Environmental DNA effectively captures functional diversity of coastal fish communities

Deciphering environmental factors influencing phytoplankton community structure in a polluted urban river

Tuojiang River Basin is a first-class tributary of the upper reaches of the Yangtze River-which is the longest river in China. As phytoplankton are sensitive indicators of trophic changes in water bodies, characterizing phytoplankton communities and their growth influencing factors in polluted urban rivers can provide new ideas for pollution control. Here, we used direct microscopic count and environmental DNA (eDNA) metabarcoding methods to investigate phytoplankton community structure in Tuojiang River Basin (Chengdu, Sichuan Province, China). The association between phytoplankton community structure and water environmental factors was evaluated by Mantel analysis. Additional environmental monitoring data were used to pinpoint major factors that influenced phytoplankton growth based on structural equation modeling. At the phylum level, the dominant phytoplankton taxa identified by the conventional microscopic method mainly belonged to Bacillariophyta, Chlorophyta, and Cyanophyta, in contrast with Chlorophyta, Dinophyceae, and Bacillariophyta identified by eDNA metabarcoding. In α-diversity analysis, eDNA metabarcoding detected greater species diversity and achieved higher precision than the microscopic method. Phytoplankton growth was largely limited by phosphorus based on the nitrogen-to-phosphorus ratios > 16:1 in all water samples. Redundancy analysis and structural equation modeling also confirmed that the nitrogen-to-phosphorus ratio was the principal factor influencing phytoplankton growth. The results could be useful for implementing comprehensive management of the river basin environment. It is recommended to control the discharge of point- and surface-source pollutants and the concentration of dissolved oxygen in areas with excessive nutrients (e.g., Jianyang-Ziyang). Algae monitoring techniques and removal strategies should be improved in 201 Hospital, Hongrihe Bridge and Colmar Town areas.

Streamlining large-scale oceanic biomonitoring using passive eDNA samplers integrated into vessel's continuous pump underway seawater systems

Passive samplers are enabling the scaling of environmental DNA (eDNA) biomonitoring in our oceans, by circumventing the time-consuming process of water filtration. Designing a novel passive sampler that does not require extensive sample handling time and can be connected to ocean-going vessels without impeding normal underway activities has potential to rapidly upscale global biomonitoring efforts onboard the world's oceanic fleet. Here, we demonstrate the utility of an artificial sponge sampler connected to the continuous pump underway seawater system as a means to enable oceanic biomonitoring. We compared the performance of this passive sampling protocol with standard water filtration at six locations during a research voyage from New Zealand to Antarctica in early 2023. Eukaryote metabarcoding of the mitochondrial COI gene revealed no significant difference in phylogenetic α-diversity between sampling methods and both methods delineated a progressive reduction in number of Zero-Radius Operational Taxonomic Units (ZOTUs) with increased latitudes. While both sampling methods revealed comparable trends in geographical community compositions, distinct clusters were identified for passive samplers and water filtration at each location. Additionally, greater variability between replicates was observed for passive samplers, resulting in an increased estimated level of replication needed to recover 90 % of the biodiversity. Furthermore, traditional water filtration failed to detect three phyla observed by passive samplers and extrapolation analysis estimated passive samplers recover a larger number of ZOTUs compared to water filtration for all six locations. Our results demonstrate the potential of this passive eDNA sampler protocol and highlight areas where this emerging technology could be improved, thereby enabling large-scale offshore marine eDNA biomonitoring by leveraging the world's oceanic fleet without interfering with onboard activities.

Metropolitan pressures: Significant biodiversity declines and strong filtering of functional traits in fish assemblages

Accelerating global urbanization is leading to drastic losses and restructuring of biodiversity. Although it is crucial to understand urban impacts on biodiversity to develop mitigation strategies, there is a dearth of knowledge on the functional structure of fish assemblages spanning the entire city-scale spectrum of urbanization intensity. Here, using environmental DNA sampled from 109 water sites in Beijing, we investigated the taxonomic and functional diversity patterns of fish assemblages across the city and uncovered community-, trait-, and species-level responses to various environmental stressors. By ranking sampling sites into three disturbance levels according to water physiochemical and landcover conditions, we found that both native and non-native fish taxonomic and functional α-diversity decreased significantly with elevating disturbance, as strong disturbance led to the disappearance of many species. However, the quantitative taxonomic and functional β-diversity components of native and non-native fish showed distinct patterns; assemblage turnover dominated native fish β-diversity and decreased with increasing disturbance, whereas species/trait richness differences dominated non-native fish β-diversity and increased with disturbance intensity particularly in lotic waters. RLQ and fourth-corner analyses revealed that fish size, fecundity, diet, and reproductive behaviors were significantly correlated with water quality, with pollution-tolerant, larger-sized native and omnivorous non-native fishes being urban winners, which indicates strong trait-dependent environmental filtering. Potential ecological indicator species were identified based on the sensitivity of fish responses to pollution loads; these were mostly small native species, and many have bivalve-dependent reproduction. Our results demonstrate that, along with native fish assemblage simplification and homogenization, urban stressors exert profound impacts on community trait composition, highlighting the need to consider both biodiversity loss and functional reorganization in combating disturbance of aquatic ecosystems under global urbanization. Furthermore, correlations between cropland cover and water nutrient level suggested that the management of agricultural runoff might be critically important for safeguarding urban water quality.

