<p>Examination of metabarcoding plant DNA traces from Malaise trap samples. A dataset of 79 samples from 21 sites in Germany was analyzed using the ITS2 barcode. This study is part of the project DINA (Diversity of insects in Nature Reserves) to study insect communities in 21 nature reserves in Germany.</p>
<p>Biological invasions are a major challenge for natural systems in the Anthropocene, yet their underlying dynamics often remain insufficiently understood. This project establishes Johnstone’s Whistling Frog (Eleutherodactylus johnstonei) as a new alien amphibian model and reevaluates long-held assumptions about invasion processes and patterns. Native to a small Lesser Antillean island, E. johnstonei has achieved an unexpectedly broad exotic distribution. By integrating ecological, genetic, and microbiome perspectives, this work reveals that the species’ invasion success is driven less by intrinsic biological superiority and more by its compatibility with human-dominated environments.Field surveys conducted 25 years after the frog’s introduction to Colombia demonstrate that its distribution remains tightly associated with urban habitats and their characteristic environmental conditions. Comparative genetic analyses across E. johnstonei, its successful alien congener E. antillensis, and the island endemic E. portoricensis show consistently low genetic diversity in both native and exotic populations, indicating that genetic impoverishment does not preclude invasion success. Instead, species distribution models highlight human footprint as a key predictor of the frog’s wide exotic range. Furthermore, microbiome analyses reveal distinct microbial communities between native and introduced populations, suggesting that microbial restructuring accompanies range expansion and may reflect underlying adaptive or transfer processes.Together, these findings challenge conventional invasion theory by illustrating that islands can act as sources instead of sinks and that species with low genetic diversity can thrive across continents when human-mediated disturbances create favorable conditions. The study argues that conservation strategies should prioritize protecting native habitats over targeting adaptable alien species that succeed largely because of anthropogenic change. More broadly, it calls for a rethinking of "nativeness" in an era of rapid environmental transformation and underscores that the resilience of both macro- and micro-communities - rather than species origin - will shape biodiversity outcomes in the Anthropocene.</p>
<p>TRIO (Transformative intercropping systems for One Health) is a project funded by the Hessian LOEWE excellence cluster program, that investigates the effect of intercropping annual and perennial wheat with medicinal and aromatic plants (MAPs). The project proposes a targeted approach for the integration of deep-rooted annual or perennial taproot plants into crop rotation as a strategy for achieving ecological functional intensification of food production. The scientific objective is to improve the understanding of complex soil–plant, plant–plant, plant–microbiome, and plant–agroecosystem interactions as a foundation for sustainable crop production in the future. Under the stress conditions associated with climate change, this approach aims to achieve increased water and nutrient uptake from soil zones that have previously been underutilized, more complete utilization of solar radiation, greater sequestration of atmospheric carbon in the soil, more diverse and resilient microbiomes in soil, roots, and harvested crops, greater attractiveness to flower-visiting insects, and higher yields and product quality. The targeted improvements in production and quality, modelled using Hesse as an exemplary region, are to be achieved through the intensification of ecological processes. This approach is designed to promote the health of soil, plants, animals, humans, and the planet, and thus follows the One Health approach.</p><p>Related data are available at https://www.ebi.ac.uk/ena/browser/view/PRJEB102902 and https://www.ebi.ac.uk/ena/browser/view/PRJEB102999.</p>
