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191 results for “marine ecosystem”
Data from: A sedimentary eDNA record of the Atacama Trench reveals biodiversity changes in the most productive marine ecosystem
<p>The hadopelagic environment remains highly understudied due to the inherent difficulties in sampling at these depths. The use of sediment eDNA can overcome some of these restrictions as settled and preserved DNA represent an archive of the biological communities. We use sediment eDNA to assess changes in the community within one of the world's most productive open ocean ecosystems: the Atacama Trench. The ecosystems around the Atacama Trench have been intensively fished and are affected by climate oscillations, but the understanding of potential impacts on the marine community is limited. We sampled five sites using sediment cores at water depths from 2400 to ~8000m. The chronologies of the sedimentary record were determined using 210Pbex. Environmental DNA was extracted from core slices and metabarcoding was used to identify the eukaryote community using two separate primer pairs for different sections of the 18S rDNA gene (V9 and V7) effectively targeting pelagic taxa. The reconstructed communities were similar among markers and mainly composed of chordates and members of the Chromista kingdom. Alpha-diversity was estimated for all sites in intervals of 15 years (from 1842 to 2018), showing a severe drop in biodiversity from 1970 to 1985 that aligns with one of the strongest known El Niño events. We argue that the harsh adverse ENSO events potentially combined with extensive fishing efforts during this period of time resulted in a distinct reduction of marine biodiversity. Fish and cnidarian read abundance was examined separately to determine if fishing had a direct impact, but no direct relation was found. These results demonstrate that sediment eDNA can be a valuable emerging tool providing insight in historical perspectives on ecosystem developments. This study constitutes one of the first steps toward an improved understanding of the importance of environmental and anthropogenic drivers in affecting open and deep ocean communities.</p>
Fig. 2 in A report of 30 unrecorded bacterial species in Korea, isolated from marine ecosystems in 2021
Fig. 2. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showing the relationship between the strains isolated in this study and their closest bacterial species in classes Alphaproteobacteria, Bacilli, Cytophagia, Flavobacteriia, Fusobacteriia, and Clostridia. Bootstrap values over 70% are shown.
Fig. 1 in A report of 30 unrecorded bacterial species in Korea, isolated from marine ecosystems in 2021
Fig. 1. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showing the relationship between the strains isolated in this study and their closest bacterial species in the class Gammaproteobacteria. Bootstrap values over 70% are shown.
Fig. 3 in A report of 30 unrecorded bacterial species in Korea, isolated from marine ecosystems in 2021
Fig. 3. Transmission electron micrographs of scanning electron micrographs of cells of the strain isolated in this study. Strains: 1, HNI- BRBA38; 2, HNIBRBA54; 3, HNIBRBA100; 4, HNIBRBA151; 5, HNIBRBA189; 6, HNIBRBA220; 7, HNIBRBA244; 8, HNIBRBA255; 9, HNIBRBA270; 10, HNIBRBA272; 11, HNIBRBA274; 12, HNIBRBA350; 13, HNIBRBA370; 14, HNIBRBA397; 15, HNIBRBA406; 16, HNIBRBA489; 17, HNIBRBA506; 18, HNIBRBA601; 19, HNIBRBA666; 20, HNIBRBA682; 21, HNIBRBA683; 22, HNIBRBA684; 23, HNIBRBA685; 24, HNIBRBA688; 25, HNIBRBA773; 26, HNIBRBA833; 27, HNIBRBA853; 28, HNIBRBA855; 29, HNIBRBA866; 30, HNIBRBA1036. Scale bars are indicated in parenthesis after strain ID.
Spread of the non-native anemone Anemonia alicemartinae Häussermann & Försterra, 2001 along the Humboldt-current large marine ecosystem: an ecological niche model approach
<p>Environmental variables and script</p>
Figure 5. Sentinel 3 in Marine mucilage in the Sea of Marmara and its effects on the marine ecosystem: mass deaths
Figure 5. Sentinel 3 imagery of the chlorophyll-a concentration in the study area on April 22, 2021.
Figure 3 in Marine mucilage in the Sea of Marmara and its effects on the marine ecosystem: mass deaths
Figure 3. Some dead species were collected during sampling. The orange circle indicates Atherina sp., and the yellow square indicates other affected species.
Figure 2 in Marine mucilage in the Sea of Marmara and its effects on the marine ecosystem: mass deaths
Figure 2. Regional map and sampling stations in the southern of Sea of Marmara (1: Misakça, 2: Şirinçavuş, 3: Narlı, 4: Tatlısu)
Figure 1 in Marine mucilage in the Sea of Marmara and its effects on the marine ecosystem: mass deaths
Figure 1. Mucilage aggregation examples on the water surface in the Sea of Marmara, a) on April 23, 2021, on the coast of Misakça and b) on May 25, 2021, in Erdek Harbor.