Is it worthy to use environmental DNA instead of scientific trawling or video survey to monitor taxa in soft-bottom habitats?

Non-extractive techniques such as video analysis are increasingly used by scientists to study marine communities instead of extractive methods such as trawling. Currently, environmental DNA (eDNA) analysis is seen as a revolutionary tool to study taxonomic diversity. We aimed to determine which method is the most appropriate to describe fish and commercial invertebrate diversity comparing bottom trawl hauls, video transects and seawater eDNA. Our results reveal that video detected the lowest number of taxa and trawling the highest. eDNA analysis is powerful to describe marine bony fish communities, but some taxa of importance for the ecosystem such as elasmobranchs, crustaceans or molluscs are poorly detected. This may be due to several factors such as marker specificity, incomplete reference gene databases or low DNA release in the environment. For now, the various methods provide different information and none is exhaustive enough to be used alone for biodiversity characterisation.

Human activities strengthen the influence of deterministic processes in the mechanisms of fish community assembly in tropical rivers of Yunnan, China

Human-induced global alterations have worsened the severe decrease in fish biodiversity in rivers. To successfully reduce the pace of reduction in fish diversity, it is crucial to prioritize the understanding of how human activities impact the processes that shape and maintain fish diversity. Traditional fish survey methods are based on catch collection and morphological identification, which is often time-consuming and ineffective. Hence, these methods are inadequate for conducting thorough and detailed large-scale surveys of fish ecology. The rapid progress in molecular biology techniques has transformed environmental DNA (eDNA) technique into a highly promising method for studying fish ecology. In this work, we conducted the first systematic study of fish diversity and its formation and maintenance mechanism in the Xishuangbanna section of the Lancang River using eDNA metabarcoding. The eDNA metabarcoding detected a total of 159 species of freshwater fishes spanning 13 orders, 34 families, and 99 genera. The fishes in the order cypriniformes were shown to be overwhelmingly dominant. At different intensities of anthropogenic activity, we found differences in fish community composition and assembly. The analysis of the Sloan's neutral community model fitting revealed that stochastic processes were the dominant factor in the shaping of fish communities in the Xishuangbanna section of the Lancang River. We have further confirmed this result by using the phylogenetic normalized stochasticity ratio. Furthermore, our findings indicate that as human activities get more intense, the influence of stochastic processes on the shaping of fish communities decreases, while the influence of deterministic processes eventually becomes more prominent. Finally, we discovered that salinity positively correlated with fish community changes in the high-intensity anthropogenic sample sites, but all environmental factors had little effect on fish community changes in the low-intensity and moderate-intensity anthropogenic sample sites. Our study not only validated the potential application of eDNA metabarcoding for monitoring fish diversity in tropical rivers, but also revealed how fish communities respond to human activities. This knowledge will serve as a solid foundation for the protection of fish resources in tropical rivers.

Environmental DNA Reveals the Impact of Submarine Groundwater Discharge on the Spatial Variability of Coastal Fish Diversity

Submarine groundwater discharge (SGD) has recently been recognized as an influential factor in coastal ecosystems; however, little research has been conducted on its effects on coastal fish diversity. To investigate the relationship between SGD and fish diversity, we conducted a survey at the coastal island scale using the environmental DNA (eDNA) method. Our findings indicate that fish species richness and functional richness peak at stations with high SGD. Environmental variables, such as salinity, dissolved inorganic nitrogen (DIN) concentration, and SGD, significantly influence fish diversity. Carnivore fish richness was negatively correlated with salinity, while planktivore fish richness was positively correlated. Additionally, SGD and DIN concentrations were found to be crucial in shaping omnivorous and pelagic communities, respectively. This study highlights the role of SGD in enhancing nutrient conditions favorable for diverse fish communities and demonstrates the effectiveness of eDNA metabarcoding for rapid marine biodiversity assessment. These findings provide valuable insights for coastal ecosystem monitoring and management.

Stochastic process is main factor to affect plateau river fish community assembly

Plateau river ecosystems are often highly vulnerable and responsive to environmental change. The driving mechanism of fish diversity and community assembly in plateau rivers under changing environments presents a significant complexity to the interdisciplinary study of ecology and environment. This study integrated molecular biological techniques and mathematical models to identify the mechanisms influencing spatial heterogeneity of freshwater fish diversity and driving fish community assembly in plateau rivers. By utilizing environmental-DNA metabarcoding and the null model, this study revealed the impact of the stochastic process on fish diversity variations and community assembly in the Huangshui Plateau River of the Yellow River Basin (YRB) in China. This research identified 30 operational taxonomic units (OTUs), which correspond to 20 different fish species. The findings of this study revealed that the fish α-diversity in the upstream region of Xining is significantly higher than in the middle-lower reach (Shannon index: P = 0.017 and Simpson: P = 0.035). This pattern was not found to be related to any other environmental factors besides altitude (P = 0.023) that we measured. Further, the study indicated that the assembly of fish communities in the Huangshui River primarily depends on stochastic ecological processes. These findings suggested that elevation was not the primary factor impacting the biodiversity patterns of fish in plateau rivers. In plateau rivers, spatial heterogeneity of fish community on elevation is mainly determined by stochastic processes under habitat fragmentation, rather than any other physicochemical environmental factors. The limitations of connectivity in the downstream channel of the river could be taken the mainly responsibility for stochastic processes of fish community in Huangshui River. Incorporating ecological processes in the eDNA approach holds great potential for future monitoring and evaluation of fish biodiversity and community assembly in plateau rivers.

