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44 results for “Marine biology”
Fig. 2 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species
Fig. 2 | Limit of detection, sample exclusion, and microbial biomassestimation for FMP101 dataset. a Application of KatharoSeq formula to calculate limit of detection of microbiota platesusing the Bacillus/Paracoccus mock community (1150 reads at 90%). b Limit of detection based on cell counts of Bacillus/ Paracoccus mock community (~16 cells into extraction at 90%). c Model fit of the log(sequencing read counts) of positive extraction controls vs. the log cell counts of those positive extraction controls (empirically determined using plate counts. The linear regression of the line is indicative of the quality of method to estimate microbial biomass from sequencing read counts. Con- fidenceintervalsof 95% aredisplayedas dottedlines. Thismethodissimilar to a qPCR curvewherethe log (Ct) would beequivalent to the log(read counts).This equation is then used to estimate the number of "microbial density" of the existing samples which is then further normalized by the volume of the DNA extraction,biomass of materialgoinginto theextraction and finallynormalized to at estimated microbial cells per gram of tissue. d Community analysis comparison and validation of compositionality of controls of twosets of mock community controls (section 1 = Bacillus/Paracoccus mock community; section 2 = zymo mock community). Putative contaminant g__Geobacillus identified (presentin 93% of negatives and higherrelative abundance ascompared to positives and samples). e Number of samples successful across the four body sites collected from the broad fish microbiota dataset. QC quality control, g__ refers to a genus of bacteria, HM mock homemade mock or human made mixture of bacteria to use as a control whereas zymo mock = mock microbial community created by a company "Zymo".
Fig. 1 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species
Fig. 1 | Samplingdesignof 116 speciesof marine fish. a Using ArcGIS todepictthe general area from which fish were sampled: black dots indicate the locations of the 101 unique species of marine fish sampled from the California Current Ecosystem in the Eastern Pacific Ocean primarily in the waters of San Diego CA. Red circles depict the locations of an additional 17 species of fish (15 unique species with 2 species duplicates) collected from the Western Atlantic primarily in the waters of New York. When multiple species of fish were caught in the same location, a single circle is used to indicate the location. b Fish were sampled across a gradient of depth and distances from shore. c Biometric measurements taken for nearly all fish include total length, fork length, mass, gape, and GI length. Various ratios from these lengths were also calculated. Microbiota samples from the gill were primarily whole tissue specimens from the entire left second gill arch or a section of the top middle and bottom of the entire filament. Skin mucus samples were taken by scraping using a razor blade. Midgut digesta material was collected from directly posterior of the stomach or if stomach was absent, the beginning of the GI tract. Hindgut digesta samples were taken from near the anus. Image from phylopic. MG midgut, HG hindgut, GI gastrointestinal tract, m meters.
Biological and biogeochemical responses of benthic communities to marine heatwaves - BioHeat
<p>The dataset presents data from a laboratory experiment exploring the effect of heatwaves of different intensities on benhic bioturbation, community excretion and biogeochemical cycling of solutes. <span>We tested the effects of short-term, moderate and strong marine heatwaves on macrofauna bioturbation and associated solute fluxes as examples of ecosystem functioning. We also measured macrofaunal excretion rates to assess effects of temperature on macrofauna metabolism. For this experiment, we used unmanipulated sediment cores with natural animal communities collected from a muddy location at 32 m depth in the northern Baltic Sea. Despite the mechanistic effect of bioturbation remaining unchanged between the treatments, there were significant differences in oxygen consumption, solute fluxes and excretion. Biogeochemical and biological processes were boosted by the moderate heatwave, whereas biogeochemical cycling seemed to decrease under a strong heatwave.</span></p>
Biological and biogeochemical responses of benthic communities to marine heatwaves - BioHeat
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Data from: The core of the matter – Importance of identification method and biological replication for benthic marine monitoring
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Integrating univariate niche dynamics in species distribution models: a step forward for marine research on biological invasions
