Dataset supporting the use of nematodes as bioindicators of polluted sediments.

We provide the dataset supporting the research article "Nematodes as bioindicators of polluted sediments using metabarcoding and microscopic taxonomy" [1]. Nematodes are frequently used as bioindicators and the NemaSPEAR[%] is an validated index that is originally based on morphological data. The index was compared to molecular sequence data for the 28S rDNA, 18S rDNA and COI gene for 7 locations. This dataset includes chemical analyses of the sediments for 33 different substances. The sequence data for OTU-based analyses for the 28S rDNA, 18S rDNA and COI gene is given, together with the read distribution during bioinformatics processing. We furthermore include alternative ASV data, based on a cluster-independent approach. The morphological data is presented, including the biomass for each species, as well as an overview about whether the species is represented in the NCBI database. Furthermore, rarefaction analysis is given for the morphological data, and furthermore NMDS plots for the species and genus level based on morphological and molecular data. The correlation between the mean PEC-Q and the NemaSPEAR[%] values is given in order to compare the efficiency of the index, based on morphological and molecular data.

Nematodes as bioindicators of polluted sediments using metabarcoding and microscopic taxonomy.

The use of bioindicator species is a widely applied approach to evaluate ecological conditions, and several indices have been designed for this purpose. To assess the impact of pollution, especially in sediments, a pollution-sensitive index based on nematodes, one of the most abundant and species-rich groups of metazoa, was developed. The NemaSPEAR[%] index in its original form relies on the morphological inspection of nematode species. The application of a morphologically based NemaSPEAR[%] at the genus-level was previously validated. The present study evaluated a NemaSPEAR[%] index based on metabarcoding of nematode communities and tested the potential of fragments from the 28S rDNA, 18S rDNA and cytochrome c oxidase subunit I (COI) genes. In general, molecular-based results tended to show a poorer condition than morphology-based results for the investigated sites. At the genus level, NemaSPEAR[%] values based on morphological data strongly correlated with those based on molecular data for both the 28S rDNA and the 18S rDNA gene fragments (R2 = 0.86 and R2 = 0.74, respectively). Within the dominant genera (>3%) identified by morphology, 68% were detected by at least one of the two ribosomal markers. At the species level, however, concordance was less pronounced, as there were several deviations of the molecular from the morphological data. These differences could mostly be attributed to shortcomings in the reference database used in the molecular-based assignments. Our pilot study shows that a molecularly based, genus-level NemaSPEAR[%] can be successfully applied to evaluate polluted sediment. Future studies need to validate this approach further, e.g. with bulk extractions of whole meiofaunal communities in order to circumvent time-consuming nematode isolation. Further database curation with abundant NemaSPEAR[%] species will also increase the applicability of this approach.

Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities.

Biomonitoring approaches and investigations of many ecological questions require assessments of the biodiversity of a given habitat. Small organisms, ranging from protozoans to metazoans, are of great ecological importance and comprise a major share of the planet's biodiversity but they are extremely difficult to identify, due to their minute body sizes and indistinct structures. Thus, most biodiversity studies that include small organisms draw on several methods for species delimitation, ranging from traditional microscopy to molecular techniques. In this study, we compared the efficiency of these methods by analyzing a community of nematodes. Specifically, we evaluated the performances of traditional morphological identification, single-specimen barcoding (Sanger sequencing), and metabarcoding in the identification of 1500 nematodes from sediment samples. The molecular approaches were based on the analysis of the 28S ribosomal large and 18S small subunits (LSU and SSU). The morphological analysis resulted in the determination of 22 nematode species. Barcoding identified a comparable number of operational taxonomic units (OTUs) based on 28S rDNA (n = 20) and fewer OTUs based on 18S rDNA (n = 12). Metabarcoding identified a higher OTU number but fewer amplicon sequence variants (AVSs) (n = 48 OTUs, n = 17 ASVs for 28S rDNA, and n = 31 OTUs, n = 6 ASVs for 18S rDNA). Between the three approaches (morphology, barcoding, and metabarcoding), only three species (13.6%) were shared. This lack of taxonomic resolution hinders reliable community identifications to the species level. Further database curation will ensure the effective use of molecular species identification.

Dapsone in a Large Tertiary Center: Outdated Therapeutic Option or Timeless Agent?

BACKGROUND: The ancient drug dapsone has antimicrobial and anti-inflammatory features. In dermatology, dapsone is primarily used for neutrophil-dominant skin diseases. However, real-life data assessing the long-term efficacy of dapsone across multiple dermatological diseases is missing. -Objectives: To determine the efficacy and safety of dapsone in patients with inflammatory skin diseases treated at the Department of Dermatology of the University Hospital Zurich. METHODS: The hospital database was searched for patients treated with dapsone in the last 20 years (from January 1, 1998, to December 31, 2017). Overall, 175 patients were included in our study. RESULTS: Thirty-four patients received dapsone for eosinophilic dermatoses, 82 for neutrophilic dermatoses and 59 for other dermatoses. After 3 months, 8% of all patients reached complete remission, 40.6% showed improvement, 30.3% had stable disease, and only 9.1% had disease progression. Final treatment evaluation revealed complete response in 13.2%, disease improvement in 47.4%, stable disease in 25.7% and disease progression in only 12.0%. Patients who showed remission or improvement after 3 months were significantly older than patients with stable or progressive disease. In addition, remission after 3 months was associated with a significantly lower dose of dapsone compared to improvement only. Hemolysis was the most common adverse event (21.7%). CONCLUSIONS: Our data show that dapsone is a valid treatment option in various dermatological diseases, leading to a favorable response in the vast majority of patients. In addition, it is well tolerated, safe and inexpensive. Randomized, controlled trials are needed to further elucidate the role of this high-potential drug.