CESM2.2-8P4Z data supporting Yu et al. (2024): Simulating ecosystem dynamics and marine biogeochemical cycles with multiple plankton functional types
<p><span>This dataset contains the model output from CESM2.2-8P4Z, used in Yu et al. (2024) and</span><span> </span><span>submitted to</span><span> the Journal of Advances in Modeling Earth Systems (JAMES). These are the last 20-year averaged output files from 310 years of the model simulations, which are analyzed in Yu et al., (2024). CESM2.2-8P4Z contains twelve plankton groups, including eight types of phytoplankton:</span><span> </span><span>1</span><span>) picophytoplankton groups: <em>Prochlorococcus</em>, <em>Synechococcus</em>, picoeukaryotes and diazotrophs; 2) nanophytoplankton groups:</span><span> </span><em><span><em>P</em></span></em><em><span><em>haeocystis</em></span></em><span>, <em>coccolithophores</em></span><span> </span><span>and a generic other nanophytoplankton; 3) micro-sized phytoplankton: diatoms</span><span>; and four types of zooplankton:</span><span> </span><span>small microzooplankton (5-20 u</span><span>m, such as ciliates, nanoflagellates), large microzooplankton (20-200 u</span><span>m, such as copepod nauplii, small dinoflagellates etc.), mesozooplankton (200-2000 u</span><span>m, such as smaller copepod, large dinoflagellates) and macrozooplankton (>2000 u</span><span>m, such as larger copepod, krill).</span><span> </span><span>The MARBL-8P4Z model improves seasonal simulation of the spring bloom compared with more simplified MARBL configurations, benefiting from dampened diatom blooms at higher latitudes due to a combination of bottom-up and top-down drivers.</span></p>
Daily Anomalies and High Productivity Zone Mask for Northern Peruvian Coastal Marine Ecosystem during the 2017 Coastal El Niño (December 2016 - May 2017)
<p>This dataset is part of the manuscript entitled "Chlorophyll Response and High Productivity Zone Contraction in Northern Perú During the 2017 Coastal El Niño."</p> <p>The dataset is designed to assess the atmospheric and oceanographic drivers of productivity changes during the 2017 Coastal El Niño. It allows detailed analysis of the interactions between physical processes (e.g., wind-driven upwelling rates, heat flux changes) and biological responses (e.g., chlorophyll concentration variations) in a region highly susceptible to ENSO-related variability. This comprehensive dataset provides valuable insight into the physical-biological coupling and the impacts of rapid climate events on marine ecosystems. The dataset, covering the period from December 1, 2016, to May 31, 2017, includes:</p> <p>1. Chlorophyll-a Anomalies (chla): Represents deviations in surface chlorophyll concentrations, a proxy for phytoplankton biomass, highlighting variations in primary productivity during the event.</p> <p>2. Sea Surface Temperature Anomalies (sst): Captures changes in sea surface temperatures relative to the climatological mean, providing insight into the warming pattern typical of marine heatwaves associated with the Coastal El Niño.</p> <p>3. Sea Level Anomaly (sla): Indicates changes in sea surface height, which reflects thermal expansion of water masses and potential contributions from coastal trapped waves propagating along the Peruvian coast.</p> <p>4. Wind Component Anomalies (u,v): Daily anomalies for both zonal (east-west) and meridional (north-south) wind components, which are critical for understanding changes in wind patterns including upwelling and Ekman transport processes.</p> <p>5. Ekman Pumping Anomalies (w): Represents variations in vertical water movement forced by wind stress curl, highlighting the suppression or enhancement of upwelling during the event.</p> <p>6. Latent Heat Flux Anomalies (lathf): Indicates deviations in heat loss from the ocean surface due to evaporation, affecting surface temperature regulation.</p> <p>7. Shortwave Radiation Anomalies (swrad): Shows changes in solar radiation (and also a proxy for PAR) reaching the ocean surface, influencing upper ocean heat content and the light availability for phytoplankton.</p> <p>8. High Productivity Zone (mask): A binary mask with daily values of 1 indicating areas meeting the HPZ criterion and 0 otherwise, allowing for spatial tracking of the HPZ's extent during the period of study.</p> <p> </p>
Data and code for FishMIP global marine ecosystem model ensemble projections summarised by countries and territories and other selected marine spatial regions.
