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89 results for “Biomonitoring”

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dryad32/100

Data from: Exploring the temporal variability of a food web using long-term biomonitoring data

Ecological communities are constantly being reshaped in the face of environmental change and anthropogenic pressures. Yet, how food webs change over time remains poorly understood. Food web science is characterized by a trade-off between complexity (in terms of the number of species and feeding links) and dynamics. Topological analysis can use complex, highly resolved empirical food web models to explore the architecture of feeding interactions but is limited to a static view, whereas ecosystem models can be dynamic but use highly aggregated food webs. Here, we explore the temporal dynamics of a highly resolved empirical food web over a time period of 18 years, using the German Bight fish and benthic epifauna community as our case study. We relied on long-term monitoring ecosystem surveys (from 1998 to 2015) to build a metaweb, i.e. the meta food web containing all species recorded over the time span of our study. We then combined time series of species abundances with topological network analysis to construct annual food web snapshots. We developed a new approach, "node-weighted" food web metrics by including species abundances to represent the temporal dynamics of food web structure, focusing on generality and vulnerability. Our results suggest that structural food web properties change through time; however, binary food web structural properties may not be as temporally variable as the underlying changes in species composition. Further, the node-weighted metrics enabled us to detect that food web structure was influenced by changes in species composition during the first half of the time series and more strongly by changes in species dominance during the second half. Our results demonstrate how ecosystem surveys can be used to monitor temporal changes in food web structure, which are important ecosystem indicators for building marine management and conservation plans.

opencc-zeroAug 2019View details →

dryad32/100

Microplastics in Eurasian otter (Lutra lutra) spraints and their potential as a biomonitoring tool in freshwater systems

The ubiquitous nature of microplastics in aquatic ecosystems may have serious implications for aquatic biota. While microplastic research in freshwater ecosystems is increasing, very few studies have assessed the physical presence of microplastics among top predators. The Eurasian otter (Lutra lutra), a top predator of aquatic ecosystems, is one of the most widely distributed otter species and has a broad habitat niche. The opportunistic collection of otter spraints (i.e. feces) presents a valuable opportunity to assess pollutants of freshwater ecosystems through non-invasive means. Here we assessed the prevalence, abundance and concentration of microplastics (100 µm to 5 mm), as well as dietary remains, in 53 spraint samples collected over eight river catchments spanning three regions of Ireland. We found microplastics present in 57% of spraints at an abundance of 1.2 ± 0.1 microplastics (MPs)/spraint (mean ± SE) and a concentration of 3.8 ± 0.6 MPs/g (dry weight). Fibers were the dominant particle type recovered (85%), followed by film (10%). No significant differences in microplastic concentrations were detected between the three regions assessed, or between spraints collected from areas upstream (i.e. 'lower' exposure) or downstream ('higher' exposure) of putative microplastic sources, which were defined using spatial vector data. While microplastic concentrations were not explained by spraint condition (i.e. fresh, drying or dry), spraints collected in autumn had a significantly higher concentration than spring and summer. Furthermore, microplastic abundance or concentration could not be linked to dietary composition based on the items identified. From a trophic perspective, this study showed that the presence of microplastics in the feces of otter are most likely being obtained through its prey (i.e. secondary ingestion). While there may be limitations associated with using spraints as a biomonitoring tool for microplastics in freshwater systems, particularly with respect to otter home range and dietary niche breadth, they could still be employed for a regional assessment of microplastic levels.

opencc-zeroDec 2020View details →

dryad32/100

Raw data for Urine DNA (uDNA) as a non-lethal method for endoparasite biomonitoring: development and validation

