cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26008/1912/bco-dmo.954262.1
title: Sequence read accession (SRA) numbers and collection metadata for coral microbiome collected in Moorea, French Polynesia from Jul 2018 to Aug 2020

description: This dataset contains the complete sample information for the 16S rRNA gene V4 region amplicon sequencing data associated with the NCBI SRA accession from BioProject PRJNA994532. All raw sequencing data can be found at this publicly available NCBI SRA BioProject. 

The associated samples were collected from an in situ coral manipulative experiment in Moorea, French Polynesia between 2018-2020 from Acropora retusa, Porites lobata, and Pocillopora spp. Data collection was a multi-university collaborative effort between the Vega Thurber Laboratory,  at Oregon State University during the time of the experiment, and the Burkepile Community Ecology Laboratory at UC Santa Barbara. The experiment, conducted on the fore reef on the north shore of the island, evaluated the interaction of consumer pressure level (termed &quot;Herbivory&quot; in the dataset and in Vompe et al., 2023) and nutrient enrichment on coral microbiome composition and host success. The experiment also captured two severe and sequential marine heatwaves in 2019 and 2020. This experiment aimed to  evaluate whether managing local inputs, including water column nutrient levels and fishing regimes, interacts with heat stress to affect coral success. Coral microbiomes were sampled as these microbial communities are known to interact with host health during heat stress. The data herein correspond to the microbiomes of the sampled corals.
DOI: 10.26008/1912/bco-dmo.3773.2
title: Niskin bottle water samples and associated CTD measurements from the Hawaii Ocean Time-Series cruises from 1988-2019

description: Monthly measurements of the thermohaline structure, water column chemistry, and primary production were collected at station ALOHA as part of the Hawaii Ocean Time-series (HOT) program. This dataset presents biogoeochemical data from water samples collected on cruises HOT-001 through HOT-317 from October 1988 through December 2019.
DOI: 10.26008/1912/bco-dmo.942939.1
title: Micromorphological analyses of Pocillopora damicornis overall skeleton collected from reef of Heron Island, southern Great Barrier Reef from Jan 2021 to Feb 2021

description: Corals residing in habitats that experience frequent seawater pCO2 variability may possess an enhanced capacity to cope with ocean acidification. Yet, we lack a clear understanding of the molecular toolkit enabling acclimatization to environmental extremes, and how life-long exposure to pCO2 variability influences biomineralization. We examined the gene expression responses and micro-skeletal characteristics of Pocillopora damicornis originating from the reef flat and reef slope of Heron Island, southern Great Barrier Reef. The reef flat (454 ± 3.0) and reef slope (418 ± 1.9) had similar mean seawater pCO2 (µatm; mean ± SE), but the reef flat experienced twice the mean daily pCO2 amplitude (range of 797v. 399  µatm day-1, respectively). A controlled mesocosm experiment was conducted over eight weeks, exposing P. damicornis from the reef slope and reef flat to stable (218±9) or variable (911±31) diel pCO2 fluctuations (µatm; mean ± SE). 

This dataset includes the data and analyses for the overall skeletal micromorphological analyses of P. damicornis, including the origin reef environment, treatment, colony ID, feature of interest, image magnification, image name, observer, replicate, size of image, area of image, number of corallites within image, number of corallites area-1, corallite diameter (mm), and distance between corallites (mm).
DOI: 10.26008/1912/bco-dmo.942962.1
title: Micromorphological analyses of Pocillopora damicornis calyxes collected from reef of Heron Island, southern Great Barrier Reef from Jan 2021 to Feb 2021

description: Corals residing in habitats that experience frequent seawater pCO2 variability may possess an enhanced capacity to cope with ocean acidification. Yet, we lack a clear understanding of the molecular toolkit enabling acclimatization to environmental extremes, and how life-long exposure to pCO2 variability influences biomineralization. We examined the gene expression responses and micro-skeletal characteristics of Pocillopora damicornis originating from the reef flat and reef slope of Heron Island, southern Great Barrier Reef. The reef flat (454 ± 3.0) and reef slope (418 ± 1.9) had similar mean seawater pCO2 (µatm; mean ± SE), but the reef flat experienced twice the mean daily pCO2 amplitude (range of 797v. 399 µatm day-1, respectively). A controlled mesocosm experiment was conducted over eight weeks, exposing P. damicornis from the reef slope and reef flat to stable (218±9) or variable (911±31) diel pCO2 fluctuations (µatm; mean ± SE).