Unlocking Antarctic molecular time-capsules - Recovering historical environmental DNA from museum-preserved sponges

Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of sponges to accumulate eDNA provides an exciting opportunity to reconstruct contemporary communities and ecosystems with high temporal and spatial precision. However, the use of historical eDNA, trapped within the vast number of specimens stored in scientific collections, opens up the opportunity to begin to reconstruct the communities and ecosystems of the past. Here, we define the term 'heDNA' to denote the historical environmental DNA that can be obtained from the recent past with high spatial and temporal accuracy. Using a variety of Antarctic sponge specimens stored in an extensive marine invertebrate collection, we were able to recover information on Antarctic fish biodiversity from specimens up to 20 years old. We successfully recovered 64 fish heDNA signals from 27 sponge specimens. Alpha diversity measures did not differ among preservation methods, but sponges stored frozen had a significantly different fish community composition compared to those stored dry or in ethanol. Our results show that we were consistently and reliably able to extract the heDNA trapped within marine sponge specimens, thereby enabling the reconstruction and investigation of communities and ecosystems of the recent past with a spatial and temporal resolution previously unattainable. Future research into heDNA extraction from other preservation methods, as well as the impact of specimen age and collection method, will strengthen and expand the opportunities for this novel resource to access new knowledge on ecological change during the last century.

Exploring uncharted territory: new frontiers in environmental DNA for tropical fisheries management

Tropical ecosystems host a significant share of global fish diversity contributing substantially to the global fisheries sector. Yet their sustainable management is challenging due to their complexity, diverse life history traits of tropical fishes, and varied fishing techniques involved. Traditional monitoring techniques are often costly, labour-intensive, and/or difficult to apply in inaccessible sites. These limitations call for the adoption of innovative, sensitive, and cost-effective monitoring solutions, especially in a scenario of climate change. Environmental DNA (eDNA) emerges as a potential game changer for biodiversity monitoring and conservation, especially in aquatic ecosystems. However, its utility in tropical settings remains underexplored, primarily due to a series of challenges, including the need for a comprehensive barcode reference library, an understanding of eDNA behaviour in tropical aquatic environments, standardized procedures, and supportive biomonitoring policies. Despite these challenges, the potential of eDNA for sensitive species detection across varied habitats is evident, and its global use is accelerating in biodiversity conservation efforts. This review takes an in-depth look at the current state and prospects of eDNA-based monitoring in tropical fisheries management research. Additionally, a SWOT analysis is used to underscore the opportunities and threats, with the aim of bridging the knowledge gaps and guiding the more extensive and effective use of eDNA-based monitoring in tropical fisheries management. Although the discussion applies worldwide, some specific experiences and insights from Indian tropical fisheries are shared to illustrate the practical application and challenges of employing eDNA in a tropical context.

The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves

Coastal areas host a major part of marine biodiversity but are seriously threatened by ever-increasing human pressures. Transforming natural coastlines into urban seascapes through habitat artificialization may result in loss of biodiversity and key ecosystem functions. Yet, the extent to which seaports differ from nearby natural habitats and marine reserves across the whole Tree of Life is still unknown. This study aimed to assess the level of α and β-diversity between seaports and reserves, and whether these biodiversity patterns are conserved across taxa and evolutionary lineages. For that, we used environmental DNA (eDNA) metabarcoding to survey six seaports on the French Mediterranean coast and four strictly no-take marine reserves nearby. By targeting four different groups-prokaryotes, eukaryotes, metazoans and fish-with appropriate markers, we provide a holistic view of biodiversity on contrasted habitats. In the absence of comprehensive reference databases, we used bioinformatic pipelines to gather similar sequences into molecular operational taxonomic units (MOTUs). In contrast to our expectations, we obtained no difference in MOTU richness (α-diversity) between habitats except for prokaryotes and threatened fishes with higher diversity in reserves than in seaports. However, we observed a marked dissimilarity (β-diversity) between seaports and reserves for all taxa. Surprisingly, this biodiversity signature of seaports was preserved across the Tree of Life, up to the order. This result reveals that seaports and nearby marine reserves share few taxa and evolutionary lineages along urbanized coasts and suggests major differences in terms of ecosystem functioning between both habitats.

