Search Results (6)

The SPEcies At Risk index for metals (${\mathrm{SPEAR}}_{metal}$ index) was refined using updated physiological sensitivity data and validated to assess the ecological impact of metal contamination on benthic macroinvertebrate communities in the upper Nakdong River, near a Zn smelter in Korea. Biosurvey and chemical monitoring data were collected at 18 sites surrounding the smelter and nearby mines. Acute ecotoxicity tests on 20 indigenous species from the Korean peninsula were conducted and used to update taxon-specific metal sensitivity data. The refined ${\mathrm{SPEAR}}_{metal}$ index, based on this updated sensitivity, was significantly lower than previous versions, with most values below the severe impact threshold (0.5) in the main stream. The correlation between hazard quotients in water and the SPEAR index improved, with the correlation coefficient increasing from 0.63 to 0.70. Despite consistently high benthic macroinvertebrate indices (BMIs) across the study area, generic ecological indices, such as total richness, EPT (Ephemeroptera, Plecoptera, and Trichoptera taxa richness), and Shannon’s diversity index, showed correlations with metal contamination levels. Principal component analysis identified the ${\mathrm{SPEAR}}_{metal}$ index as the primary indicator associated with metal contamination in both water and sediment. These findings highlight the improved performance of the refined ${\mathrm{SPEAR}}_{metal}$ index as a more sensitive and specific tool for assessing the ecological status of metal-impacted aquatic ecosystems compared to traditional indices. Full article

Biodiversity response-based diagnostic tools are nonlinear approaches that simultaneously consider complex environmental stressors. Such approaches have been used to quantify biological responses to environmental changes. This study identified the major environmental stressors of community turnover and corresponding thresholds by applying diagnostic tools that use multiple biological assemblages in a large river with artificially controlled flow. Four Gradient Forest models were constructed using the relationships between stream biological assemblage and 66 parameters over 12 years. The multi-stressors that caused community turnover and their thresholds differed depending on the biological assemblage, even under the same environmental conditions. Specifically, they showed that operation of weirs has increased the importance of certain species (e.g., non-native species). In addition, specific-taxon response to multi-stressors analysis identified the ecological or management thresholds of endangered species, Korean endemic species, non-native species, and legal pollution indicator species, which must be managed from a biodiversity perspective. These thresholds are significant as the first reference points presented in similar ecological environments and can be used as guidelines for species over the long term. We propose that ‘true’ threshold identification requires efforts to recognize and improve the limitations of GF techniques confirmed in this study. This may ultimately enable a sustainable aquatic ecosystems maintenance and biodiversity preservation. Full article

Copper (Cu), zinc (Zn), and nickel (Ni) are essential micronutrients for aquatic life, but they produce adverse effects on aquatic organisms when environmental concentrations exceed a certain threshold. The objective of this study was to analyze the taxon-specific sensitivities of aquatic life to the three metals and assess ecological risks at exposure levels prevalent in the Songhua River, China. The results showed that sensitivities to these metals varied among different taxonomic groups, with intra-taxon sensitivities being lower than inter-taxa sensitivities, and the consistency of intra-taxon sensitivity increased from phylum to order. The maximum detected concentrations of Cu, Zn, and Ni in the Songhua River were 52.7, 166.0, and 65.3 μg/L, respectively, which met the water quality standards set by China but exceeded the chronic criteria established by the USA. A probabilistic risk assessment based on chronic toxicity data revealed that these three metals posed an intermediate to high risk to aquatic animals, with maximum risk products of 36.4% for Cu, 14.3% for Ni, and 6.2% for Zn, respectively. These results indicate that the ecological damage of heavy metals in the Songhua River cannot be ignored. Full article

Climate warming is expected to drive an upward altitudinal shift of species distributions in mountain areas. In this study, we consider how environmental variables constrain the distribution of freshwater mollusks across elevations based on an extensive survey of the entire Pyrenean range. Results show that several altitude-related variables are significantly relevant for the distribution of all mollusks (i.e., temperature, sediment organic content). Others respond more precisely to some variables: fine substrate proportion increases the probability of finding Pisidium sensu lato (mostly Euglesa species), and the latter, the macrophyte presence, and Ampullaceana balthica. Despite the low acid-neutralizing capacity in many of the lakes, only the distribution of A. balthica was significantly constrained by this factor, independent from elevation. The results confirm a likely altitudinal expansion of the distributions of all species, particularly toward lakes with a summer surface temperature increasing above 12 °C. The pace of change is expected to differ among species according to different nonlinear thresholds in thermal response, which temperature value increases from Pisidium s.l. to Ampullaceana to Ancylus, and the taxon-specific sensitivity to substrates and chemical conditions. Full article

Emerging virus diseases present a global threat to public health. To detect viral pathogens in time-critical scenarios, accurate and fast diagnostic assays are required. Such assays can now be established using mass spectrometry-based targeted proteomics, by which viral proteins can be rapidly detected from complex samples down to the strain-level with high sensitivity and reproducibility. Developing such targeted assays involves tedious steps of peptide candidate selection, peptide synthesis, and assay optimization. Peptide selection requires extensive preprocessing by comparing candidate peptides against a large search space of background proteins. Here we present Purple (Picking unique relevant peptides for viral experiments), a software tool for selecting target-specific peptide candidates directly from given proteome sequence data. It comes with an intuitive graphical user interface, various parameter options and a threshold-based filtering strategy for homologous sequences. Purple enables peptide candidate selection across various taxonomic levels and filtering against backgrounds of varying complexity. Its functionality is demonstrated using data from different virus species and strains. Our software enables to build taxon-specific targeted assays and paves the way to time-efficient and robust viral diagnostics using targeted proteomics. Full article

We have recently developed a computational approach for hierarchical, genome-based classification of viruses of a family (DEmARC). In DEmARC, virus clusters are delimited objectively by devising a universal family-wide threshold on intra-cluster genetic divergence of viruses that is specific for each level of the classification. Here, we apply DEmARC to a set of 56 filoviruses with complete genome sequences and compare the resulting classification to the ICTV taxonomy of the family Filoviridae. We find in total six candidate taxon levels two of which correspond to the species and genus ranks of the family. At these two levels, the six filovirus species and two genera officially recognized by ICTV, as well as a seventh tentative species for Lloviu virus and prototyping a third genus, are reproduced. DEmARC lends the highest possible support for these two as well as the four other levels, implying that the actual number of valid taxon levels remains uncertain and the choice of levels for filovirus species and genera is arbitrary. Based on our experience with other virus families, we conclude that the current sampling of filovirus genomic sequences needs to be considerably expanded in order to resolve these uncertainties in the framework of genetics-based classification. Full article