This dataset includes the data and analyses for the overall skeletal micromorphological analyses of P. damicornis, including the origin reef environment, treatment, colony ID, feature of interest, image magnification, image name, observer, replicate, corallite diameter, distance between corallites, area, perimeter, and circularity.
DOI: 10.26008/1912/bco-dmo.942948.1
title: Micromorphological analyses of Pocillopora damicornis spine structures collected from reef of Heron Island, southern Great Barrier Reef from Jan 2021 to Feb 2021

description: Corals residing in habitats that experience frequent seawater pCO2 variability may possess an enhanced capacity to cope with ocean acidification. Yet, we lack a clear understanding of the molecular toolkit enabling acclimatization to environmental extremes, and how life-long exposure to pCO2 variability influences biomineralization. We examined the gene expression responses and micro-skeletal characteristics of Pocillopora damicornis originating from the reef flat and reef slope of Heron Island, southern Great Barrier Reef. The reef flat (454 ± 3.0) and reef slope (418 ± 1.9) had similar mean seawater pCO2 (µatm; mean ± SE), but the reef flat experienced twice the mean daily pCO2 amplitude (range of 797v. 399 µatm day-1, respectively). A controlled mesocosm experiment was conducted over eight weeks, exposing P. damicornis from the reef slope and reef flat to stable (218±9) or variable (911±31) diel pCO2 fluctuations (µatm; mean ± SE).

This dataset includes the data and analyses for the spine structures micromorphological analyses of P. damicornis, including the origin reef environment, treatment, colony ID, feature of interest, image magnification, image name, observer, replicate, spine length, spine width, and number of spines.
DOI: 10.26008/1912/bco-dmo.942955.1
title: Micromorphological analyses of Pocillopora damicornis Spine RADs on samples collected from reef of Heron Island, southern Great Barrier Reef from Jan 2021 to Feb 2021

description: Corals residing in habitats that experience frequent seawater pCO2 variability may possess an enhanced capacity to cope with ocean acidification. Yet, we lack a clear understanding of the molecular toolkit enabling acclimatization to environmental extremes, and how life-long exposure to pCO2 variability influences biomineralization. We examined the gene expression responses and micro-skeletal characteristics of Pocillopora damicornis originating from the reef flat and reef slope of Heron Island, southern Great Barrier Reef. The reef flat (454 ± 3.0) and reef slope (418 ± 1.9) had similar mean seawater pCO2 (µatm; mean ± SE), but the reef flat experienced twice the mean daily pCO2 amplitude (range of 797v. 399  µatm day-1, respectively). A controlled mesocosm experiment was conducted over eight weeks, exposing P. damicornis from the reef slope and reef flat to stable (218±9) or variable (911±31) diel pCO2 fluctuations (µatm; mean ± SE). 

This dataset includes the data and analyses for the overall skeletal micromorphological analyses of P. damicornis, including the origin reef environment, treatment, colony ID, feature of interest, image magnification, image name, observer, replicate, number of RADs, and area of RADs.
DOI: 10.26008/1912/bco-dmo.958698.1
title: NCBI accession numbers and related metadata for an SRA archive of the seagrass, Zostera marina

description: 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.
DOI: 10.26008/1912/bco-dmo.947757.1
title: Algal consumption data from Tegula in the presence of the predator Pisaster ochraceus, displaying anti-predatory responses or not within mesocosms at Bodega Marine Lab in 2018

description: To examine the impacts of fear removal on the strength of trophic cascades, we measured the amount of algae (Ulva spp.) consumed by Tegula funebralis that either displayed either an anti-predatory response to its predators, Pisaster ochraceus and Cancer productus, or ignored the predators. Additionally, we used two species of predators with differing consumption rates to test how predator traits might mediate the effect of removal on trophic cascade strength. The experiment was conducted within laboratory mesocosms at Bodega Marine Lab in 2018.

