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Supplementary data to this article can be found online at https://doi. org/10.1016/j.scitotenv.2021.151783, Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring., The work is the result of the DNAqua-Net workshop held in Rome, on June 10–12, 2019, organised by IRSA-CNR and supported by European Cooperation in Science and Technology (COST) grant CA15219 (DNAqua-Net). It largely benefited from the discussions with DNAqua-Net members during this event as well as other DNAqua-Net conferences.This study was carried out within the UNIVPM VIRIDE Project (n. 2017EKFA98) funded by the Ministry of University and Research of Italy (MUR) and the Italian National Project on the use of environmental DNA for the identification of marine non-indigenous species funded by the Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA). JP, TC, and LAPG were supported by the Swiss National Science Foundation (grant 31003A_179125) as well as FL with an Early Postdoc.Mobility grant (P2GEP3_171829). MS-M was supported by the Ministry of Education, Youth and Sports of the Czech Republic, European Regional Development Fund-Project CZ.02.1.01/0.0/0.0/16_019/0000845 and LTC 20063. KP was supported by the European Regional Development Fund within National Programme for Addressing Socio-Economic Challenges through R&D (L190003VLVI RITA1/02-60-05) and base financed project P190250PKKH of Estonian University of Life Sciences, IM was supported by the Slovenian Research Agency (ARRS) programme P4-0085. SD was supported by the Portuguese Foundation for Science and Technology (FCT) (CEECIND/00667/2017). LC was supported by the PON AIM 1854833 – PON Ricerca e Innovazione 2014–2020 – Azione I.2 – D.D. n. 407, 27/02/2018 – Attraction and International Mobility.VK was supported by grants PUT1389 (ETAg) and Institute of Technology, University of Tartu basic funding grant.

In many urban catchments, the discharge of effluents from wastewater treatment plants (WWTPs), as well as untreated wastewaters (UWWs), presents a major challenge for the maintenance of river sediment and water quality. The discharge of these effluents cannot only increase the concentration of metals, nutrients and organic compounds in fluvial ecosystems, but also alter the abundance, structure and function of river bacterial communities. Here, we present data on chemical and biological quality parameters in wastewater-impacted and non-impacted river surface sediment and water samples. Overall, the concentration of nutrients (inorganic nitrogen) and some heavy metals (Zn, Ni and Cr) was positively correlated with the nirS/16S rRNA ratio, while nirK- and nosZ-denitrifier populations were negatively affected by the presence of ammonium in sediments. Bacterial community structure was significantly correlated with the (i) combined influence of nutrient and metal concentrations, (ii) the contamination level (non-impacted vs. impacted sites), (iii) type of contamination (WWTP or UWW), and (iv) location of the sampling sites. Moreover, the higher abundance of five genera of the family Rhodocyclaceae detected in wastewater-impacted sites is also likely to be an effect of effluent discharge. The data presented here complement a broader study (Martínez-Santos et al., 2018) [1] and they are particularly useful for those interested in understanding the impact of wastewater effluents on the abundance, structure and function of river bacterial communities involved in nitrogen cycling. Keywords: Wastewater, River sediment, Nutrients, Metals, Denitrifying genes, Rhodocyclaceae

Increased exploitation of resources in sensitive marine ecosystems emphasizes the importance of knowledge regarding ecological impacts. However, current bio-monitoring practices are limited in terms of target-organisms and temporal resolution. Hence, developing new technologies is vital for enhanced ecosystem understanding. In this study, we have applied a prototype version of a phylogenetic microarray to assess the eukaryote community structures of marine sediments from an area with ongoing oil and gas drilling activity. The results were compared with data from both sequencing (metabarcoding) and morphology-based monitoring to evaluate whether microarrays were capable of detecting ecosystem disturbances. A significant correlation between microarray data and chemical pollution indicators, as well as sequencing-based results, was demonstrated, and several potential indicator organisms for pollution-associated parameters were identified, among them a large fraction of microorganisms not covered by traditional morphology-based monitoring. This suggests that microarrays have a potential in future environmental monitoring. acceptedVersion