<p>R code to extract and create data tables and summary plots of FishMIP mean ensemble projections provided are for percentage change in "exploitable fish biomass", which is a proxy for the biomass available to fisheries, consisting of marine animals spanning the size range 10 g to 100 kg: this is typically dominated by fish, but is also inclusive of other animals such as crustaceans and cephalopods.</p> <p>This release contains scripts and summary data for producing figures in Part A of the following report:</p> <p>Blanchard, J.L., Novaglio, C., eds. (2024). Climate change risks to marine ecosystems and fisheries: Future projections from the Fisheries and Marine Ecosystems Model Intercomparison Project. FAO Fisheries and Aquaculture Technical Paper No. 707. Rome, FAO.</p> <p>Please refer to the above report to cite and for more information.</p> <p>The summary data are here:</p> <p>https://github.com/Fish-MIP/FAO_Report/blob/main/data/table_stats_formatted_admin_full.csv</p> <p>Where the column 'spatial_scale' refers to the type of aggregation:</p> <p>FAO_area = High Sea areas grouped by FAO Major Fishing Areas</p> <p>countries = Exclusive Economic Zones</p> <p>countries_admin = Exclusive Economic Zones results aggregated into Administrative Countries</p> <p>Please note that these results can also be visualised and downloaded from our shiny app: https://rstudio.global-ecosystem-model.cloud.edu.au/shiny/FAO_report_shiny/</p> <p> </p>
Data from: Restoring marine ecosystems: spatial reef configuration triggers taxon-specific responses among early colonizers
<p>1. The longstanding debate in conservation biology on the importance of single large or several small (SLOSS) habitats for preserving biodiversity remains highly relevant, given the ongoing degradation and loss of natural habitats worldwide. Restoration efforts are often constrained by limited resources, and insights from SLOSS studies therefore have important implications if restoration efforts can be optimized by manipulating the spatial configuration of restored habitats. Yet, the relevance of SLOSS for habitat restoration remains largely unexplored.</p> <p>2. Here, we report the effects of spatial reef configuration on early colonization of marine organisms after restoring boulder reef habitats. Reefs were restored in single large (SL) and several small (SS) designs in the western Baltic Sea, where century-long boulder extraction has severely degraded large reef areas and likely exacerbated regional declines in commercially important gadoids (<i>Gadidae spp.</i>). We sampled the field sites using remote underwater video systems in a before-after control-impact (BACI) design and obtained probabilistic inferences on restoration and SLOSS effects from Bayesian hierarchical models.</p> <p>3. Probabilities of a positive restoration effect were high (>95%) for gadoids, labrids and demersal gobies, moderate (60-75%) for species richness and sand gobies, and low (<5%) for flatfish abundance. Notably, gadoid abundance increased 60-fold and 129-fold on average at SL and SS, respectively. The species composition at restored reefs deviated from control sites, mainly driven by large-bodied piscivores.</p> <p>4. Spatial reef configuration had the strongest effect on small-bodied mesopredators, including gobies, which were more abundant and driving a distinct species assemblage at SS. In addition to providing suitable conditions for reef species, results suggest that SS can also benefit soft-bottom taxa, possibly through a dispersed predator-mediated effect relative to SL. </p> <p><i>5. Synthesis and applications.</i> This study demonstrates that boulder reef restoration can strongly promote the abundance of exploited gadoids and is therefore a promising management tool to support top-down controls by predatory fishes in degraded marine systems. The higher abundance of mesopredators at SS reefs suggests that SLOSS could have long-term implications for trophic structure and resilience of restored habitats, and should therefore become an important facet within restoration strategies. </p>
High trophic level feedbacks on global ocean carbon uptake and marine ecosystem dynamics under climate change (Dupont et al., GBC)
<p>Files used to make the analysis in the paper "High trophic level feedbacks on global ocean carbon uptake and marine ecosystem dynamics under climate change" (Dupont et al., accepted in GBC)</p> <p>- HTL_LTL_figures.ipynb is the python notebook in which are computed the different terms to make the figures of the paper </p> <p>- histrcp85.1-PISAPE-N-OW** and piCtrl2-PISAPE-N-OW** files contain the raw outputs of the one way (OW) simulation</p> <p>- histrcp85.1-PISAPE-N-TW* and piCtrl2-PISAPE-N-TW* files contain the raw outputs of the two way (TW) simulation</p> <p>- all files ending with *rmp_f.nc/ *regrid.nc/ *f20.nc are regridded files to make maps used in the paper. More details can be found in the python noteboook (briefly, dAT_* = change in active export, dDIC_*= change in dissolved inorganic carbon, dEPC200_* = change in carbon export at 200m depth, OW/TW_<a href="https://zenodo.org/api/files/cc2ae8cc-a150-4bc6-9125-04d9e3465859/TW_dBMapermp_f.nc">dBMape</a>* = OW/TW change in small high trophic levels biomass, OW/<a href="https://zenodo.org/api/files/cc2ae8cc-a150-4bc6-9125-04d9e3465859/TW_dBMapermp_f.nc">TW_dBM</a>meszo* = OW/TW change in mesozooplankton biomass)</p> <p>- <a href="https://zenodo.org/api/files/cc2ae8cc-a150-4bc6-9125-04d9e3465859/egestt2_2.nc">egestt2_2.nc</a>, excrett2_2.nc and graztt2_2.nc are the outputs of egestion, excretion and grazing terms used to compute the active export (AT). </p>
