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129 results for “coastal communities”
Figure 5 in Temporal dynamics of parasite populations and communities of blue sea catfish Ariopsis guatemalensis (Günther, 1864), in a eutrophic coastal lagoon from Mexican Pacific
Figure 5. Scatter plot of principal component analysis (PCA) of factors that influence the species richness and diversity of the parasite infracommunities of Ariopsis guatemalensis, from Tres Palos lagoon. 'Predictor variables': Season = climatic season, Month = sampling month, GRI = gastric repletion index, GSI = gonadosomatic index, CF = condition factor, Size = host body size (total length), Sex = sex of the host. Infracommunity parameters: Richness = number of parasite species per host, Diversity = Brillouin diversity index values, Load = total number of parasites per infracommunity, Evenness = species evenness, RHsp = number of heteroxenous parasite species, THsp = total number of heteroxenous parasites, TMsp = total number of monoxenous parasites. Ellipses represent sampling months.
Data from: A year in hypoxia: epibenthic community responses to severe oxygen deficit at a subsea observatory in a coastal inlet
Changes in ocean ventilation driven by climate change result in loss of oxygen in the open ocean that, in turn, affects coastal areas in upwelling zones such as the northeast Pacific. Saanich Inlet, on the west coast of Canada, is a natural seasonally hypoxic fjord where certain continental shelf species occur in extreme hypoxia. One study site on the VENUS cabled subsea network is located in the hypoxic zone at 104 m depth. Photographs of the same 5 m2 area were taken with a remotely-controlled still camera every 2/3 days between October 6th 2009 and October 18th 2010 and examined for community composition, species behaviour and microbial mat features. Instruments located on a near-by platform provided high-resolution measurements of environmental variables. We applied multivariate ordination methods and a principal coordinate analysis of neighbour matrices to determine temporal structures in our dataset. Responses to seasonal hypoxia (0.1–1.27 ml/l) and its high variability on short time-scale (hours) varied among species, and their life stages. During extreme hypoxia, microbial mats developed then disappeared as a hippolytid shrimp, Spirontocaris sica, appeared in high densities (200 m22) despite oxygen below 0.2 ml/l. The slender sole Lyopsetta exilis was abundant in severe hypoxia and diminished as oxygen increased in the summer. This planktivore may be responding to changes in the depth of the diurnal migration of zooplankton. While the squat lobster Munida quadrispina was common at all times, juveniles disappeared in fluctuating conditions. Despite low oxygen conditions, animal densities were high indicating that the risk from hypoxia is balanced by factors such as food availability and escape from less tolerant predators. As hypoxia increases on the continental shelf, we expect benthic communities to become dominated by low diversity, hypoxia-tolerant species of low commercial significance.
Data from: Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean
<p><span>Pollution in human-made fishing ports caused by petroleum </span><span>from</span><span> boats, dead fish, toxic </span><span>chemicals</span><span>, and effluent </span><span>poses</span><span> a challenge to the organisms in seawater. To decipher the impact of pollution on the microbiome, we collected surface water </span><span>from</span><span> a fishing port and a nearby offshore island in northern Taiwan facing the </span><span>Northwestern Pacific Ocean. By employing 16S </span><span>rRNA gene</span><span> amplicon sequencing and whole-genome shotgun sequencing, we discovered that </span><span>Rhodobacteraceae, Vibrionaceae, and Oceanospirillaceae emerged as the dominant species in the fishing port</span><span>,</span><span> where we found many genes harboring the functions of </span><span>antibiotic</span><span> resistance (</span><span>ansamycin, nitroimidazole, and aminocoumarin), metal tolerance (copper, chromium, iron and multimetal), virulence factors (chemotaxis, flagella, T3SS1), carbohydrate metabolism (biofilm formation and remodeling of bacterial cell </span><span>walls</span><span>), nitrogen metabolism (denitrification, N<sub>2</sub> fixation, and ammonium assimilation), and ABC transporters (phosphate, lipopolysaccharide, and branched-chain amino </span><span>acids</span><span>). The dominant bacteria at the nearby offshore island (</span><span>Alteromonadaceae, Cryomorphaceae, Flavobacteriaceae, Litoricolaceae, and Rhodobacteraceae) were partly similar to those in the South China Sea and the East China Sea. Furthermore, we inferred</span><span> that</span><span> the microbial community network of </span><span>the cooccurrence</span><span> of dominant bacteria </span><span>on the</span><span> offshore island was connected to dominant bacteria in </span><span>the </span><span>fishing port by mutual</span> <span>exclusion. By examining the assembled microbial genomes collected from the coastal seawater of the fishing port, we revealed four genomic islands containing large gene-containing sequences</span><span>,</span><span> including phage integrase, DNA</span> <span>invertase, restriction enzyme, DNA gyrase inhibitor, and antitoxin HigA-1.</span><span> In this study, </span><span>we provided </span><span>clues </span><span>for the possibility of genomic islands as the units of horizontal transfer and as the tools of microbes for facilitating adaptation in a human-made port environment.</span></p>
A community and functional comparison of coral and reef fish assemblages between four decades of coastal urbanisation and thermal stress.