This dataset reports results for experiments with Pisaster ochraceus as the predator.  See &quot;Related Datasets&quot; section for results from the experiments with Cancer productus as the predator along with results of other experiments to be published in Ng & Gaylord (2025, in-prep).
DOI: 10.26008/1912/bco-dmo.958631.1
title: NCBI accession numbers and related metadata for an SRA archive of the Pacific oyster, Magallana gigas

description: The massive geographic expansion of terrestrial plant crops, livestock, and marine aquacultured species during the 19th and 20th centuries provided local economic benefits, stabilized food demands, and altered local ecosystems. The invasion history of these translocations remains uncertain for most species, limiting our understanding of their future adaptive potential and historical roles as vectors for co-invaded species. We provide a framework for filling this gap in invasion biology using the widely transplanted Pacific oyster (Magallana gigas) as a case study. A two-dimensional summary of population-level variation in single nucleotide polymorphisms (SNPs) in native Japan reflected the geographical map of Japan and allowed identification of the source regions for the worldwide expansion. Pacific oysters proliferate in non-native areas with environmental temperatures similar to those areas where native lineages evolved.
DOI: 10.26008/1912/bco-dmo.821289.2
title: RNA-Seq sample information and accessions numbers for the copepods Neocalanus flemingeri (Prince William Sound, Gulf of Alaska)(2015-2017) and Labidocera madurae (Kane‘ohe Bay, Oahu, Hawaii)(2017)

description: This dataset includes accession information for RNA-seq data for the copepods Neocalanus flemingeri and Labidocera madurae used to generate de novo reference transcriptomes and for gene expression analysis. N. flemingeri adult females (CVI) were collected in Prince Williams Sound (Gulf of Alaska) during the fall (September 2015 and 2017) oceanographic cruises of the Seward line long-term observation program (ltop)(http://www.sfos.uaf.edu/sewardline/) and Northern Gulf of Alaska Long-Term Ecological Research Program (NGA LTER). For each sample collection date and preservation dates are listed. Labidocera madurae adult females (CVI) and mixed copepodid stages (CIII-CV) were collected in Kane‘ohe Bay, Oahu (Hawaii) in August 2015.
DOI: 10.26008/1912/bco-dmo.947753.1
title: Algal consumption data from Tegula in the presence of the predator Cancer productus, displaying anti-predatory responses or not within mesocosms at Bodega Marine Lab in 2018

description: To examine the impacts of fear removal on the strength of trophic cascades, we measured the amount of algae (Ulva spp.) consumed by Tegula funebralis that either displayed either an anti-predatory response to its predators, Pisaster ochraceus and Cancer productus, or ignored the predators. Additionally, we used two species of predators with differing consumption rates to test how predator traits might mediate the effect of removal on trophic cascade strength. The experiment was conducted within laboratory mesocosms at Bodega Marine Lab in 2018.

This dataset reports results for experiments with Cancer productus as the predator.  See &quot;Related Datasets&quot; section for results from the experiments with Pisaster ochraceus as the predator along with results of other experiments to be published in Ng & Gaylord (2025, in-prep).
DOI: 10.26008/1912/bco-dmo.954189.1
title: Microplankton microscopy and biovolume analysis from Lugol's samples collected in Resurrection Bay, AK from January to March of 2023

description: The Gulf of Alaska is a highly seasonal environment characterized by an order-of-magnitude increase in copepod biomass in the photic zone between winter and spring. The study focused on copepod recruitment to characterize species-specific naupliar production. Concurrent environmental monitoring included taxonomic identification of microplankton using microscopy.
DOI: 10.6084/m9.figshare.30565478
title: Units used for motif enrichment (30 bp)

description: The fasta used for the motif enrichment. The fasta were collected by the potential modified sites.
DOI: 10.6084/m9.figshare.30565478.v1
title: Units used for motif enrichment (30 bp)

description: The fasta used for the motif enrichment. The fasta were collected by the potential modified sites.
DOI: 10.26008/1912/bco-dmo.737393.3
title: Sediment trap flux measurements for the Hawaii Ocean Time-Series (HOT) project from December 1988 to December 2023 at Station ALOHA