Experimental addition of marine-derived nutrients affects wildflower traits in a coastal meta-ecosystem
<p>Organismal movement can bring individuals, resources, and novel interactions across ecosystem boundaries and into recipient habitats, thereby forming meta-ecosystems. For example, Pacific salmon ecosystems receive large marine-derived nitrogen subsidies during annual spawning events, which can have a wide range of effects on aquatic and terrestrial plant species and communities. In this study, we evaluate the effects of cross-ecosystem nutrient subsidies on terrestrial plant growth and reproduction. We conducted a large-scale field experiment with four treatments: (1) addition of a pink salmon (<em>Oncorhynchus</em> <em>gorbuscha</em>) carcass, (2) addition of the drift seaweed rockweed (<em>Fucus</em> <em>distichus</em>), (3) addition of both salmon + rockweed, and (4) a control. We examined treatment effects on leaf nitrogen and fitness-associated floral traits in four common estuarine wildflower species. We found elevated leaf ∂<sup>15</sup>N in all plant species and all sampling years in treatments with salmon carcass additions but did not observe any differences in leaf percent nitrogen. We also observed larger leaf area in two species, a context-dependent increase in floral display area in two species, and a limited increase in plant seed set in response to both salmon carcass treatments. In sum, our study suggests that marine nutrients can affect terrestrial plant growth and reproduction.</p>
Data and code to next-generation ensemble projections reveal higher climate risks for marine ecosystems
<p>Data products: <strong>Tittensor et al. (2021). Next-generation ensemble projections reveal higher climate risks for marine ecosystems, Nature Climate Change. DOI: <a href="https://doi.org/10.1038/s41558-021-01173-9">https://doi.org/10.1038/s41558-021-01173-9</a> </strong></p> <p>This data was produced using R scripts available on the GitHub repository <a href="https://github.com/Fish-MIP/CMIP5vsCMIP6">https://github.com/Fish-MIP/CMIP5vsCMIP6</a>, and was used for analysis and plotting in Tittensor et al. (2021). These R scripts are also available here as CMIP5vsCMIP6_code.zip </p> <p>Data_CMIP5.Rdata and Data_CMIP6.RData include all data used to produce global maps of percentage change in total consumer biomass. </p> <p>Data_trends_CMIP5.Rdata and Data_trends_CMIP6.RData include all data used to produce temporal trends of percentage change in total consumer biomass. </p> <p>Data_inputs_CMIP5.Rdata and Data_trends_CMIP6.RData include all data used to produce global maps of percentage change in phytoplankton biomass, zooplankton biomass, net primary production and sea surface temperature. </p> <p>Data_trends_inputs_CMIP5.Rdata and Data_trends_CMIP6.RData include all data used to produce temporal trends of percentage change in phytoplankton biomass, zooplankton biomass, net primary production and sea surface temperature.</p> <p>The suffix _reducedModelSet refers to the case when only the subset of Fish-MIP models in Lotze et al. (2019) - Global ensemble projections reveal trophic amplification of ocean biomass declines with climate change, PNAS, DOI: https://doi.org/10.1073/pnas.1900194116 - are considered. This data was used to produce some of the supplementary figures in Tittensor et al. (2021).</p> <p>Please contact Derek Tittensor (derek.tittensor@dal.ca), Camilla Novaglio (camilla.novaglio@gmail.com), or Julia Blanchard (julia.blanchard@utas.edu.au) for data interpretation and use. </p>
Replication Data for: "Marine latitudinal diversity gradients are generally absent in intertidal ecosystems"
<p>Datasets used in the paper "Marine latitudinal diversity gradients are generally absent in intertidal ecosystems"</p>
Terrain variables used for ensemble distribution modelling of vulnerable marine ecosystems indicator taxa on data-limited seamounts of Cabo Verde (NW Africa)
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Data from: A sedimentary eDNA record of the Atacama Trench reveals biodiversity changes in the most productive marine ecosystem
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Experimental addition of marine-derived nutrients affects wildflower traits in a coastal meta-ecosystem
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.