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  • Wiley  (1,037,719)
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  • 1
    Publication Date: 2024-06-05
    Description: Pattern-triggered immunity (PTI) is an integral part of the innate immune system of many eukaryotic hosts, assisting in the defence against pathogen invasions. In plants and animals, PTI exerts a selective pressure on the microbiota that can alter community composition. However, the effect of PTI on the microbiota for non-model hosts, including seaweeds, remains unknown. Using quantitative polymerase chain reaction complemented with 16S rRNA gene and transcript amplicon sequencing, this study profiled the impact that PTI of the red seaweed Gracilaria gracilis has on its microbiota. PTI elicitation with agar oligosaccharides resulted in a significant reduction in the number of bacteria (by 〉75% within 72 h after treatment). However, the PTI elicitation did not cause any significant difference in the community diversity or structure. These findings demonstrated that PTI can be non-selective, and this might help to maintain a stable microbiota by uniformly reducing bacterial loads.
    Type: Article , PeerReviewed
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  • 2
    Publication Date: 2024-06-05
    Description: Low-level jets (LLJs), vertical profiles with a wind speed maxima in the lowest hundred meters of the troposphere, have multiple impacts in the Earth system, but a global present-day climatology based on contemporary data does not exist. We use the spatially and temporally complete data set from ERA5 reanalysis to compile a global climatology of LLJs for studying the formation mechanisms, characteristics, and trends during the period of 1992–2021. In the global mean, LLJs are detected 21% of the time with more cases over land (32%) than over the ocean (15%). We classified the LLJs into three categories: non-polar land (LLLJ), polar land (PLLJ), and coastal (CLLJ) LLJs. For LLLJ, the averaged frequency of occurrence is 20% and 75% of them are associated with a near-surface temperature inversion as a prerequisite for an inertial oscillation. PLLJs are also associated with a temperature inversion and occur even more frequently with 59% of the time. These are also the lowest and the strongest LLJs among the three categories. CLLJs are particularly frequent in some marine hotspots, situated along the west coast of continents, with neutral to unstable stratification close to the surfaces and a stably stratified layer aloft. We found distinct regional trends in both the frequency and intensity of LLJs over the past decades, which can have implications for the emission and transport of aerosols, and the transport of atmospheric moisture. Future studies could address changes in LLJs and the associated implications in more detail, based on the here released ERA5-based LLJ data. Key Points: - First global comprehensive low-level jet (LLJ) climatology using ERA5 - Polar LLJs are the strongest and most frequent among the detected types - Distinct past trends in regional LLJ frequency and intensity
    Type: Article , PeerReviewed
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  • 3
    Publication Date: 2024-06-05
    Description: Aim Species have different distribution patterns across the globe and among biogeographical regions. The Nearctic and Palaearctic regions share lineages because of their parallel biogeographic histories and ecological conditions. As the number of phylogenetic studies increases, there are more insights into past exchange events between these two regions and their effects on the current distribution of diversity. However, several groups have not been tested and an overall generalization is still missing. Here, we analyse the biogeographic history across multiple genera of odonates to elucidate a general process of species exchange, vicariance and species divergence between these two regions. Location The Holarctic, including the entire Nearctic and the East and West Palaearctic. Taxon 14 genera of Odonata (Insecta). Methods We reconstructed a time-calibrated phylogenetic tree for each genus to determine species relationships and divergence time using 3614 COI sequences of 259 species. Biogeographic ancestral range estimation was inferred for each phylogeny using BioGeoBEARS. Preferred habitat (lotic versus lentic) was established for each species. Results Exchange events were not restricted in time, direction or either lentic habitat or lotic habitat. Most genera crossed between both regions only once, and it was mainly across the Beringia, while three diverse anisopteran genera revealed multiple exchanges. Recent exchanges during the Pleistocene were associated with cold-dwelling and lentic species. Main Conclusions Our finding reveals the absence of a generalizable pattern of species exchange and divergence between the Nearctic and Palaearctic regions; instead, we found lineage-specific biogeographic patterns. This finding highlights the complexity of drivers and functional traits that shaped current diversity patterns. Moreover, it emphasizes that general conclusions cannot be formulated based on one single clade.