<p>Aim The development of approaches to predict the distribution and potential expansion of invasive species is still an open challenge. Here our goal is to improve the modelling procedure for marine invaders by coupling Species Distribution Models (SDMs) with an analysis of their univariate niche dynamics. In particular, we tested for the first time whether choosing model predictors among the stable niche dimensions was effective in improving predictions of invasive species expansion.<br> Location Mediterranean Sea<br> Taxon Dusky spinefoot, Siganus luridus.<br> Methods We analysed the univariate niche dynamics for S. luridus across its native and invaded ranges, by applying a standardized framework that allowed the identification of cases of niche stability or shift. We compared inter-range transferability of SDMs fitted with different combinations of labile or stable predictors. Finally, we evaluated interactions in SDM settings (calibration area, model technique and predictors set) on models' predictive ability, using independent data from the most recent phase of invasion.<br> Results We detected a pattern of niche stability for several variables, especially salinity and bathymetry, which positively influenced model inter-ranges transferability: when the models calibrated in the native range include only stable niche axes, predictive ability is improved. We also identified a shift toward lower surface temperatures in the introduced range, which were almost never experienced by the species before invasion. The model calibrated within the combined ranges was the most ecologically congruent. Also, models calibrated in the invaded range allowed a correct prediction of range expansion, with the predicted suitable areas only slightly underestimated.<br> Main conclusions We provide the first evidence that using conserved predictors in SDMs improves inter-range projections of expanding invasive species. Variable selection, calibration area and modelling technique all matter when modelling invasive species, with important interaction effects. We provide guidelines on how to improve SDMs applications in biological invasion research.</p>
Code and data sets analysed in: "Marine heatwave bleaching causes mass mortality and drives a microbial community reorganisation in an ecologically important temperate sponge" Bell et al. (2024). Global Change Biology
<p>The attached zipped folder contains in-situ, satellite, reanalysis and laboratory measurements, together with R and MATLAB scripts, to reproduce the results in Bell et al. (2024). Marine heatwave bleaching causes mass mortality and drives a microbial community reorganisation in an ecologically important temperate sponge. Global Change Biology. Each folder contains a read me file that describes the enclosed data sets and scripts.</p>
Data from: Environmental and biological controls on the diversity and ecology of Late Cretaceous through early Paleogene marine ecosystems in the U.S. Gulf Coastal Plain
The late Mesozoic through early Cenozoic is an interval of significant biologic turnover and ecologic reorganization within marine assemblages, but the timing and causes of these changes remain poorly understood. Here, we quantify the pattern and timing of changes in the diversity (richness and evenness) and ecology of local (i.e., sample level) mollusk-dominated assemblages during this critical interval using field-collected and published datasets from the US Gulf Coastal Plain. We test whether the biologic and ecologic changes observed primarily at the global level during this time are also expressed at the local level, and whether the end Cretaceous (K/Pg) mass extinction and recovery moderated these trends. To explore whether environment had any effect on these patterns, we examine data from shallow subtidal and offshore settings. Assemblages from both settings recovered to pre-extinction diversity levels rapidly, in less than 7 million years. Following initial recovery, diversity remained relatively unchanged in both settings. The trajectory of ecological restructuring was distinct for each setting in the wake of the K/Pg extinction. In offshore assemblages, the abundance and number of predatory carnivorous taxa dramatically increased, and surficial sessile suspension feeders were replaced by more active suspension feeders. In contrast, shallow subtidal assemblages did not experience ecological reorganization following the K/Pg extinction. The distinct ecological patterns displayed in each environment follow onshore-offshore patterns of innovation, whereby evolutionary novelties first appear in onshore settings relative to offshore habitats. Increased predation pressure may explain the significant ecological restructuring of offshore assemblages, whereby the explosive radiation of predators drove changes in their prey. Habitat-specific ecological restructuring, and its occurrence solely during the recovery interval, implies that disturbance and incumbency were also key in mediating these ecological changes.
PLATE 1 in Holotypes of ostracods of Order Podocopida from the collection of the Museum of A.V.Zhirmunsky Institute of Marine Biology FEB RAS (Vladivostok)
PLATE 1. SEM images of ostracod valves. 1, Trapezicandona taurica, RV f, holotype; 2, Heterocythereis reticulata, LV f, holotype; 3–6, Semicytherura calamitica: RV and LV f, holotype; 5, 6, LV m (No. 13416) and f (No. 13418), tuberculate variation, paratypes, the Black Sea near Crimea; 7–10, Semicytherura virgata: 7, 8, RV and LV f, holotype; 9, 10, RV and LV m, paratype (No. 13419), the Black Sea near Crimea, Planerskoye Village, 25 m depth, muddy sand. Scale 60 µm.
