From biomarkers to community composition: Negative effects of UV/chlorine-treated reclaimed urban wastewater on freshwater biota.

The use of urban wastewater reclaimed water has recently increased across the globe to restore stream environmental flows and mitigate the effects of water scarcity. Reclaimed water is disinfected using different treatments, but their effects into the receiving rivers are little studied. Physiological bioassays and biomarkers can detect sub-lethal effects on target species, but do not provide information on changes in community structure.

A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species.

Metabarcoding techniques are revolutionizing studies of marine biodiversity. They can be used for monitoring non-indigenous species (NIS) in ports and harbors. However, they are often biased by inconsistent sampling methods and incomplete reference databases.

DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets.

DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors.

To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography.

Background: The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies.

Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?

In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic communities requires destructive direct sampling or the setting-up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer.

From metabarcoding to metaphylogeography: separating the wheat from the chaff.

Metabarcoding is by now a well-established method for biodiversity assessment in terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used for α- and β-diversity estimates, that is, interspecies (or inter-MOTU [molecular operational taxonomic unit]) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra-MOTU) information-mostly untapped so far.