundance values were standardized based on mesh size, tow type, and season, following the detailed procedure outlined in the Technical Validation section.