Data from: Marine protected area restricts demographic connectivity: dissimilarity in a marine environment can function as a biological barrier
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Data from: Environmental and biological controls on the diversity and ecology of Late Cretaceous through early Paleogene marine ecosystems in the U.S. Gulf Coastal Plain
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Integrating univariate niche dynamics in species distribution models: a step forward for marine research on biological invasions
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Figure 1-4 from: Younis EM, Al-Asgah NA, Abdel-Warith A-WA, Gabr MH, Shamlol FS (2020) Analysis of reproductive biology and spawning season of the pink ear emperor Lethrinus lentjan, from marine ecosystem. Zoologia 37: 1-10. https://doi.org/10.3897/zoologia.37.e48475
Figure 1-4 Photomicrographs of ovarian tissue explain the sex change of L. lentjan: (1)male reproductive cells in mature female ovaries; (2) the central cavity (remaining egg channel) inside the testicle; (3) torsion of the ovary wall to the inside to form the seminal canal; (4) brown masses (the porous layer of the remaining ovaries).
Figure 8-11 from: Younis EM, Al-Asgah NA, Abdel-Warith A-WA, Gabr MH, Shamlol FS (2020) Analysis of reproductive biology and spawning season of the pink ear emperor Lethrinus lentjan, from marine ecosystem. Zoologia 37: 1-10. https://doi.org/10.3897/zoologia.37.e48475
Figure 8-11 Histological sections in the ovary of L. lantjan showing the maturation stages of female: (8) immature; (9) early maturation; (10) maturity; (11) spawning. (AO) atretic oocytes, (CY) coalesced secondary oocytes, (EF) empty follicles, (HY) hydrated oocytes, (LP) late perinucleolar, (PP) pre-perinucleolar, (PY) primary yolk vesicle oocytes, (SY) secondary yolk vesicle oocytes.
Figure 5-7 from: Younis EM, Al-Asgah NA, Abdel-Warith A-WA, Gabr MH, Shamlol FS (2020) Analysis of reproductive biology and spawning season of the pink ear emperor Lethrinus lentjan, from marine ecosystem. Zoologia 37: 1-10. https://doi.org/10.3897/zoologia.37.e48475
Figure 5-7 Histological sections in the testis of L. lantjan showing the maturation stages of male: (5) immature; (6) maturity; (7) spawning. (Ps) primary spermatocytes, (Ss) secondary spermatocytes, (S) sperm, (St) spermatids, (Sg) spermatogonia, (Sc& S) sperm cells and sperms outside the seminal vesicles
Fig. 2 in Ichthyoplankton of Arvoredo Biological Marine Reserve, Santa Catarina, Brazil
Fig. 2. Average densities of (a) eggs and (b) larvae collected during the winter and summer periods to six stations in the Arvoredo Biology Marine Reserve (Brazil) in different campaign (1- 1997/1998, 2- 2007/2008, and 3- 2008/2009). The vertical bar represents the confidence interval.
Fig. 4 in Ichthyoplankton of Arvoredo Biological Marine Reserve, Santa Catarina, Brazil
Fig. 4. Relative abundance (%) of eggs collected in the Arvoredo Biology Marine Reserve (Brazil) during the winter (a) and summer (b) in campaign 1 (1997/1998), 2 (2007/2008) and 3 (2008/2009). SI: not identified species.
Fig. 3 in Ichthyoplankton of Arvoredo Biological Marine Reserve, Santa Catarina, Brazil
Fig. 3. Average densities of (a) eggs and (b) larvae collected in the Arvoredo Biology Marine Reserve (Brazil) in to six stations in campaign 1 (1997/1998), twelve stations in campaign 2 (2007/2008) and twelve stations in campaign 3 (2008/2009), during the winter and summer periods. The vertical bar represents the confidence interval.
EduLifeDesks Archive: Biology 260 Occidental College - Biodiversity & Organization of Marine Ecosystems
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Grassystatin G, a new cathepsin D inhibitor from marine cyanobacteria: discovery, synthesis, and biological characterization
GEO Series GSE313283. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing.
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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.