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We reviewed the current methodology and practices of the DNA metabarcoding approach using a universal PCR primer pair MiFish, which co-amplifies a short fragment of fish DNA (approx. 170 bp from the mitochondrial 12S rRNA gene) across a wide variety of taxa. This method has mostly been applied to biodiversity monitoring using environmental DNA (eDNA) shed from fish and, coupled with next-generation sequencing technologies, has enabled massively parallel sequencing of several hundred eDNA samples simultaneously. Since the publication of its technical outline in 2015, this method has been widely used in various aquatic environments in and around the six continents, and MiFish primers have demonstrably outperformed other competing primers. Here, we outline the technical progress in this method over the last 5 years and highlight some case studies on marine, freshwater, and estuarine fish communities. Additionally, we discuss various applications of MiFish metabarcoding to non-fish organisms, single-species detection systems, quantitative biodiversity monitoring, and bulk DNA samples other than eDNA. By recognizing the MiFish eDNA metabarcoding strengths and limitations, we argue that this method is useful for ecosystem conservation strategies and the sustainable use of fishery resources in “ecosystem-based fishery management” through continuous biodiversity monitoring at multiple sites.

Effects of fragmentation on the ecology of organisms occupying dendritic ecological networks (DENs) have recently been described through both conceptual and mathematical models, but few hypotheses have been tested in complex, real-world ecosystems. Stream fishes provide a model system for assessing effects of fragmentation on the structure of communities occurring within DENs, including how fragmentation alters metacommunity dynamics and biodiversity. A recently developed habitat-availability measure, the \"dendritic connectivity index\" (DCI), allows for assigning quantitative measures of connectivity in DENs regardless of network extent or complexity, and might be used to predict fish community response to fragmentation. We characterized stream fish community structure in 12 DENs in the Great Plains, USA, during periods of dynamic (summer) and muted (fall) discharge regimes to test the DCI as a predictive model of fish community response to fragmentation imposed by road crossings. Results indicated that fish communities in stream segments isolated by road crossings had reduced species richness (alpha diversity) relative to communities that maintained connectivity with the surrounding DEN during summer and fall. Furthermore, isolated communities had greater dissimilarity (beta diversity) to downstream sites not isolated by road crossings during summer and fall. Finally, dissimilarity among communities within DENs decreased as a function of increased habitat connectivity (measured using the DCI) for summer and fall, suggesting that communities within highly connected DENs tend to be more homogeneous. Our results indicate that the DCI is sensitive to community effects of fragmentation in riverscapes and might be used by managers to predict ecological responses to changes in habitat connectivity. Moreover, our findings illustrate that relating structural connectivity of riverscapes to functional connectivity among communities might aid in maintaining metacommunity dynamics and biodiversity in complex dendritic ecosystems.

Marine biodiversity monitoring in the Mediterranean’s increasingly threatened ecosystems is crucial for effective ecosystem conservation and management. Here, we leveraged the Mediterranean International Trawl Survey program (MEDITS) to implement eDNA sampling through the recently tested ‘metaprobe’ procedure and characterize fish assemblages in three separate areas off the Italian coasts: Northern Adriatic Sea (NoAS), Ligurian and Northern Tyrrhenian Sea (LNTS), and Sardinian Sea (SaS). By combining the information from two homologous mitochondrial 12S metabarcodes––i.e., Elas02 and Tele02 targeting elasmobranchs and teleosts, respectively––we identified 108 species, over 60% of which overlapped with those caught by the trawl net. We produced an accurate reconstruction of fish community composition of the examined sites, reflecting differences in species assemblages linked with both geographic area and depth range. Metaprobe eDNA data consistently returned a biodiversity ‘bonus’ mostly consisting of pelagic taxa not captured through bottom trawl surveys, including rare and endangered taxa (e.g., elasmobranchs). Overall, the spatial characterisation of the assemblages across the surveyed areas was better delineated and more robust using eDNA metabarcoding than trawl data. Our results support the operationalisation of the metaprobe as a simple, inexpensive, versatile sampling tool, in association with pre-existing ship surveys, to overcome many of the limitations of marine data collection and strengthen marine management.