<p>The dataset comprises presence data of arthropods, but also on the groups 'Annelida', 'Bacillariophyta', 'Ascomycota', 'Basidiomycota', 'Bryozoa', 'Chordata', 'Cnidaria', 'Echinodermata', 'Glomeromycota', 'Haptophyta', 'Mollusca', 'Mucoromycota', 'Nematoda', 'Nemertea', 'Ochrophyta', 'Oomycota', 'Porifera', 'Pseudomonadota', 'Rhodophyta', 'Rotifera' and 'Tardigrada'. The arthropods were collected in four different life stages of short rotation coppices (harvested, young (2 years), mature (3 years) and old (4 years)) using 3 different trapping techniques: branch sampling (BS), coloured canopy Malaise traps (MT) and pitfall traps (PIT). In each life stage, three sets of traps were placed (3 sites per life stage) and activated for two weeks, each in May, June, July and August. Once in a month, a branch sampling was conducted. In the branch sampling, 16 trees within a radius of 20m around the canopy Malaise traps were randomly selected and shaken for 10 s. Arthropods fell on a plastic tarpaulin of 1x1 m that was emptied into a collection bottle where the arthropods were stored in 96.7% ethanol.</p><p>The samples were analysed using DNA metabarcoding. In DNA metabarcoding, the Cytochrome Oxidase I-Region was targeted using the primers fwhF2 (forward) and fwhR2n (reverse) from Vamos et al 2017 (https://doi.org/10.3897/mbmg.1.14625) The sequences found in the samples were matched with sequences in the BOLD database. The sequences displayed are already grouped like it is known from OTUs. For this grouping, all sequences with a similarity of 97% were compiled, which means that the grouped sequences finally comprise different genetic variants of the same taxa. For each hit in the database, a plausibility check was performed by comparing the distribution range of a species (calculated from GBIF coordinates) and the trapping locations. For each detection of a sequence in a sample, the number of reads is also given. A flagging system helps the user to estimate the degree of uncertainty arising from each species hit.</p><p>This data and the data in the datasets "https://doi.org/10.15468/9pzhm6" and "https://doi.org/10.15468/9pzhm6" belongs to one study.</p>
The project examined the effects of substrate type, water depth, oxygen, temperature and proximity to shore for macrofaunal invertebrates inhabiting mineral-rich hardgrounds in the southern California Borderland, USA. Rocks were collected individually in isolated compartments by the Hercules and SuBastian ROVs. A total of 3,555 macrofauna individuals were counted, and 416 different morphospecies (excluding encrusting bryozoans and hydrozoans) were identified from 82 rocks at depths between 231 and 2,688 m. Details are provided in Guraieb M, Mendoza G, Mizell K, Rouse G, McCarthy RA, Pereira OS, Levin LA. 2024. Deep-ocean macrofaunal assemblages on ferromanganese and phosphorite-rich substrates in the Southern California Borderland. Some of the specimens reside in the Scripps Institution of Oceanography Benthic Invertebrate Collection. This research was supported by NOAA OER awards NA19OAR110305 and NA23OAR0110520. The Ocean Exploration Trust and the Schmidt Ocean Institute funded additional ship time. Our research benefited immensely from the expertise of taxonomic specialists Oliver Ashford, Tim O’Hara, and Charlotte Seid, who played crucial roles in identifying specimens. Additionally, we acknowledge Ailish Ullman, Ximena Flores, and Ana Patricia Galindo for their important contributions in the laboratory; and Devin Vlach for his contributions aboard R/V Falkor and E/V Nautilus. This work would not have been possible without the collective efforts and dedication of all involved.
<p>The De Maten pond dataset contains data on local pond conditions and taxonomic community composition of phytoplankton, zooplankton, macro-invertebrates and fish from 34 interconnected fish ponds in the "De Maten" nature reserve (Limburg, Belgium).</p>
<p>The B-BLOOMS2 dataset resulted from the monitoring of 4 Belgian reference lakes during the bloom seasons in 2007 and 2008. It is composed of 278 sample events for which 17 environmental parameters are available, as well as HPLC based pigment analysis, zooplankton counting, proportion of cyanobacterial populations (from genus to species), and MC-LR concentrations determined by ELISA. Molecular data acquired during this project are also available (http://hdl.handle.net/2268/213145). </p><p>These data were acquired with the financial support of BELSPO in the frame of the Science for a Sustainable Development programme funding the project B-BLOOMS2 (SD/TE/01). The final report is available at: http://www.bblooms.be/BBLOOMS2_FinalReport.pdf</p>
<p>The database of the PONDSCAPE project (Towards a sustainable management of pond diversity at the landscape level) comprises taxon occurrence data of eight different organism groups (bacteria, phytoplankton, diatoms, cladoceran, macro-invertebrates (mollusks, heteropterans and coleopterans), macrophytes, amphibians and fish) and data on physical, chemical and morphometric variables of 125 farmland ponds covering five biogeographic regions in Belgium/Luxembourg</p>
