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Nutrients introduced to the environment by finfish aquaculture pose environmental risks, which can be mitigated by robust environmental monitoring. Biological communities in soft sediments are good indicators of aquaculture derived environmental changes. Traditionally, monitoring programs have visually surveyed macrofauna communities. However, DNA metabarcoding is a potentially more efficient alternative. We compared alpha diversity, multivariate dispersion and taxonomic composition of macrofauna communities with metabarcoding derived bacterial and eukaryote communities along an organic enrichment gradient at a salmon farm in Tasmania, Australia. Additionally, we conducted a cost-benefit analysis comparing the approaches. All methods identified indicator taxa that changed in abundance over the enrichment gradient. Macrofauna analysis was the most sensitive method for detecting changes in alpha diversity, while metabarcoding was most sensitive for multivariate dispersion. Taxonomic composition of animal communities derived from the two methods differed drastically. Metabarcoding was cheaper than macrofauna for ≥93 samples and quicker for ≥14 samples. • 16S and 18S rRNA metabarcoding both detect aquaculture derived organic enrichment. • Sediment metazoan communities derived from metabarcoding and visual methods differ. • Metabarcoding was faster than visual identification for 14 or more samples. • Metabarcoding was cheaper than visual identification for 96 or more samples. [ABSTRACT FROM AUTHOR]

This study thoroughly examines three cetacean monitoring methods and assessing their advantages and limitations, establishing a foundational basis for comprehensive information on composition, distribution, and behavior. While real-time and non-invasive, visual surveys favor surface-active cetaceans and are weather-dependent. Local ecological knowledge supplements insights into group behavior. Environmental DNA (eDNA) analysis efficiently detects species like the narrow-ridged finless porpoise (Neophocaena asiaeorientalis) and common bottlenose dolphin (Tursiops truncatus), offering non-invasive, and spatially adept monitoring. Furthermore, eDNA provides prey species information, revealing the narrow-ridged finless porpoise's winter migration to deeper waters due to prey distribution. The study identifies prevalent prey species, like the Japanese Anchovy (Engraulis japonicus) and Osbeck's grenadier anchovy (Coilia mystus), offering insights into the porpoise's feeding ecology and adaptation to changing prey availability in winter. This study systematically compares diverse methodologies employed in cetacean surveys, thereby yielding a comprehensive understanding of cetacean distribution, behavior, and feeding ecology. • Integrating visual surveys, LEK, and eDNA for nuanced cetacean insights. • Fishermen's knowledge enriches research, aiding policy and conservation. • Non-invasive, real-time eDNA monitors cetaceans, enhancing species identification accuracy. • Promoting sustainable fisheries, ecosystem-based strategies for marine coexistence and conservation. [ABSTRACT FROM AUTHOR]

Aquatic ecosystems are deteriorating, with the most impacted species and populations having insufficient data to inform conservation and management. Monitoring aquatic biodiversity and evaluating anthropogenic impacts typically rely on time-consuming, logistically challenging, and invasive methods (e.g., seining, trawling or electrofishing). Environmental DNA (eDNA) methods have been touted as an important advancement, especially in fish biodiversity assessment. We compare eDNA metabarcoding and seining methods along a 350 km section of the Upper St. Lawrence River (Canada) for: i) mapping the distribution of invasive and threatened fish species, ii) describing species richness and fish community structure, and iii) assessing the effect of habitat type and anthropogenic degradation of riparian zones on fish community composition and richness. eDNA detected more fish species (n = 67) than seining (n = 38) and revealed higher fish diversity in samples adjacent to intact, natural riparian zones. Fish assemblages were influenced by habitat type according to analyses using eDNA, while no effect of any environmental predictor on fish community composition was found using seining. Altogether, our results support eDNA metabarcoding as a powerful, complementary tool in fish monitoring and testing for the impacts of anthropogenic disturbances. [ABSTRACT FROM AUTHOR]

We evaluated benthic bacterial communities as bioindicators in environmental impact assessments of salmon aquaculture, a rapidly growing sector of seafood industry. Sediment samples (n = 72) were collected from below salmon cages towards distant reference sites. Bacterial community profiles inferred from DNA metabarcodes were compared to reference data from standard macrofauna biomonitoring surveys of the same samples. Deltaproteobacteria were predominant in immediate vicinity of the salmon cages. Along the transect, significant shifts in bacterial community structures were observed with Gammaproteobacteria dominating the less-impacted sites. Alpha- and beta-diversity measures of bacterial communities correlated significantly with macrofauna diversity metrics and with five ecological status indices. Benthic bacterial communities mirror the reaction of macrofauna bioindicators to environmental disturbances caused by salmon farming. The implementation of bacterial eDNA metabarcoding in future Strategic Framework Directives is an alternative cost-effective high-throughput biomonitoring solution, providing a basis for management strategies in a matter of days rather than months. [ABSTRACT FROM AUTHOR]

Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management. [Display omitted] • The workflow of eDNA metabarcoding technology is summarized. • eDNA metabarcoding technology contributes to effectively biomonitoring. • Invasive species and endangered species are vital detection targets of eDNA method. • Limitations and issues exist in the application of eDNA metabarcoding technology. • eDNA metabarcoding technology is expected to be combined with other technologies. [ABSTRACT FROM AUTHOR]

Metal contamination is a global issue impacting biodiversity in urbanised estuaries. Traditional methods to assess biodiversity are time consuming, costly and often exclude small or cryptic organisms due to difficulties with morphological identification. Metabarcoding approaches have been increasingly recognised for their utility in monitoring, however studies have focused on freshwater and marine systems despite the ecological significance of estuaries. We targeted estuarine eukaryote communities within the sediments of Australia's largest urbanised estuary, where a history of industrial activity has resulted in a metal contamination gradient. We identified specific eukaryote families with significant correlations with bioavailable metal concentrations, indicating sensitivity or tolerance to specific metals. While polychaete families Terebellidae and Syllidae demonstrated tolerance to the contamination gradient, members of the meio- and microfaunal communities including diatoms, dinoflagellates and nematodes displayed sensitivities. These may have high value as indicators but are frequently missed in traditional surveys due to sampling limitations. • We sampled a metal contamination gradient in Australia's largest estuary. • We used eDNA metabarcoding to investigate benthic eukaryote communities. • Polychaete families displayed tolerance to bioavailable metal concentrations. • We found sensitivities of members of the meio- and microfaunal communities. • Metabarcoding offers a promising alternative to traditional monitoring approaches. [ABSTRACT FROM AUTHOR]

Sugar kelp cultivation at the southern end of its range on the east coast of North America is being pursued commercially for human consumption, which demands a high-quality product. Blade quality can be compromised by attached organisms – epibionts. Biweekly examination of epibionts on sugar kelp was conducted April–May 2018, on a kelp farm in eastern Long Island Sound, CT, USA. Culturable Vibrio spp. were not present on kelp blades until May and were limited to only old sections. No Vibrio colonies were human pathogens V. parahaemolyticus or V. vulnificus , based upon ToxR -specific multiplex PCR assays. Neither epibenthic cyanobacteria Lyngbya spp. nor the dinoflagellate Prorocentrum lima, microbes of concern because of toxigenicity, were detected on kelp by microscopy or metabarcoding of partial rRNA genes. The lacy bryozoan was the only epibiotic animal observed that could cause damage to kelp, but its abundance was low. Summarizing most-common sequence reads, Gammaproteobacteria was the most abundant bacterial group on kelp blades (49%) and Alphaproteobacteria were the most abundant in seawater (39%). Bacillariophyta were the most abundant eukaryotes on kelp blades (36%) and Dinoflagellata were the most abundant eukaryotes in seawater (43%). Molecular operational taxonomic unit matrices were used for non-metric multidimensional scaling; the most prominent structure for both prokaryotic and eukaryotic communities was the separation between blade and seawater samples. This spatial separation explained 81% and 76% of the variation among prokaryotic and eukaryotic samples, respectively. Indicator Species Analysis identified Gammaproteobacteria (55%) and Bacillariophyta (56%) to be the most important blade indicator prokaryotes and eukaryotes, respectively. A closer examination of indicator species temporal patterns and their ecophysiology suggested that Aquimarina , Parcubacteria, and Peronosporomycetes are potential pathogens to sugar kelp. Ciliates may be the most important grazers that keep epiphytes (Bacillariophyta, Rhodophyta, and Phaeophyta) and Peronosporomycetes on kelp in check. • Kelp epibiotic microbial communities differ from planktonic microbial communities. • No pathogenic Vibrio or toxigenic epibenthic microalgae were detected. • Aquimarina , Parcubacteria, and Peronosporomycetes are potential kelp pathogens. • Gammaproteobacteria were abundant on kelp, including petroleum-degrading strains. • Benthic diatoms were most abundant microalgae on kelp. [ABSTRACT FROM AUTHOR]