<p>Urbanised coral reefs experience anthropogenic disturbances caused by coastal development, pollution and nutrient runoff, resulting in turbid, marginal conditions in which only certain species can persist. Mortality effects are exacerbated by increasingly regular thermal stress events, leading to shifts towards novel communities dominated by habitat generalists and species with low structural complexity.</p> <p>There is limited data on the turnover processes that occur due to this convergence of anthropogenic stressors, and how novel urban ecosystems are structured both at the community and functional level. As such, it is unclear how they will respond to future disturbance events.</p> <p>Here, we examine the patterns of coral reef community change, and determine whether ecosystem functions provided by specialist species are lost post-disturbance. We present a comparison of community and functional trait-based changes for scleractinian coral genera and reef fish species assemblages subject to coastal development, coastal modification, and mass bleaching between two time periods, 1975-6 and 2018, in Nakagusuku Bay, Okinawa, Japan.</p> <p>We observed an increase in fish habitat generalists, a dominance shift from branching to massive/ sub-massive corals and increasing site-based coral genera richness between years. Fish and coral communities significantly reassembled, but functional trait-based multivariate space remained constant, indicating a turnover of species with similar traits. A compression of coral habitat occurred, with shallow (<5m) and deep (>8m) coral genera shifting towards the mid-depths (5-8m).</p> <p>We show that although reef species assemblages altered post disturbance, new communities retained similar ecosystem functions. This result could be linked to the stressors experienced by urban reefs, which reflect those that will occur at an increasing frequency globally in the near future. Yet, even after shifts to disturbed communities, these fully functioning reef systems may maintain high conservation value.</p>
Supplementary material 1 from: Woch MW, Kapusta P, Stanek M, Możdżeń K, Grześ IM, Rożej-Pabijan E, Stefanowicz AM (2023) Effects of invasive Rosa rugosa on Baltic coastal dune communities depend on dune age. NeoBiota 82: 163-187. https://doi.org/10.3897/neobiota.82.97275
Detailed information and results of supplementary analyses on the structure of resident plant communities
Disentangling the effects of eutrophication and natural variability on macrobenthic communities across French coastal lagoons
<p>We present here the raw data and scripts to reproduce the results presented in the preprint "Disentangling the effects of eutrophication and natural variability on macrobenthic communities across French coastal lagoons" available on BioRxiv. Before using the scripts and associated data, we recommend reading the "readme" word document also available, which details the information available in the different data sheets. </p> <p>Preprint abstract : </p> <p>Coastal lagoons are transitional ecosystems that host a unique diversity of species and support many ecosystem services. Owing to their position at the interface between land and sea, they are also subject to increasing human impacts, which alter their ecological functioning. Because coastal lagoons are naturally highly variable in their environmental conditions, disentangling the effects of anthropogenic disturbances like eutrophication from those of natural variability is a challenging, yet necessary issue to address. Here, we analyze a dataset composed of macrobenthic invertebrate abundances and environmental variables (hydro-morphology, water, sediment and macrophytes) gathered across 29 Mediterranean coastal lagoons located in France, to characterize the main drivers of community composition and structure. Using correlograms, linear models and variance partitioning, we found that lagoon hydro-morphology (connection to the sea and lagoon surface), which affects the level of environmental variability (salinity and temperature), as well as lagoon-scale benthic habitat diversity (using macrophyte morphotypes) seemed to regulate macrofauna distribution, while eutrophication and associated stressors like low dissolved oxygen, acted upon the existing communities, mainly by reducing species richness and diversity. Furthermore, M-AMBI, a multivariate index composed of species richness, Shannon diversity and AMBI (AZTI's Marine Biotic Index) and currently used to evaluate the ecological state of French coastal lagoons, was more sensitive to eutrophication (18%) than to natural variability (9%), with nonetheless 49% of its variability explained jointly by both. To improve the robustness of benthic indicators like M-AMBI and increase the effectiveness of lagoon benthic habitat management, we call for a revision of the ecological groups at the base of the AMBI index and of the current lagoon typology which could be inspired by the lagoon-sea connection levels used in this study.</p>