    Keywords: biogeography ; climate change ; damselflies ; dragonflies ; Holarctic
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 4
    Publication Date: 2024-06-04
    Description: Aim: The efficiency of animal-mediated seed dispersal is threatened by the decline of animal populations, especially in tropical forests. We hypothesise that large-seeded plants with animal-mediated dispersal tend to have limited geographic ranges and face an increased risk of extinction due to the potential decline in seed dispersal by large-bodied fruit-eating and seed-dispersing animals (frugivores). Location: Atlantic Forest, Brazil, South America. Taxon: Angiosperms. Methods: First, we collected dispersal-related traits (dispersal syndrome, fruit size, and seed size), growth form (tree, climber, and other) and preferred vegetation type (open and closed) data for 1052 Atlantic Forest plant species. Next, we integrated these with occurrence records, extinction risk assessments, and phylogenetic trees. Finally, we performed phylogenetic generalised least squares regressions to test the direct and interactive effects of dispersal-related traits and vegetation type on geographical range size. Results: Large-seeded species had smaller range sizes than small-seeded species, but only for species with animal-mediated dispersal, not for those dispersed by abiotic mechanisms. However, plants with abiotic dispersal had overall smaller range sizes than plants with animal-mediated dispersal. Furthermore, we found that species restricted to forests had smaller ranges than those occurring in open or mixed vegetation. Finally, at least 29% of the Atlantic Forest flora is threatened by extinction, but this was not related to plant dispersal syndromes. Main Conclusions: Large-seeded plants with animal-mediated dispersal may be suffering from dispersal limitation, potentially due to past and ongoing defaunation of large-bodied frugivores, leading to small range sizes. Other factors, such as deforestation and fragmentation, will probably modulate the effects of dispersal on range size, and ultimately extinction. Our study sheds light on the relationship between plant traits, mutualistic interactions, and distribution that are key to the functioning of tropical forests.
    Keywords: defaunation ; extinction risk ; frugivory ; phylogeny ; range size ; seed dispersal ; tropical forest
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 5
    Publication Date: 2024-05-30
    Description: Tropical sea surface temperature (SST) biases can cause atmospheric biases on global scales, hence SST needs to be represented well in climate models. A major source of uncertainties is the representation of turbulent mixing in the oceanic boundary layer, or mixed layer (ML). In the present study we focus on near-inertial wave (NIW) induced mixing. The performance of two mixing schemes, Turbulent Kinetic Energy and K-profile parameterization (KPP), is assessed at two sites (11.5°N, 23°W and 15°N, 38°W) in the tropical Atlantic. At 11.5°N, turbulence observations (eddy diffusivities, shear and stratification) are available for comparison. We find that the schemes differ in their representation of NIWs, but both under-represent the observed enhanced diffusivities below the observed ML. However, we find that the models do mix below the ML at 15°N when a storm passes nearby. The near-inertial oscillations remain below the ML for the following 10 days. Near-inertial kinetic energy (NIKE) biases in the models are not directly correlated with the wind speed, the MLD biases, or the stratification at the ML base. Instead, NIKE biases are sensitive to the vertical mixing scheme parameterization. NIKE biases are lowest when the KPP scheme is used. Key Points: - Observations of inertial oscillations are used to evaluate the performance of two vertical mixing schemes in two high-resolution models - Both the K-profile parameterization and the Turbulent Kinetic Energy closure underestimate the NIW-induced mixing - Near-inertial kinetic energy biases are sensitive to the vertical mixing parameterization
    Type: Article , PeerReviewed
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  • 6
    Publication Date: 2024-05-30
    Description: The toxin-producing dinoflagellate Alexandrium pseudogonyaulax has become increasingly abundant in northern European waters, replacing other Alexandrium species. A. pseudogonyaulax produces goniodomins and lytic substances, which can be cytotoxic toward other organisms, including fish, but we still know little about the environmental conditions influencing its growth and toxicity. Here, we investigated the impacts of different nitrogen sources and light intensities, common bottom-up drivers of bloom formation, on the growth and toxin content of three A. pseudogonyaulax strains isolated from the Danish Limfjord. While the growth rates were significantly influenced by nitrogen source and light intensity, the intracellular toxin contents only showed strong differences between the exponential and stationary growth phases. Moreover, the photophysiological response of A. pseudogonyaulax showed little variation across varying light intensities, while light-harvesting pigments were significantly more abundant under low light conditions. This study additionally highlights considerable physiological variability between strains, emphasizing the importance of conducting laboratory experiments with several algal strains. A high physiological plasticity toward changing abiotic parameters points to a long-term establishment of A. pseudogonyaulax in northern European waters.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 7
    Publication Date: 2024-05-30
    Description: The toxin-producing dinoflagellate Alexandrium pseudogonyaulax has become increasingly abundant in northern European waters, replacing other Alexandrium species. A. pseudogonyaulax produces goniodomins and lytic substances, which can be cytotoxic toward other organisms, including fish, but we still know little about the environmental conditions influencing its growth and toxicity. Here, we investigated the impacts of different nitrogen sources and light intensities, common bottom-up drivers of bloom formation, on the growth and toxin content of three A. pseudogonyaulax strains isolated from the Danish Limfjord. While the growth rates were significantly influenced by nitrogen source and light intensity, the intracellular toxin contents only showed strong differences between the exponential and stationary growth phases. Moreover, the photophysiological response of A. pseudogonyaulax showed little variation across varying light intensities, while light-harvesting pigments were significantly more abundant under low light conditions. This study additionally highlights considerable physiological variability between strains, emphasizing the importance of conducting laboratory experiments with several algal strains. A high physiological plasticity toward changing abiotic parameters points to a long-term establishment of A. pseudogonyaulax in northern European waters.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 8
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    In:  Ecology and Evolution vol. 12 no. e9549 | H2020 European Institute of Innovation and Technology, Grant/Award Number: 813360; Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Grant/ Award Number: 16.161.301
    Publication Date: 2024-05-30
    Description: Monitoring community composition of Foraminifera (single-celled marine protists) pro-vides valuable insights into environmental conditions in marine ecosystems. Despitethe efficiency of environmental DNA (eDNA) and bulk-sample DNA (bulk-DNA) me-tabarcoding to assess the presence of multiple taxa, this has not been straightforwardfor Foraminifera partially due to the high genetic variability in widely used ribosomalmarkers. Here, we test the correctness in retrieving foraminiferal communities by me-tabarcoding of mock communities, bulk-DNA from coral reef sediment samples, andeDNA from their associated ethanol preservative using the recently sequenced cy-tochrome c oxidase subunit 1 (COI) marker. To assess the detection success, we com-pared our results with large benthic foraminiferal communities previously reportedfrom the same sampling sites. Results from our mock communities demonstrate thatall species were detected in two mock communities and all but one in the remainingfour. Technical replicates were highly similar in number of reads for each assigned ASVin both the mock communities and bulk-DNA samples. Bulk-DNA showed a signifi-cantly higher species richness than their associated eDNA samples, and also detectedadditional species to what was already reported at the specific sites. Our study con-firms that metabarcoding using the foraminiferal COI marker adequately retrieves thediversity and community composition of both the mock communities and the bulk-DNA samples. With its decreased variability compared with the commonly used nu-clear 18 S rRNA, the COI marker renders bulk-DNA metabarcoding a powerful tool toassess foraminiferal community composition under the condition that the referencedatabase is adequate to the target taxa.