Combining environmental DNA and visual surveys can inform conservation planning for coral reefs

Environmental DNA (eDNA) metabarcoding has the potential to revolutionize conservation planning by providing spatially and taxonomically comprehensive data on biodiversity and ecosystem conditions, but its utility to inform the design of protected areas remains untested. Here, we quantify whether and how identifying conservation priority areas within coral reef ecosystems differs when biodiversity information is collected via eDNA analyses or traditional visual census records. We focus on 147 coral reefs in Indonesia's hyper-diverse Wallacea region and show large discrepancies in the allocation and spatial design of conservation priority areas when coral reef species were surveyed with underwater visual techniques (fishes, corals, and algae) or eDNA metabarcoding (eukaryotes and metazoans). Specifically, incidental protection occurred for 55% of eDNA species when targets were set for species detected by visual surveys and 71% vice versa. This finding is supported by generally low overlap in detection between visual census and eDNA methods at species level, with more overlap at higher taxonomic ranks. Incomplete taxonomic reference databases for the highly diverse Wallacea reefs, and the complementary detection of species by the two methods, underscore the current need to combine different biodiversity data sources to maximize species representation in conservation planning.

Using eDNA to survey amphibians: Methods, applications, and challenges

In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.

Local climate modulates the development of soil nematode communities after glacier retreat

The worldwide retreat of glaciers is causing a faster than ever increase in ice-free areas that are leading to the emergence of new ecosystems. Understanding the dynamics of these environments is critical to predicting the consequences of climate change on mountains and at high latitudes. Climatic differences between regions of the world could modulate the emergence of biodiversity and functionality after glacier retreat, yet global tests of this hypothesis are lacking. Nematodes are the most abundant soil animals, with keystone roles in ecosystem functioning, but the lack of global-scale studies limits our understanding of how the taxonomic and functional diversity of nematodes changes during the colonization of proglacial landscapes. We used environmental DNA metabarcoding to characterize nematode communities of 48 glacier forelands from five continents. We assessed how different facets of biodiversity change with the age of deglaciated terrains and tested the hypothesis that colonization patterns are different across forelands with different climatic conditions. Nematodes colonized ice-free areas almost immediately. Both taxonomic and functional richness quickly increased over time, but the increase in nematode diversity was modulated by climate, so that colonization started earlier in forelands with mild summer temperatures. Colder forelands initially hosted poor communities, but the colonization rate then accelerated, eventually leveling biodiversity differences between climatic regimes in the long term. Immediately after glacier retreat, communities were dominated by colonizer taxa with short generation time and r-ecological strategy but community composition shifted through time, with increased frequency of more persister taxa with K-ecological strategy. These changes mostly occurred through the addition of new traits instead of their replacement during succession. The effects of local climate on nematode colonization led to heterogeneous but predictable patterns around the world that likely affect soil communities and overall ecosystem development.

Environmental DNA biomonitoring reveals the human impacts on native and non-native fish communities in subtropical river systems

Subtropical rivers are one of the hotspots of global biodiversity, facing increased risks of fish diversity changes and species extinction. However, until now, human impacts on native and non-native fish communities in subtropical rivers still lack sufficient effort. Here, we used the environmental DNA (eDNA) approach to investigate fish communities in the Dongjiang River of southeast China, a typical subtropical river, and explored the effects of regional land use and local water pollution on fish taxonomic and functional diversity. Our data showed that 90 species or genera of native fish and 15 species or genera of non-native fish were detected by the eDNA approach, and there was over 85% overlap between eDNA datasets and historical records. The taxonomic and functional diversity of all, native and non-native fish communities showed consistent spatial patterns, that is, the upstream of the tributary was significantly higher than that of the mainstream and downstream. Land use and water pollution such as COD and TP were the determinants in shaping the spatial structure of fish communities, and water pollution explained 31.56%, 29.88%, and 27.80% of the structural variation in all, native and non-native fish communities, respectively. The Shannon diversity and functional richness of native fish showed a significant downward trend driven by COD (pShannon = 0.0374; pfunctional = 0.0215) and land use (pShannon = 0.0159; pfunctional = 0.0441), but they did not have significant impacts on non-native fish communities. Overall, this study emphasizes the inconsistent response of native and non-native fish communities to human impacts in subtropical rivers, and managers need to develop strategies tailored to specific fish species to effectively protect water security and rivers.

Multiple interannual records of young-of-the-year identify an important area for the protection of the shortfin mako, Isurus oxyrinchus

The shortfin mako (Isurus oxyrinchus) is the second most fishery-exploited pelagic shark in the Mediterranean Sea, thus its conservation status is a cause for concern. Despite the species has been listed in fishery and trade regulations to hinder its population decline, the lack of knowledge on its distribution patterns and habitats essential for its persistence still hampers the implementation of sound conservation actions. Combining data from local expert knowledge, opportunistic catch records, and Baited Remote Underwater Videos, we show evidence of the interannual presence of young-of-the-year (YOY) I. oxyrinchus in the Pelagie Archipelago (Central Mediterranean Sea). A total of twenty-one individuals ranging 71-92.5 cm FL were incidentally caught (on average 2.3 YOY/1000 hooks) or documented on BRUVS in July and August over three consecutive years. These data coupled with questionnaires administered to longline fishers identify one specific area used by YOY in the summer months. Our study presents the most abundant record of YOY shortfin makos in the Mediterranean Sea within such a restricted time and limited area providing important information for improving the protection of this critically endangered species.

