[ZooProcess and Ecotaxa Output for Zooplankton Mediated Aggregates] - ZooProcess and Ecotaxa output from ZooSCANs of zooplankton collected with MOCNESS tows during six R/V Atlantic Explorer cruises from 2021 to 2023 (Collaborative Research: Zooplankton mediation of particle formation in the Sargasso Sea)

This dataset consists of ZooProcess and Ecotaxa outputs from ZooSCANs of plankton caught in the upper 600m using Multiple Opening-Closing Net and Environmental Sensing System (MOCNESS) tows during day- and night-time. It includes data for this project from Ecotaxa (export v1.0), an online machine-learning platform that assists in identifying organisms and particles. The dataset also includes particle measurements generated by ZooProcess software. These samples were collected and processed over two years, with three cruises a year to capture distinct seasons. The goal of this data was to assess high-resolution vertical distribution of zooplankton in order to distinguish diel vertical migrators from resident populations and to quantify contributions to particulate organic carbon flux via fecal pellet production.

Project description: The oceanic biological carbon pump refers to the export of dissolved and particulate organic carbon to the deep ocean, and it is a significant driver of atmospheric carbon uptake by the oceans. Evidence from long-term research carried out at the Bermuda Atlantic Time-series Study (BATS) site suggests that the spectrum of particles collected by gel-traps below the euphotic zone changes drastically below 150 m, which is attributed to resident populations of zooplankton that feed on vertically migrating zooplankton as well as sinking particles. The goals of this study are to investigate the role of different zooplankton taxa on both particle aggregate formation and in particle transformation, and to compare and characterize the particles generated by the zooplankton communities with those collected by particle traps.

cdm_data_type = Other
VARIABLES:
object_id (unitless)
latitude (Object_lat_start, degrees_north)
longitude (Object_lon_start, degrees_east)
object_date (unitless)
object_time (unitless)
time (Object_iso_datetime_utc, seconds since 1970-01-01T00:00:00Z)
object_link (unitless)
object_depth_min (Meters)
object_depth_max (Meters)
... (143 more variables)


[Zostera marina GenBank SRA accession numbers] - NCBI accession numbers and related metadata for an SRA archive of the seagrass, Zostera marina (RUI: Collaborative Research: Trait differentiation and local adaptation to depth within meadows of the foundation seagrass Zostera marina)

Using recent advances in indirect genetic methods applied to both adult plants and dispersed seeds, we find that the mean seed dispersal in a threatened marine foundation plant (the seagrass Zostera marina) is approximately 100-200 meters. We documented strong phenotypic variation and genome-wide differentiation among plants separated by less than the spatial scale of mean realized dispersal, which suggests genetic isolation by environment in response to depth-related environmental gradients. Within all meadows, the ratio of effective to census size (or Ne/Nc) approximated 0.1%, indicating that a fraction of existing plants provides the genetic variation to allow adaptation to environmental change. The SRA dataset at NCBI contains the raw sequencing reads that were used to create genotypes and genotype likelihoods.

cdm_data_type = Other
VARIABLES:
Accession (unitless)
Sample_Name (unitless)
adult_seed (unitless)
site (unitless)
SvD (unitless)
quad_name (unitless)
longitude (degrees_east)
latitude (degrees_north)
YearCollected (unitless)


[Zostera marina whole genome resequencing] - Sample collection and sequence accession information for Zostera marina whole genome resequencing from specimens collected at 16 geographic locations worldwide in 2017 (Using genomics to link traits to ecosystem function in the eelgrass Zostera marina)

This dataset includes sample collection and sequence accession information for Zostera marina whole genome resequencing from specimens collected at 16 geographic locations worldwide in 2017. Sequence accessions are housed in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).

cdm_data_type = Other
VARIABLES:
SampleID (unitless)
BioProject (unitless)
Library_Code (unitless)
Sample_Description (unitless)
Location_Name (unitless)
latitude (degrees_north)
longitude (Long, degrees_east)
SRA_accession (unitless)
Library_type (unitless)
Sampled_tissue (unitless)
Instrument (unitless)
reads (unitless)
Number_of_bases_Raw_fastq (count)
Coverage_Raw_fastq (genomes)
Number_of_bases_Clean_fastq (count)
Coverage_Clean_fastq (genomes)
Mapped_pcnt (percent)
Properly_paired_pcnt (percent)