Changes in environmental conditions alter host-parasite interactions, raising the need for effective epidemiological surveillance. Developing operational, accurate, and cost-effective methods to assess individual infection status and potential for pathogen spread is a prerequisite to anticipate future disease outbreaks in wild populations. For endoparasites, effective detection of infections usually relies on host-lethal approaches, which are barely compatible with wildlife conservation objectives. Here, we used the brown trout (Salmo trutta) - Tetracapsuloides bryosalmonae host-parasite system to develop a non-lethal method for endoparasite infection detection, hereafter called "uDNA" for urine DNA. The uDNA diagnostic test is based on the amplification of endoparasite DNA from host urine. We sampled wild fish (N = 111) from eight sites, let them excrete in individual buckets filled with mineral water and performed parasite DNA amplification from water filtration. We compared the results of the uDNA diagnostic test for host infection status and parasite load to those from kidney samples (the current standard method). uDNA was sensitive in determining host infection status (even for infected hosts showing no sign of the disease), since up to 90% of fish individuals were correctly assigned to their infection status. The quantity of uDNA detected from the hosts depended on the sampling sites, suggesting a spatial variation in the parasite spread. uDNA was positively, but weakly correlated with parasite load in the kidney. This correlation depended on the severity of macroscopic lesions caused by the disease, and was negative in fish with severely damaged kidney, likely due to impaired urine excretion. The uDNA approach provides novel avenues to non-lethally infer infection parameters from wildlife populations at large spatial scales. By targeting parasite transmission stage, uDNA is also valuable to get insights on the parasite fitness and the ecological and evolutionary dynamics of this host-parasite interaction.

opencc-zeroDec 2021View details →

dryad32/100

Data from: Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

1) Traditional biodiversity assessment is costly in time, money, and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution. 2) We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass-PCR amplification of the COI barcode gene, pyrosequencing, and bioinformatic analysis, which together we call 'metabarcoding.' 3) We construct seven communities of arthropods (mostly insects) and show that it is possible to recover a substantial proportion of the original taxonomic information. We further demonstrate, for the first time, that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information inherent to metabarcoding. 4) Alpha and beta diversity metrics are the raw materials of ecology and the environmental sciences, facilitating assessment of the state of the environment with a broad and efficient measure of biodiversity.

opencc-zeroDec 2011View details →

zenodo32/100

Measuring deposition of ammonia emitted by a dairy farm using biomonitors

Raw data for bachelor project where biomonitors were used to measure nitrogen deposition around a dairy farm.

opencc-by-4.0Jul 2022View details →

dryad32/100

Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

Conservation and management of marine biodiversity depends on biomonitoring of marine habitats, but current approaches are resource-intensive and require different approaches for different organisms. Environmental DNA (eDNA) extracted from water samples is an efficient and versatile approach to detecting aquatic animals. In the ocean, eDNA composition reflects local fauna at fine spatial scales, but little is known about the effectiveness of eDNA-based monitoring of marine communities at larger scales. We investigated the potential of eDNA to characterize and distinguish marine communities at large spatial scales by comparing vertebrate species composition among marine habitats in Qatar, the Arabian Gulf (also known as the Persian Gulf), based on eDNA metabarcoding of seawater samples. We conducted species accumulation analyses to estimate how much of the vertebrate diversity we detected. We obtained eDNA sequences from a diverse assemblage of marine vertebrates, spanning 191 taxa in 73 families. These included rare and endangered species and covered 36% of the bony fish genera previously recorded in the gulf. Sites of similar habitat type were also similar in eDNA composition. The species accumulation analyses showed that the number of sample replicates was insufficient for some sampling sites but suggested that a few hundred eDNA samples could potentially capture >90% of the marine vertebrate diversity in the study area. Our results confirm that seawater samples contain habitat-characteristic molecular signatures and that eDNA monitoring can efficiently cover vertebrate diversity at scales relevant to national and regional conservation and management.

opencc-zeroDec 2019View details →

zenodo32/100

Urinary metabolic dysregulations associated to thirdhand smoke exposure in mice: Implications for human urine biomonitoring

