Aquatic Macroinvertebrates
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA306791 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3049981_1.fastq.gz | Fastqsanger.gz | |||
| SRR3049981_2.fastq.gz | Fastqsanger.gz | |||
| SRR3049892_1.fastq.gz | Fastqsanger.gz | |||
| SRR3049892_2.fastq.gz | Fastqsanger.gz | |||
| SRR3049982_1.fastq.gz | Fastqsanger.gz |
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Project description:BackgroundAs ecosystem engineers, the construction of dams by beavers alters stream habitat physically and biologically, making them a species of interest for habitat restoration. Beaver-created habitat changes affect a wide range of aquatic invertebrate species. However, despite numerous individual studies of how beavers affect aquatic macroinvertebrate assemblages, there has been no evaluation of the consensus of these effects across studies.MethodologyWe collated and examined studies comparing beaver-created ponds to nearby lotic reaches to determine general trends in aquatic macroinvertebrate richness, density, biomass, and functional composition between habitats. From this evidence, we highight knowledge gaps in how beaver activity affects aquatic macroinvertebrates.ResultsOverall, in the majority of studies, aquatic macroinvertebrate richness was higher in nearby lotic reaches compared to beaver-created ponds, but richness at coarser scales (gamma diversity) increased with the addition of beaver ponds due to increased habitat heterogeneity. Functional feeding group (FFG) patterns were highly context-dependent, though predator taxa were generally more abundant in beaver ponds than adjacent lotic reaches. Site-specific geomorphological changes, coupled with dam or riparian zone characteristics and resulting differences in basal food resources likely shape other FFG responses.ConclusionsWe identify a lack of long-term studies at single or multiple sites and conclude that fine-scale approaches may improve our understanding of the dynamics of macroinvertebrates within the freshwater realm and beyond. Due to the context-dependent nature of each study, further systematic studies of beaver engineering effects across a wider variety of environmental conditions and wetland types will also help inform land and species management decisions, such as where to prioritize protection of beaver habitats in the face of a global freshwater biodiversity crisis, or where to restore beaver populations to deliver maximum benefit.
| S-EPMC9059751 | biostudies-literature
Project description:BackgroundThe Madeira Island (Portugal; 32°24'-33°07'N, 16°16-17°16'W; 796 km2) is an oceanic island located in the North Atlantic, about 980 km south of Portugal and about 700 km west of the African coast. The presence of freshwater invertebrates in oceanic islands has always raised questions concerning dispersal, colonisation and evolution. Therefore, the freshwater fauna of Madeira Island has attracted the interest of many researchers in the past, the first publications going back to the nineteenth century. Initial studies were mainly taxonomic, resulting in a checklist of the Madeira freshwater macroinvertebrates with 240 taxa. As typical from oceanic islands, freshwater invertebrates are characterised by low diversity, with some taxonomic groups absent. Although freshwater Madeiran macroinvertebrates are a well-studied group, geographical information of diversity distribution is still scarce. Therefore, more studies are needed, especially georeferenced data of diversity and distribution of macroinvertebrate assemblages, to provide valuable information for improving knowledge and the development of typologically appropriate monitoring and conservation programmes and restoration strategies for local stakeholders.New informationThe results of the present study revealed 713 occurrences in 40 sampling points in Madeira Island streams. The occurrence data showed 70 different aquatic taxa belonging to 21 orders and 53 families. Amongst our occurrence data, 15 endemic taxa (22.1%) from Madeira Archipelago were found. In addition, different families of Collembola and different taxa of Copepoda (Onychiuridae, Poduridae, Isotomidae, Entomobryidae, Sminthuridae) comprised new records for the Madeira streams. Therefore, further taxonomic and ecological studies on freshwater invertebrates from Madeira Island should be done with a particular focus on these lesser-known groups. Thus, our data increase the geographical data distribution of freshwater macroinvertebrates and their diversity in Madeira Island. This database is an update of geographical information of diversity distribution of Madeira freshwater macroinvertebrates known groups. This information is essential for a better understanding of community composition, diversity, occurrence or spatial distribution, which will help explore different research questions on different research areas, such as community ecology and biogeography.