Heterogeneity of Fish Taxonomic and Functional Diversity Evaluated by eDNA and Gillnet along a Mangrove-Seagrass-Coral Reef Continuum

The effective and reliable monitoring of fish communities is important for the management and protection of marine ecosystems. Environmental DNA (eDNA) metabarcoding is a relatively new method that has been widely used in recent years, while traditional sampling via fish catching (i.e., gillnets) is one of the most common and reliable fish monitoring methods used to date. We compared the taxonomic and functional diversity of fish detected within a mangrove-seagrass-coral reef continuum using both survey methods. One liter seawater and gillnet samples were collected in August 2021 from mangrove forests, seagrass meadows and coral reef habitats (n = 3 each) in Hainan, China. Surveys using eDNA and gillnets identified 139 genera belonging to 66 families and 58 genera belonging to 42 families, respectively. Regardless of the survey method, fish detected in mangrove, seagrass and coral reef habitats were heterogeneous in their communities; however, the shared species between habitats suggest some degree of connectivity. There were no significant differences between habitats in terms of taxonomic and functional diversity, but a higher taxonomic diversity was detected using eDNA. Both methods were able to distinguish fish assemblages between different habitats; however, gillnet surveys performed better than eDNA surveys for distinguishing mangrove from seagrass assemblages. Therefore, the concurrent use of eDNA and gillnet survey methods provides a more comprehensive approach to understanding the heterogeneity of fish taxonomic and functional diversity along mangrove-seagrass-coral reef continuums.

To the north: eDNA tracing of the seasonal and spatial dynamics of fish assemblages along the world's largest water diversion project

Extensive water diversion projects that have been increasingly installed worldwide transport essential water resources as well as a large number of biota. However, studies of the dynamic processes of such transport have been limited. The South-to-North Water Diversion Project of China is the largest manmade water diversion system ever constructed. Here, in a year-long project, we used environmental DNA (eDNA) metabarcoding to assess fish biodiversity and assemblage composition along the Project's 1277-km main canal, while also investigating the temporal, spatial, and functional trait drivers of changes in the fish assemblages. Together, 45 fish taxa were detected, with substantial compositional variations between seasons. The number of detected species typically dropped upon entering the canal but remained relatively constant along the canal's length. Spatial variations in fish assemblages were generally dominated by the turnover component over nestedness, and a positive spatial autocorrelation of qualitative assemblage composition was detected within 80 km in all seasons. Furthermore, several functional traits, such as smaller body size, invertivorous diet, rheophilic living, and lithophilic and demersal spawning, were positive predictors of fish presence along the length of the canal and they may boost species chances of introduction to the recipient areas. Our results provide crucial information for ecological management of diversion projects and have key implications for modelling and predicting foreign species invasion through water transfers.

Fish eDNA detections in ports mirror fishing fleet activities and highlight the spread of non-indigenous species in the Mediterranean Sea

Gathering comprehensive marine biodiversity data can be difficult, costly and time consuming, preventing adequate knowledge of diversity patterns in many areas worldwide. We propose fishing ports as "natural" sinks of biodiversity information collected by fishing vessels probing disparate habitats, depths, and environments. By combining rapid environmental DNA metabarcoding (eDNA) surveys and data from public registers and Automatic Identification Systems, we show significant positive relationships between fishing fleet activities (i.e. fishing effort and characteristics of the fishing grounds) and the taxonomic fish assemblage composition in eleven Mediterranean fishing ports. Overall, we identified 160 fish and 123 invertebrate OTUs, including at least seven non-indigenous species, in some instances well beyond their known distribution areas. Our findings suggest that eDNA assessments of fishing harbours' waters might offer a rapid way to monitor marine biodiversity in unknown or under-sampled areas, as well as to reconstruct fishing catches, often underreported in several regions.

Pragmatic applications of DNA barcoding markers in identification of fish species – a review

DNA barcoding and mini barcoding involve Cytochrome Oxidase Subunit I (COI) gene in mitochondrial genome and is used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging between 500 to 700 base pairs for fish species in DNA barcoding and 80 to 650 base pairs for DNA mini barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method focuses on the analysis of short-length DNA markers has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA meta-barcoding refers to the automated identification of multiple species from a single bulk sample. The may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini barcoding and meta-barcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.

Capturing marine microbiomes and environmental DNA: A field sampling guide

The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.

Three mitochondrial lineages and no Atlantic-Mediterranean barrier for the bogue Boops boops across its widespread distribution

Marine species exhibiting wide distributional ranges are frequently subdivided into discrete genetic units over limited spatial scales. This is often due to specific life-history traits or oceanographic barriers that prevent gene flow. Fine-scale sampling studies revealed distinct phylogeographic patterns in the northeastern Atlantic and the Mediterranean, ranging from panmixia to noticeable population genetic structure. Here, we used mitochondrial sequence data to analyse connectivity in the bogue Boops boops throughout most of its widespread distribution. Our results identified the existence of three clades, one comprising specimens from the Azores and eastern Atlantic/Mediterranean, another with individuals from the Canary Islands, Madeira and Cape Verde archipelagos, and the third with samples from Mauritania only. One of the branches of the northern subtropical gyre (Azores Current) that drifts towards the Gulf of Cádiz promotes a closer connection between the Azores, southern Portugal and the Mediterranean B. boops populations. The Almería-Oran Front, widely recognised as an oceanographic barrier for many organisms to cross the Atlantic-Mediterranean divide, does not seem to affect the dispersal of this benthopelagic species. The southward movement of the Cape Verde Frontal Zone during the winter, combined with the relatively short duration of the pelagic larval stage of B. boops, may be potential factors for preventing the connectivity between the Atlantic oceanic archipelagos and Mauritania shaping the genetic signature of this species.