Data from: Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean
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Data from: A year in hypoxia: epibenthic community responses to severe oxygen deficit at a subsea observatory in a coastal inlet
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Data from: Persistent differences between coastal and offshore kelp forest communities in a warming Gulf of Maine
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Data from: Purple pitcher plant (Sarracenia rosea) dieback and partial community disassembly following experimental storm surge in a coastal pitcher plant bog
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Data from: Tropical ancient DNA from bulk archaeological fish bone reveals the subsistence practices of a historic coastal community in southwest Madagascar
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Data from: Phytoplankton community interactions and environmental sensitivity in coastal and offshore habitats
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Data from: Effects of vicariant barriers, habitat stability, population isolation and environmental features on species divergence in the south-western Australian coastal reptile community
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A community and functional comparison of coral and reef fish assemblages between four decades of coastal urbanisation and thermal stress.
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Data from: Upgrades of coastal protection infrastructure affect benthic communities
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Long-term Spartina alterniflora invasion simplified soil seed bank and regenerated community in a coastal marsh wetland
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Data from: Post-fire recovery in coastal sage scrub: seed rain and community trajectory
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Identifying mechanisms for successful ecological restoration with salvaged topsoil in coastal sage scrub communities
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Data from: Seawater environmental DNA reflects seasonality of a coastal fish community
Coastal marine fish populations are in decline due to overfishing, habitat destruction, climate change and invasive species. Seasonal monitoring is important for detecting temporal changes in the composition of fish communities, but current monitoring is often non-existent or limited to annual or semi-annual surveys. In the present study, we investigate the potential of using environmental DNA (eDNA) metabarcoding of seawater samples to detect the seasonal changes in a coastal marine fish community. Water sampling and snorkelling visual census were performed over 1 year (from 23rd of August 2013 to 11th of August 2014) at a temperate coastal habitat in Denmark (55°45′39″N, 12°35′59″E) and compared to long-term data collected over a 7-year period. We used Illumina sequencing of PCR products to demonstrate that seawater eDNA showed compositional changes in accordance with seasonal changes in the fish community. The vast majority of fish diversity observed in the study area by snorkelling was recovered from sequencing, although the overlap between methods varied widely among sampling events. In total, 24 taxa were detected by both methods, while five taxa were only detected using eDNA and three taxa were only detected by snorkelling. A limitation of the applied primers was the lack of resolution to species level in a few diverse families, and varying sequencing depth between samples represents a potential bias. However, our study demonstrates the utility of eDNA for recovering seasonal variation in marine fish communities, knowledge of which is essential for standardised long-term monitoring of marine biodiversity.
Supplementary Material to: Hannon, M. C. & Schulze, A: Two-year survey of Alitta succinea (Annelida: Nereididae) in fouling communities with notes on morphology and reproduction. Ocean and Coastal Resources
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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.