This dataset contains all raw LC-MS and GC-MS data of urine extracts from mice exposed to thirdhand smoke (THS) used in the paper Urinary metabolic dysregulations associated to thirdhand smoke exposure in mice: Implications for human urine biomonitoring. Objective: The goal of this study is to characterize the THS-induced molecular alterations in urine using an LC-MS and GC-MS based untargeted metabolomic approaches. We have selected urine as a target matrix because it is a non-invasive valuable diagnostic biofluid, rich in metabolites that reflect dysregulations of all biochemical pathways, which also has been one of the most widely used biofluid to assess human exposure to tobacco smoke. Experimental groups: Urine extracts were from two mice groups: control group (CTRL, n=5), which was never exposed to THS; and THS exposed group (THS, n=5), which was exposed to THS from weaning (three weeks of age) to 24 weeks weeks without exposure to SHS during the study. Sample extraction: Metabolites were extracted using a mixture of methanol and Milli-Q water. In the case of GC-MS, samples were pre-treated with urease prior metabolite extraction and dried under nitrogen, lyophilized, and derivatized after extraction. Quality control samples (QCs) were prepared by pooling equal volumes of each extract and analysed every five samples to ensure data quality and reproducibility. LC-MS analysis: LC-MS urine extracts were analysed using a 1290 UHPLC system coupled to a 6550 quadrupole time of flight (QTOF) mass spectrometer from Agilent Technologies operated in ESI+ mode. Chromatographic separation was conducted on a ACQUITY UPLC HSS T3 C18 column (1.8 µm, 150 × 2.1 mm, Waters). MS/MS was performed in targeted mode, and the instrument was set to acquire over the m/z range 50-1000, with a default iso width of 4 m/z. The collision energy was fixed at 20 V. GC-MS analysis: GC-MS urine extracts were analysed using a 7890A gas chromatograph coupled to a 7200 QTOF mass spectrometer from Agilent Technologies. The MS was operated in the electron impact ionization mode at 70 eV, with a fixed emission current of 20 µA. Files are named following this code: <ol> <li>Folders: mzDATA: contains GC-MS and LC-MS raw data in mzXML format; LC-MSMS: contains LC-MS/MS data used for identification of metabolites in mzXML format.</li> <li>Analytical approaches: GCMS: data from GC-MS urine extracts; LCMS: data from LC-MS urine extracts.</li> <li>Samples: CTRL: control group; THS: THS exposed group.</li> </ol> Technical information <ol> <li>Sample extraction and data acquisition (single date, range, approximate date): 2016-2017</li> <li>Data analysis (single date, range, approximate date): 2017-2021</li> <li>Geographic location of data collection: <ul> <li>Mice exposure: Department of Molecular, Cell and Systems Biology, University of California, Riverside CA 92521, U.S.A.</li> <li>Sample extraction and data acquisition: Universitat Rovira i Virgili, Departament d’Enginyeria Electrònica, Elèctrica i Automàtica, Tarragona, Spain.</li> </ul> </li> <li>Information about funding sources that supported the collection of the data: This research was funded by the European Union’s Horizon 2020 research and innovation pro-gramme under the Marie Sklodowska-Curie grant agreement No. 660034; the Secretaria d’Universitats i Recerca del Departament d’Empresa i Coneixement de la Generalitat de Catalunya through C.M.’s predoctoral grant number 2020 FI_B2 00118; the Spanish Ministry of Science & Innovation through N.R.’s Juan de la Cierva Incorporación grant No. (IJCI- 2015-23158); N.R.’s Miguel Servet contract (CP19/00060) from Instituto de Salud Carlos III, co-financed by Fondo Europeo de Desarrollo Regional (FEDER), Unión Europea, “Una manera de hacer Europa”; and the Tobacco-Related Disease Research Program (TRDRP) of the University of California under projects 22RT- 0121 and 23DT-0103.</li> </ol>

opencc-by-4.0Oct 2021View details →

ClinicalTrials.gov32/100

Remote Biomonitoring (RBM) for Temperature Surveillance of Mothers and Newborns: Pre-clinical and Clinical Evaluation

ClinicalTrials.gov study NCT04608565. IPD Sharing: NO. Countries: 1. Publications: 10.

closedIPD-NOFeb 2026View details →

ClinicalTrials.gov32/100

Evaluation of Ambulatory Monitoring of Patients After High-risk Acute Coronary Syndrome Using Two Different Systems: Biomonitor-2 and Kardia Mobile

ClinicalTrials.gov study NCT03940066. IPD Sharing: Not stated. Countries: 1. Publications: 6.

restrictedIPD-UNDECIDEDFeb 2026View details →

ClinicalTrials.gov32/100

Biomonitoring and Cardiorenal Syndrome in Heart Failure(BIONICS-HF) Trial

ClinicalTrials.gov study NCT01570153. IPD Sharing: Not stated. Countries: 2. Publications: 22.

restrictedIPD-UNDECIDEDFeb 2026View details →

dryad32/100