description: This dataset presents 35 years of particle flux measurements from Hawaii Ocean Time-Series (HOT) cruises during December 1988 to December 2023 at Station ALOHA in the Pacific Ocean north of Hawaii. Particle flux was measured at a standard reference depth using multiple cylindrical particle interceptor traps deployed on a free-floating array for approximately 60 hours during each cruise. Sediment trap design and collection methods are described in Winn et al. (1991). Passively sinking particulate matter was collected, prescreened (335 µm) to remove zooplankton and micronekton carcasses, then the sample materials analyzed for particulate carbon, nitrogen, phosphorus, silica, and mass flux.
DOI: 10.26008/1912/bco-dmo.954173.1
title: Chlorophyll a and flow cytometry data from bi-weekly vertical profiles in Resurrection Bay, AK from January to March of 2023 from bi-weekly vertical profiles in Resurrection Bay, AK from January to March of 2023

description: The Gulf of Alaska is a highly seasonal environment that is characterized by an order-of-magnitude increase in copepod biomass in the photic zone between winter and spring. The study focused on copepod recruitment to characterize species-specific naupliar production. Concurrent environmental monitoring included measurements of chlorophyll α and flow cytometry as indicators of prey field. Bi-weekly vertical profiles of temperature, salinity and fluorescence were recorded at an established station (RES2.5) in Resurrection Bay, AK. Discrete water samples were obtained for size-fractionated chlorophyll α samples and cell counts using flow cytometry. The water column was stratified by salinity with the lowest salinities recorded in the surface layer. A moderate increase in chlorophyll α concentrations occurred during March prior to the spring phytoplankton bloom.
DOI: 10.26008/1912/bco-dmo.957527.1
title: Open cell and single-step method for total alkalinity titrations from samples collected on R/V Mirai cruises MR23-06C and MR23-07 in the North Pacific and Western Arctic from September to November 2023

description: Duplicate samples were collected for total alkalinity on two cruises in 2023 aboard the R/V Mirai (MR23-06C and MR23-07) in order to compare two different methods of total alkalinity titrations: the open cell with non-linear least squares fitting and single step with spectrophotometric endpoint detection. Measurements of dissolved inorganic carbon and pH on the total scale were also made as quality control checks. GLODAPv2 hinted at a potential offset between laboratories in the Pacific Ocean. We hypothesized that if non-negligible amounts of organic alkalinity were present, the different methods could be titrating different amounts leading to differences between the methods. The results show that any offset is within the uncertainty of the analytical precision and presence of organic alkalinity in open ocean waters remains inconclusive.
DOI: 10.26008/1912/bco-dmo.957644.1
title: Total alkalinity determined through experiments comparing usage of high-density polyethylene (HDPE) and borosilicate glass bottles for collection and storage of water samples collected on the GEOTRACES GP17-OCE cruise (R/V Roger Revelle RR2214)

description: Total alkalinity plays an important role in buffering seawater and determining how much anthropogenic carbon dioxide the oceans can absorb and mitigate the rise in atmospheric concentrations. Total alkalinity varies with location, depth, and time making it an important variable needed to quantify and monitor ocean acidification, and potentially for ocean alkalinity enhancement interventions. Currently, best practices are to use expensive high quality borosilicate glass bottles for collecting and storing these samples. However, unlike other carbon system variables, total alkalinity is not affected by gas exchange meaning plastic bottles may be suitable for total alkalinity sample storage. Plastic bottles are lighter, cheaper, and less prone to breakage making them easier to handle and ship. Here, we test the suitability of high-density polyethylene (HDPE) for collection and long-term storage of total alkalinity samples. Duplicate samples were collected in standard borosilicate glass bottles and HDPE bottles on GEOTRACES GP17-OCE. The samples were analyzed in the laboratory over a year later and the storage methods were compared. It was determined that HDPE is not suitable for long-term storage of total alkalinity samples as there were large changes in total alkalinity over time and precision of duplicate samples was very poor. We hypothesize that HDPE plastic is slightly porous leading to leaching of alkalinity either into or out of the bottle over time impacting the value of the sample. Use of HDPE bottles for total alkalinity samples is not recommended for long term sample storage.
DOI: 10.26008/1912/bco-dmo.958359.1
title: Restriction site-associated DNA sequence metadata of Kelletia kelletii collected in California, USA and Baja, Mexico in 2015 to 2017

description: Climate-driven warming and changes in major ocean currents enable poleward transport and range expansions of many marine species. Here, we report the population genetic structure for the gastropod Kelletia kelletii, a commercial fisheries species and subtidal predator with top-down food web effects, whose populations have recently undergone climate-driven northward range expansion. 