<p>The dataset contains data on arthropods which was derived from DNA metabarcoding. The DNA metabarcoding was performed for samples from coloured canopy Malaise traps, caterpillar traps, branch sampling and blue and white pan traps. The traps were selected to capture predominantly flying insects, especially butterflies and hoverflies. They were placed as a defined set in four different habitat types: 'Forest (Beech and oak)', 'Centre of a short rotation coppice', 'Margin of a short rotation coppice' and 'Maize field'. There existed three replicates of each habitat type. The coloured canopy Malaise traps were equipped with blue, yellow and white cotton cloth panels (50 x 35 cm) and hung in a wooden frame four metres above ground. The caterpillar traps consisted of a dark-green plastic tarpaulin, which was stretched between trees and tapered towards the ground. At its lowest point, insects were collected with a capture bottle, which was attached to the tarpoulin with a fine gauze. The branch sampling was conducted by tabbing 100 tree branches and shaking ten trees at each site. In the corn fields, the shaking was replaced by another interval of tabbing. The blue and white pan traps were placed next to each other on a wooden table, one metre above ground. The pans were enlarged at the top with fine gauze to prevent from overfloating in the case of rain. All insects were captured and stored in 96.6% ethanol. The traps were operated in 15-day sampling intervals, each in June, July and August 2021. For DNA metabarcoding, the samples of each sampling interval and method were compiled. The DNA metabarcoding was performed following the method of Hausmann et al (2020): 'Toward a standardized quantitative and qualitative insect monitoring scheme. Ecology and Evolution, 10, 4009–4020'. Briefly, a lysis volume of 5-10 ml of the dried and homogenized composite samples was used for DNA extraction. The mitochondrial Cytochrome c Oxidase subunit I gene (COI) was amplified for species identification (see Leray et al. (2013): 'A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Frontiers in Zoology, 10, 34' and Morinière et al. (2016): 'Species Identification in Malaise Trap Samples by DNA Barcoding Based on NGS Technologies and a Scoring Matrix. PLOS ONE, 11, e0155497'. The resulting metabarcoding data contains the OTU sequences from the samples and their corresponding identities from the Barcode of Life database (BOLD, Ratnasingham and Hebert 2007), the database of the National Center for Biotechnology Information (NCBI) and the Ribosomal Database Project (RDP) classifier. For the two databases, the overlap between the OTU sequence and the database entry determined the determination depth (97-100%: species, 95-97%: genus; 90-95%. family, 85-90%: order, 80-85%: class, 75-80%: phylum, <75%: domain). Each taxonomic determination level of the RDP-classifier is additionally displayed with a bootstrap value. The table also provides data on the red list Germany and Bavaria for each entry.</p><p>The dataset is used in: Hoffmann, L. & Stoll, S. (2025) Catch effectiveness, complementarity and costs of five sampling techniques for flying insects across different land use types. Insect Conservation and Diversity, 1–12. Available from: https://doi.org/10.1111/icad.12839</p>
<p>This dataset presents newly collected records of amphipod specimens gathered during the 2024 scientific benthic survey (Cruise DOG24) at the Dogger Bank, North Sea, part of an ongoing annual monitoring effort that has taken place from 1991 to 2024. A total of 8,444 specimens of 14 species belonging to 13 families, 14 genera, and 10 species were identified using morphological methods with Leica M60 and DM750 microscopes. Amphipods, key components of marine benthic ecosystems, were sampled by beam trawl over the Dogger Bank’s stable sandy substrate. This dataset supports a broader research project aimed at (i) developing a taxonomic key for Dogger Bank amphipods, (ii) identifying environmental drivers of species distribution and diversity, and (iii) predicting responses to climate change. Data were structured following the Darwin Core standard.</p><p>The Dogger Bank epibenthos is sampled with a 2 m beam trawl at 37 stations on a yearly basis since 1991 by Senckenberg Marine Zoology. At each station, the catch is sieved to preserve the fine fraction (1 cm - 1 mm), while megafaunal animals are sorted, identified and recorded by their abundance on board of RV Senckenberg. The crustacean and Ichthyology collections at Senckenberg Marine Zoology house the fine fractions from these cruises. In this project, we aim to identify the amphipod species composition and relative abundance from these fine fractions. Starting with the analysis of the fine fractions from the year 2024, we will step by step enhance the dataset with identifications of amphipod fine fractions from other years, back until 1991.</p>
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