Assessment of Fish Diversity in the Ma'an Archipelago Special Protected Area Using Environmental DNA

This study aimed to investigate the practical validity of the environmental DNA (eDNA) method for evaluating fish composition and diversity in different habitats. We evaluated the fish composition and diversity characteristics of seven different habitats in the Ma'an Archipelago Special Protected Area in April 2020. The results showed that a total of twenty-seven species of fishes belonging to six orders, eighteen families, and twenty-three genera of the Actinopterygii were detected in the marine waters of the Ma'an Archipelago Special Protected Area. The dominant species in each habitat were Larimichthys crocea, Paralichthys olivaceus, and Lateolabrax maculatus. The mussel culture area had the highest number of species, with 19 fish species, while the offshore bulk load shedding platform had the lowest number of species, with 12 fish species. The rest of the habitat was not significantly different. The results showed that the mussel culture area had the highest diversity index (average value of 2.352 ± 0.161), and the offshore bulk load shedding platform had the lowest diversity index (average value of 1.865 ± 0.127); the rest of the habitat diversity indices did not differ significantly. A comparison with historical surveys showed that the eDNA technique can detect species not collected by traditional methods such as gillnets and trawls. Our study demonstrates the role of eDNA technology in obtaining fish diversity in different habitats and provides a theoretical basis for the continuous monitoring and management of fish biodiversity in protected areas.

Fine-scale diversity of prey detected in humpback whale feces

Predator diets are largely influenced by prey availability and abundance. Yet, in heterogenous marine environments, identifying the prey species consumed by diving mammals remains a fundamental challenge. For rorqual whales, the energetic constraints of prey engulfment require that the whales seek areas of high prey abundance and execute discrete lunge feeding events on patches of high-density prey. Prey occurrences in feces should therefore provide meaningful insight into the dominant taxa in food patches selected by the animal. We investigated the prey consumed by humpback whales in three regions in southern British Columbia (BC), Canada, using opportunistic fecal sampling, microscopy, and DNA metabarcoding of 14 fecal samples. Fish including Pacific herring (Clupea pallasii), hake (Merluccius productus), and eulachon (Thaleichthys pacificus) were the most common fish species potentially targeted by humpback whales in two regions. The krill Euphausia pacifica was the most prevalent invertebrate DNA detected in all three regions, while sergestid and mysid shrimp may also be important. High DNA read abundances from walleye pollock (Gadus chalcogrammus) and sablefish (Anoplopoma fimbria) were also recovered in one sample each, suggesting that juveniles of these semi-pelagic species may occasionally be targeted. In general, we observed heavily digested fecal material that drove substantial dissimilarities in taxonomic resolution between polymerase chain reaction-based and morphological analyses of the feces. Pacific herring and walleye pollock were the only prey species confirmed by both methods. Our results highlight that molecular and visual analyses of fecal samples provide a complementary approach to diet analysis, with each method providing unique insight into prey diversity.

Environmental DNA persistence and fish detection in captive sponges

Large and hyperdiverse marine ecosystems pose significant challenges to biodiversity monitoring. While environmental DNA (eDNA) promises to meet many of these challenges, recent studies suggested that sponges, as "natural samplers" of eDNA, could further streamline the workflow for detecting marine vertebrates. However, beyond pilot studies demonstrating the ability of sponges to capture eDNA, little is known about the dynamics of eDNA particles in sponge tissue, and the effectiveness of the latter compared to water samples. Here, we present the results of a controlled aquarium experiment to examine the persistence and detectability of eDNA captured by three encrusting sponge species and compare the sponge's eDNA capturing ability with established water filtration techniques. Our results indicate that sponges and water samples have highly similar detectability for fish of different sizes and abundances, but different sponge species exhibit considerable variance in performance. Interestingly, one sponge appeared to mirror the eDNA degradation profile of water samples, while another sponge retained eDNA throughout the experiment. A third sponge yielded virtually no DNA sequences at all. Overall, our study suggests that some sponges will be suitable as natural samplers, while others will introduce significant problems for laboratory processing. We suggest that an initial optimization phase will be required in any future studies aiming to employ sponges for biodiversity assessment. With time, factoring in technical and natural accessibility, it is expected that specific sponge taxa may become the "chosen" natural samplers in certain habitats and regions.

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.