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Project description:In this study, a trait-based macroinvertebrate sensitivity modeling tool is presented that provides two main outcomes: (1) it constructs a macroinvertebrate sensitivity ranking and, subsequently, a predictive trait model for each one of a diverse set of predefined Modes of Action (MOAs) and (2) it reveals data gaps and restrictions, helping with the direction of future research. Besides revealing taxonomic patterns of species sensitivity, we find that there was not one genus, family, or class which was most sensitive to all MOAs and that common test taxa were often not the most sensitive at all. Traits like life cycle duration and feeding mode were identified as important in explaining species sensitivity. For 71% of the species, no or incomplete trait data were available, making the lack of trait data the main obstacle in model construction. Research focus should therefore be on completing trait databases and enhancing them with finer morphological traits, focusing on the toxicodynamics of the chemical (e.g., target site distribution). Further improved sensitivity models can help with the creation of ecological scenarios by predicting the sensitivity of untested species. Through this development, our approach can help reduce animal testing and contribute toward a new predictive ecotoxicology framework.
| S-EPMC6535724 | biostudies-literature
Project description:In niche-based community assembly theory, it is presumed that communities in habitats with high natural disturbance regimes are less likely to be structured by competitive mechanisms. Laurentian Great Lakes (hereafter Great Lakes) coastal wetlands can experience drastic diel fluctuations in dissolved oxygen levels, severe wave action, ice scour, and near complete freezing during the winter such that conditions are inhospitable for most organisms. The high natural disturbance levels are thought to cause high interannual turnover for aquatic macroinvertebrate communities and support the hypothesis that these communities are less likely to experience less competitive interactions and negative co-occurrence structure. We hypothesize that non-random co-occurrence patterns will be rare in Great Lake coastal wetlands and non-competitive processes (e.g., through shared or differential microhabitat affinities, pollution tolerances, or biotic homogenization) will be more common than competitively driven negative co-occurrence patterns. Null model analysis was performed on 134 macroinvertebrate communities sampled from across the Great Lakes basin from 2000 to 2013. To disentangle the effects of alternative structuring mechanisms (i.e., shared/differential habitat affinities, shared/differential pollution tolerance, and biological homogenization/competitive exclusion), communities were parsed based on the year sampled, the vegetation type from which community samples were collected, and lastly species' functional feeding group assignment or taxonomic group. As expected, very few communities were non-randomly structured; however, all of those that were non-random exhibited showed more negative co-occurrences than by chance. Upon further investigation, these communities consisted of species that are known to overwinter in wetlands, and therefore, avoid having to recolonize after each spring thaw. With expected changes in habitat conditions due to climate change, we propose that null model analyses can be used as an early warning system for community change.
| S-EPMC11612260 | biostudies-literature
Project description:Dispersal is an essential process in population and community dynamics, but is difficult to measure in the field. In freshwater ecosystems, information on biological traits related to organisms' morphology, life history and behaviour provides useful dispersal proxies, but information remains scattered or unpublished for many taxa. We compiled information on multiple dispersal-related biological traits of European aquatic macroinvertebrates in a unique resource, the DISPERSE database. DISPERSE includes nine dispersal-related traits subdivided into 39 trait categories for 480 taxa, including Annelida, Mollusca, Platyhelminthes, and Arthropoda such as Crustacea and Insecta, generally at the genus level. Information within DISPERSE can be used to address fundamental research questions in metapopulation ecology, metacommunity ecology, macroecology and evolutionary ecology. Information on dispersal proxies can be applied to improve predictions of ecological responses to global change, and to inform improvements to biomonitoring, conservation and management strategies. The diverse sources used in DISPERSE complement existing trait databases by providing new information on dispersal traits, most of which would not otherwise be accessible to the scientific community.
| S-EPMC7658241 | biostudies-literature
Project description:Exposure patterns in ecotoxicological experiments often do not match the exposure profiles for which a risk assessment needs to be performed. This limitation can be overcome by using toxicokinetic-toxicodynamic (TKTD) models for the prediction of effects under time-variable exposure. For the use of TKTD models in the environmental risk assessment of chemicals, it is required to calibrate and validate the model for specific compound-species combinations. In this study, the survival of macroinvertebrates after exposure to the neonicotinoid insecticide was modelled using TKTD models from the General Unified Threshold models of Survival (GUTS) framework. The models were calibrated on existing survival data from acute or chronic tests under static exposure regime. Validation experiments were performed for two sets of species-compound combinations: one set focussed on multiple species sensitivity to a single compound: imidacloprid, and the other set on the effects of multiple compounds for a single species, i.e., the three neonicotinoid compounds imidacloprid, thiacloprid and thiamethoxam, on the survival of the mayfly Cloeon dipterum. The calibrated models were used to predict survival over time, including uncertainty ranges, for the different time-variable exposure profiles used in the validation experiments. From the comparison between observed and predicted survival, it appeared that the accuracy of the model predictions was acceptable for four of five tested species in the multiple species data set. For compounds such as neonicotinoids, which are known to have the potential to show increased toxicity under prolonged exposure, the calibration and validation of TKTD models for survival needs to be performed ideally by considering calibration data from both acute and chronic tests.