This dataset includes sample id, collection site and year, tissue type, length, and extraction information for samples sequenced. We genotyped 598 adults from 13 locations across the species’ historical and expanded range (∼800 km) using reduced representation genomic sequencing (RAD-seq). Analyses of 40,747 SNPs show evidence for long-distance larval dispersal of K. kelletii larvae from a central historical range site (Point Loma, CA) hundreds of km into the expanded northern range (Big Creek, CA), which seems most likely to result from transport during an El Niño Southern Oscillation (ENSO) event rather than consistent on-going gene flow. Furthermore, despite smaller geographic distances among some sampled expanded-range populations, their genetic divergence exceeds that among the historical range sampled populations, suggesting multiple origins of the expanded-range populations. Given the frequency and magnitude of ENSO events are predicted to increase with climate change, understanding the factors driving changes in population connectivity is crucial for establishing effective management strategies to ensure the persistence of this and other economically and ecologically important species.
DOI: 10.26008/1912/bco-dmo.3986.2
title: Dissolved iron-binding ligands and their respective conditional stability constants in upper water column, R/V Knorr KN192-05, S. Atlantic subtropical gyre and Benguela upwelling region, Nov. 2007 (CoFeMUG project)

description: This dataset includes dissolved iron-binding ligands and their respective conditional stability constants in the upper water column from R/V Knorr cruise KN192-05 in the South Atlantic subtropical gyre and Benguela upwelling region, collected in November 2007 as part of the CoFeMUG project.
DOI: 10.26008/1912/bco-dmo.957694.1
title: Total alkalinity from an experiment testing the suitability of high-density polyethylene (HDPE) for collection and long-term storage of total alkalinity samples using laboratory-manipulated oligotrophic Atlantic surface water

description: Total alkalinity plays an important role in buffering seawater and determining how much anthropogenic carbon dioxide the oceans can absorb and mitigate the rise in atmospheric concentrations. Total alkalinity varies with location, depth, and time making it an important variable needed to quantify and monitor ocean acidification, and potentially for ocean alkalinity enhancement interventions. Currently, best practices are to use expensive high quality borosilicate glass bottles for collecting and storing these samples. However, unlike other carbon system variables, total alkalinity is not affected by gas exchange meaning plastic bottles may be suitable for total alkalinity sample storage. Plastic bottles are lighter, cheaper, and less prone to breakage making them easier to handle and ship. Here, we test the suitability of high-density polyethylene (HDPE) for collection and long-term storage of total alkalinity samples through laboratory experiments where HDPE bottles were treated to different cleaning methods and then filled with surface seawater and stored for 15-17 months before analyzing for total alkalinity. It was determined that HDPE is not suitable for long-term storage of total alkalinity samples as there were large changes in total alkalinity over time and precision of duplicate samples was very poor. We hypothesize that HDPE plastic is slightly porous leading to leaching of alkalinity either into or out of the bottle over time impacting the value of the sample. Use of HDPE bottles for total alkalinity samples is not recommended for long term sample storage.
DOI: 10.26008/1912/bco-dmo.773674.1
title: Nutrients, metals, and CTD observations from CTD casts and bottles from R/V Knorr cruise KN192-05 in the South Atlantic subtropical gyre and Benguela upwelling region from November to December 2007 (CoFeMUG project)

description: This dataset includes nutrient and metal data along with CTD data collected on R/V Knorr cruise KN192-05, &quot;CoFeMUG&quot;, from November to December 2007.
DOI: 10.26008/1912/bco-dmo.773715.1
title: Combined CTD profiles for two CTD sensor packages on R/V Knorr cruise KN192-05 from November to December 2007

description: This dataset contains the combined CTD profiles from two CTD sensor packages deployed on R/V Knorr cruise KN192-05, &quot;CoFeMUG&quot;, from November to December 2007.