Assessing a megadiverse but poorly known community of fishes in a tropical mangrove estuary through environmental DNA (eDNA) metabarcoding

Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010–2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species—stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.

eDNA metabarcoding as a promising conservation tool to monitor fish diversity in Beijing water systems compared with ground cages

Fish diversity, an important indicator of the health of aquatic ecosystems, is declining sharply due to water pollution, overfishing, climate change, and species invasion. For protecting fish diversity, effective surveying and monitoring are prerequisites. In this study, eDNA (environmental DNA) metabarcoding and ground cages were used to survey the fish diversity of the Chaobai and Beiyun Rivers in Beijing. Based on the two methods, we identified 40 species, belonging to 35 genera, 18 families, and six orders. The richness of fish identified by eDNA metabarcoding was significantly higher than that captured by ground cages in both rivers. The fish captured by the ground cage method were all recognized by eDNA metabarcoding, except Squalidus wolterstorffi and Saurogobio dabryi, which were captured only in ground cages. The correlation of relative abundance between the two methods was affected by the properties of the rivers, such as the flow rate. Fish caught by ground cage in the Beiyun River were identified by eDNA, but not in the Chaobai River. Our results also suggest that the Chaobai River has higher fish diversity than the Beiyun River and different community assemblage. In addition to differences in the natural properties of the focal rivers, the development of urbanization is also an important contributor to different community structures overserved. eDNA metabarcoding as a new survey tool has great application prospects, it provides certain theoretical data and methodological references for the protection and management of river fish diversity.

Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary

Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome of these efforts are dependent upon either de novo primer design or selecting an appropriate primer set from the dozens that have already been published. Unfortunately, there is a lack of studies that have directly compared the efficacy of different metabarcoding primers in marine and estuarine systems. Here we evaluate five commonly used primer sets designed to amplify rRNA barcoding genes in fishes and compare their performance using water samples collected from estuarine sites in the highly biodiverse Indian River Lagoon in Florida. Three of the five primer sets amplify a portion of the mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp of the mitochondrial 16S gene (Berry_16S), and the other amplifies 271 bp of the nuclear 18S gene (MacDonald_18S). The vast majority of the metabarcoding reads (> 99%) generated using the 18S primer set assigned to non-target (non-fish) taxa and therefore this primer set was omitted from most analyses. Using a conservative 99% similarity threshold for species level assignments, we detected a comparable number of species (55 and 49, respectively) and similarly high Shannon’s diversity values for the Riaz_12S and Berry_16S primer sets. Meanwhile, just 34 and 32 species were detected using the MiFish_12S and Valentini_12S primer sets, respectively. We were able to amplify both bony and cartilaginous fishes using the four primer sets with the vast majority of reads (>99%) assigned to the former. We detected the greatest number of elasmobranchs (six species) with the Riaz_12S primer set suggesting that it may be a suitable candidate set for the detection of sharks and rays. Of the total 76 fish species that were identified across all datasets, the combined three 12S primer sets detected 85.5% (65 species) while the combination of the Riaz_12S and Berry_16S primers detected 93.4% (71 species). These results highlight the importance of employing multiple primer sets as well as using primers that target different genomic regions. Moreover, our results suggest that the widely adopted MiFish_12S primers may not be the best choice, rather we found that the Riaz_12S primer set was the most effective for eDNA-based fish surveys in our system.

Holistic Impact Evaluation of Human Activities on the Coastal Fish Biodiversity in the Chinese Coastal Environment

Ecological qualities and resources in coasts are threatened by various human activities, such as pollution and fishery. Impact evaluation of environmental stressors over a wide coastal stretch has been limited due to lack of efficient and standardizable biodiversity monitoring and assessment tools. Integrating environmental DNA (eDNA) and ecological traits, a holistic approach was developed to assess the impact of pollution and aquaculture on fish biodiversity in Chinese coastal areas. Taking the Yalujiang Estuary (YLJK) from the Yellow Sea and the Nan'ao Island Area (NAO) from the South China Sea as cases, the performance of the eDNA biomonitoring workflow was validated. First, the eDNA results of 22 sampling sites reached more than 85% of the asymptotes of species or ASVs in each area. A total of 115 fish species in both areas were detected and NAO was 1.8 times richer than YLJK using eDNA and the fish eDNA composition was consistent with the historical data. eDNA recovered distinct variations of fish sequence, taxonomic and functional diversity, and the corresponding trends following the offshore distance between the two areas. Fish sequence diversity was decreased primarily by estuarine pollution factors (chemical oxygen demand and zinc) in the YLJK. Compared with no breeding areas, lower fish sequence diversity was in breeding areas in the NAO. By integrating ecological traits, the eDNA approach offers promising opportunities for future fish biodiversity monitoring and assessment in national and global coastal environments.

A, Pouyaud L, Stuart-Smith RD, Sugeha HY, Valentini A, Vigliola L, Vimono IB, Pellissier L, Manel S. Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.