| S-EPMC6132984 | biostudies-literature
Project description:<p>The study of antimicrobial resistance (AMR) in infectious diarrhea has generally been limited to cultivation, antimicrobial susceptibility testing and targeted PCR assays. When individual strains of significance are identified, whole genome shotgun (WGS) sequencing of important clones and clades is performed. Genes that encode resistance to antibiotics have been detected in environmental, insect, human and animal metagenomes and are known as "resistomes". While metagenomic datasets have been mined to characterize the healthy human gut resistome in the Human Microbiome Project and MetaHIT and in a Yanomani Amerindian cohort, directed metagenomic sequencing has not been used to examine the epidemiology of AMR. Especially in developing countries where sanitation is poor, diarrhea and enteric pathogens likely serve to disseminate antibiotic resistance elements of clinical significance. Unregulated use of antibiotics further exacerbates the problem by selection for acquisition of resistance. This is exemplified by recent reports of multiple antibiotic resistance in Shigella strains in India, in Escherichia coli in India and Pakistan, and in nontyphoidal Salmonella (NTS) in South-East Asia. We propose to use deep metagenomic sequencing and genome level assembly to study the epidemiology of AMR in stools of children suffering from diarrhea. Here the epidemiology component will be surveillance and analysis of the microbial composition (to the bacterial species/strain level where possible) and its constituent antimicrobial resistance genetic elements (such as plasmids, integrons, transposons and other mobile genetic elements, or MGEs) in samples from a cohort where diarrhea is prevalent and antibiotic exposure is endemic. The goal will be to assess whether consortia of specific mobile antimicrobial resistance elements associate with species/strains and whether their presence is enhanced or amplified in diarrheal microbiomes and in the presence of antibiotic exposure. This work could potentially identify clonal complexes of organisms and MGEs with enhanced resistance and the potential to transfer this resistance to other enteric pathogens.</p> <p>We have performed WGS, metagenomic assembly and gene/protein mapping to examine and characterize the types of AMR genes and transfer elements (transposons, integrons, bacteriophage, plasmids) and their distribution in bacterial species and strains assembled from DNA isolated from diarrheal and non-diarrheal stools. The samples were acquired from a cohort of pediatric patients and controls from Colombia, South America where antibiotic use is prevalent. As a control, the distribution and abundance of AMR genes can be compared to published studies where resistome gene lists from healthy cohort sequences were compiled. Our approach is more epidemiologic in nature, as we plan to identify and catalogue antimicrobial elements on MGEs capable of spread through a local population and further we will, where possible, link mobile antimicrobial resistance elements with specific strains within the population.</p>
| phs001260 | dbGaP
Project description:The aims of the present study were to present a methodology for toxicity tests that can be used when analytical resources to verify the test concentrations are limited, and to evaluate whether the sensitivity of a limited number of Ethiopian species to pesticides differs from literature values for, mainly, temperate species. Acute toxicity tests were performed using three Ethiopian aquatic invertebrate species, one crustacean (Diaphanosoma brachyurum) and two insects (Anopheles pharoensis and Culex pipiens) and using the pesticides endosulfan and diazinon. All species-pesticide combinations were tested in duplicate to estimate the consistency, i.e. the intra-laboratory variation, in test results. Daphnia magna was tested as well to allow the test results to be compared directly with values from the literature. Results indicate that the differences between the EC50s obtained for D. magna in this study and those reported in the literature were less than a factor of 2. This indicates that the methodology used is able to provide credible toxicity values. The results of the duplicated tests showed intra-laboratory variation in EC50 values of up to a factor of 3, with one test showing a difference of a factor of 6 at 48 h. Comparison with available literature results for arthropod species using species sensitivity distributions indicated that the test results obtained in this study fit well in the log-normal distribution of the literature values. We conclude that the methodology of performing multiple tests to check for consistency of test results and performing tests with D. magna for comparison with literature values to check for accuracy is able to provide reliable effect threshold levels and that the tested Ethiopian species did not differ in sensitivity from the arthropod species reported on in the literature.
| S-EPMC4921108 | biostudies-literature
Project description:Hydraulic Fracturing Produced Water Metagenomic assembly
| PRJNA341965 | ENA