    Keywords: bulk-sample ; DNA ; community composition ; coral reef ; environmental DNA ; foraminifera ; metabarcoding
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 9
    Publication Date: 2024-05-28
    Description: Persistently high marine temperatures are escalating and threating marine biodiversity. The Baltic Sea, warming faster than other seas, is a good model to study the impact of increasing sea surface temperatures. Zostera marina, a key player in the Baltic ecosystem, faces susceptibility to disturbances, especially under chronic high temperatures. Despite the increasing number of studies on the impact of global warming on seagrasses, little attention has been paid to the role of the holobiont. Using an outdoor benthocosm to replicate near-natural conditions, this study explores the repercussions of persistent warming on the microbiome of Z. marina and its implications for holobiont function. Results show that both seasonal warming and chronic warming, impact Z. marina roots and sediment microbiome. Compared with roots, sediments demonstrate higher diversity and stability throughout the study, but temperature effects manifest earlier in both compartments, possibly linked to premature Z. marina die-offs under chronic warming. Shifts in microbial composition, such as an increase in organic matter-degrading and sulfur-related bacteria, accompany chronic warming. A higher ratio of sulfate-reducing bacteria compared to sulfide oxidizers was found in the warming treatment which may result in the collapse of the seagrasses, due to toxic levels of sulfide. Differentiating predicted pathways for warmest temperatures were related to sulfur and nitrogen cycles, suggest an increase of the microbial metabolism, and possible seagrass protection strategies through the production of isoprene. These structural and compositional variations in the associated microbiome offer early insights into the ecological status of seagrasses. Certain taxa/genes/pathways may serve as markers for specific stresses. Monitoring programs should integrate this aspect to identify early indicators of seagrass health. Understanding microbiome changes under stress is crucial for the use of potential probiotic taxa to mitigate climate change effects. Broader-scale examination of seagrass–microorganism interactions is needed to leverage knowledge on host–microbe interactions in seagrasses.
    Type: Article , PeerReviewed
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  • 10
    Publication Date: 2024-05-28
    Description: 1. The expansion of scientific image data holds great promise to quantify individuals, size distributions and traits. Computer vision tools are especially powerful to automate data mining of images and thus have been applied widely across studies in aquatic and terrestrial ecology. Yet marine benthic communities, especially infauna, remain understudied despite their dominance of marine biomass, biodiversity and playing critical roles in ecosystem functioning. 2. Here, we disaggregated infauna from sediment cores taken throughout the spring transition (April-June) from a near-natural mesocosm setup under experimental warming (Ambient, +1.5 degrees C, +3.0 degrees C). Numerically abundant mudsnails were imaged in batches under stereomicroscopy, from which we automatically counted and sized individuals using a superpixel-based segmentation algorithm. Our segmentation approach was based on clustering superpixels, which naturally partition images by low-level properties (e.g., colour, shape and edges) and allow instance-based segmentation to extract all individuals from each image. 3. We demonstrate high accuracy and precision for counting and sizing individuals, through a procedure that is robust to the number of individuals per image (5-65) and to size ranges spanning an order of magnitude (〈750 mu m to 7.4 mm). The segmentation routine provided at least a fivefold increase in efficiency compared with manual measurements. Scaling this approach to a larger dataset tallied 〉40k individuals and revealed overall growth in response to springtime warming. 4. We illustrate that image processing and segmentation workflows can be built upon existing open-access R packages, underlining the potential for wider adoption of computer vision tools among ecologists. The image-based approach also generated reproducible data products that, alongside our scripts, we have made freely available. This work reinforces the need for next-generation monitoring of benthic communities, especially infauna, which can display differential responses to average warming.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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