Evaluating eDNA for Use within Marine Environmental Impact Assessments

In this review, the use of environmental DNA (eDNA) within Environmental Impact Assessment (EIA) is evaluated. EIA documents provide information required by regulators to evaluate the potential impact of a development project. Currently eDNA is being incorporated into biodiversity assessments as a complementary method for detecting rare, endangered or invasive species. However, questions have been raised regarding the maturity of the field and the suitability of eDNA information as evidence for EIA. Several key issues are identified for eDNA information within a generic EIA framework for marine environments. First, it is challenging to define the sampling unit and optimal sampling strategy for eDNA with respect to the project area and potential impact receptor. Second, eDNA assay validation protocols are preliminary at this time. Third, there are statistical issues around the probability of obtaining both false positives (identification of taxa that are not present) and false negatives (non-detection of taxa that are present) in results. At a minimum, an EIA must quantify the uncertainty in presence/absence estimates by combining series of Bernoulli trials with ad hoc occupancy models. Finally, the fate and transport of DNA fragments is largely unknown in environmental systems. Shedding dynamics, biogeochemical and physical processes that influence DNA fragments must be better understood to be able to link an eDNA signal with the receptor’s state. The biggest challenge is that eDNA is a proxy for the receptor and not a direct measure of presence. Nonetheless, as more actors enter the field, technological solutions are likely to emerge for these issues. Environmental DNA already shows great promise for baseline descriptions of the presence of species surrounding a project and can aid in the identification of potential receptors for EIA monitoring using other methods.

Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho‐taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA‐based community assessment across all of these studies has hitherto been lacking. Here, we performed the first meta‐analysis of available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including plankton, microphytobentos, macroinvertebrates, and fish. Across 215 data sets, we found that DNA metabarcoding provides richness estimates that are globally consistent to those obtained using traditional methods, both at local and regional scale. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, species inventories of plankton, microphytobenthos and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates, plankton and microphytobenthos, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.

Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities

Environmental DNA (eDNA) is genetic material that has been shed from macroorganisms. It has received increased attention as an indirect marker for biodiversity monitoring. This article reviews the current status of eDNA metabarcoding (simultaneous detection of multiple species) as a noninvasive and cost-effective approach for monitoring marine fish communities and discusses the prospects for this growing field. eDNA metabarcoding coamplifies short fragments of fish eDNA across a wide variety of taxa and, coupled with high-throughput sequencing technologies, allows massively parallel sequencing to be performed simultaneously for dozens to hundreds of samples. It can predict species richness in a given area, detect habitat segregation and biogeographic patterns from small to large spatial scales, and monitor the spatiotemporal dynamics of fish communities. In addition, it can detect an anthropogenic impact on fish communities through evaluation of their functional diversity. Recognizing the strengths and limitations of eDNA metabarcoding will help ensure that continuous biodiversity monitoring at multiple sites will be useful for ecosystem conservation and sustainable use of fishery resources, possibly contributing to achieving the targets of the United Nations' Sustainable Development Goal 14 for 2030.

Use of environmental DNA in assessment of fish functional and phylogenetic diversity

Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long-term remote video to assess species' phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.

Environmental DNA gives comparable results to morphology-based indices of macroinvertebrates in a large-scale ecological assessment

Anthropogenic activities are changing the state of ecosystems worldwide, affecting community composition and often resulting in loss of biodiversity. Rivers are among the most impacted ecosystems. Recording their current state with regular biomonitoring is important to assess the future trajectory of biodiversity. Traditional monitoring methods for ecological assessments are costly and time-intensive. Here, we compared monitoring of macroinvertebrates based on environmental DNA (eDNA) sampling with monitoring based on traditional kick-net sampling to assess biodiversity patterns at 92 river sites covering all major Swiss river catchments. From the kick-net community data, a biotic index (IBCH) based on 145 indicator taxa had been established. The index was matched by the taxonomically annotated eDNA data by using a machine learning approach. Our comparison of diversity patterns only uses the zero-radius Operational Taxonomic Units assigned to the indicator taxa. Overall, we found a strong congruence between both methods for the assessment of the total indicator community composition (gamma diversity). However, when assessing biodiversity at the site level (alpha diversity), the methods were less consistent and gave complementary data on composition. Specifically, environmental DNA retrieved significantly fewer indicator taxa per site than the kick-net approach. Importantly, however, the subsequent ecological classification of rivers based on the detected indicators resulted in similar biotic index scores for the kick-net and the eDNA data that was classified using a random forest approach. The majority of the predictions (72%) from the random forest classification resulted in the same river status categories as the kick-net approach. Thus, environmental DNA validly detected indicator communities and, combined with machine learning, provided reliable classifications of the ecological state of rivers. Overall, while environmental DNA gives complementary data on the macroinvertebrate community composition compared to the kick-net approach, the subsequently calculated indices for the ecological classification of river sites are nevertheless directly comparable and consistent.

The Case of Lionfish (Pterois miles) in the Mediterranean Sea Demonstrates Limitations in EU Legislation to Address Marine Biological Invasions

The European Regulation (EU) 1143/2014 on Invasive Alien Species entered into force in 2015, with the aim to fulfill regional and international biodiversity goals in a concerted manner. To date, the Regulation listed 66 Invasive Alien Species (IAS) that are subject to legal controls. Only one of these is marine. A recent lionfish (Pterois miles) invasion has been closely monitored in the Mediterranean and a detailed risk assessment was made about the profound impacts that this invasive fish is likely to have on the fisheries and biodiversity of the region. In 2016–21, lionfish rapidly became dominant predators along Eastern Mediterranean coasts, yet the process for their inclusion on the EU IAS list has been lengthy and is ongoing. There is an urgent need to learn from this experience. Here, we recommend improvements to the Regulation 1143/2014 and the risk assessment process to protect marine ecosystems and secure the jobs of people that rely on coastal resources.