Large rivers exhibit dynamic and complex geomorphic features, supporting some of the most biodiverse and ecologically productive ecosystems. However, their aquatic ecology is increasingly threatened by human modifications to natural channel morphology. The lack of systematic investigation and understanding of the interactions between hydrodynamics, water quality, and aquatic ecology within large‐scale, morphologically complex rivers has led to fragmented ecological management. This study investigates the large‐scale responses of fish communities to complex channel morphologies through two comprehensive field surveys of hydrodynamics, water quality, and fish distribution along a ∼30 km reach of the Yangtze River, encompassing channel narrowing, bifurcation, and the Yangtze River‐Poyang Lake cascading confluence system. Both surveys observed elevated fish densities at the confluence and narrowing section, particularly with a distinct Confluence Hydro‐Ecological Zone (CHEZ) within the post‐confluence channel, marked by a pronounced increase in fish density and species diversity relative to both upstream and downstream sections. Mixing dynamics driven by the confluence momentum ratio (Mr) regulate the CHEZ: slow mixing in the equivalent momentum regime (Mr ≈ 1) amplified the increase in fish density within the CHEZ, while rapid mixing in the unequal momentum regime (Mr >> 1) weakened such effect but expanded the CHEZ. Density of large fish was primarily influenced by water depth and water‐quality variability, whereas density of small fish was driven by seasonal population dynamics and hydrodynamic conditions. This study highlights that a comprehensive understanding of hydrodynamic configurations, water‐quality contrasts, and seasonal biological dynamics at confluences can inform process‐based strategies for sustainable river management.

The present study used multivariate techniques, to analyze the fish species diversity and distribution patterns in order to determine the possible role of environmental parameters as drivers of fish community structure and composition in the Yangtze River Estuary (YRE). This analysis was conducted using data obtained in the YRE from February 2012 to December 2014. Analysis of the catch data showed that species composition, total density, and total biomass varied significantly between stations and seasons. Thirty-eight species belonging to 18 families were collected. Sciaenidae was the most dominant family accounting for 40.8% of total captured specimens. In descending order, Collichthys lucidus , Cynoglossus gracilis , Chaeturichthys stigmatias , and Lophiogobius ocellicauda dominated catches in the YRE. These four species constituted 64.2% of the total catches and showed average dissimilarities of 74.19% between stations and 81.3% between months. The highest number of fish specimens captured was recorded in August 2012 while the highest species richness was observed in December 2013. The mean fish density and biomass for the YRE was 0.35 individuals/m 2 and 2.5 g/m 2 , respectively. The mean density and biomass for the most important and dominant species changed significantly between stations and seasons. Canonical correspondence analysis indicated that salinity and chlorophyll-a were the key variables that structured the fish assemblage in the YRE. High total species density and biomass were recorded in high saline stations (North Branch) of the YRE. This study confirms that most species captured in the YRE needs estuarine conditions to complete their growth and development. Hence, the findings in this study are important to understanding and developing suitable conservation plans for the management of fish resources in the YRE.

The Upper Mississippi River System, including the Illinois River, has been invaded by a number of nonnative species including silver carp Hypophthalmichthys molitirx and bighead carp H . nobilis , collectively referred to here as Asian carps. Silver carp densities in the Illinois River have increased dramatically and now represent some of the highest densities of wild silver carp anywhere in the world. Asian carps have the potential to alter existing ecosystems by consuming planktonic resources and therefore, could have the ability to alter existing fish communities as most fishes are dependent on planktonic resources during early development. However, identifying the relationship of fish community structure to the establishment of Asian carps has yet to be thoroughly investigated. Using long-term fish community data collected by the Upper Mississippi River Restoration’s Long Term Resource Monitoring element, we investigate changes in fish community structure pre- and post-establishment of Asian carps. Significant differences in the pre- and post-establishment communities were observed for the majority of gears and habitats. Species contributing to changes between establishment periods included most sportfish species and catostomids, which were less abundant post-establishment of Asian carps, while shortnose gar, grass carp, and emerald shiner were more abundant. While our analyses show Asian carps are likely contributing to major differences in fish community structure, future research and long-term monitoring should investigate the mechanisms and interactions responsible for community changes as well as identifying any potential concurrent or confounding factors such as changes in river hydrology or sedimentation.

The river–lake transitional zone of Poyang Lake is a key water area connecting the Yangtze River and Poyang Lake. A good understanding of the relationship between fish communities, hydrological dynamics, and other water environment factors in these waters is important. In this study we examined the status of fish resources in the river–lake transitional zone of Poyang Lake, from 2021 to 2022. We collected 3880 fish individuals, belonging to five orders, ten families, and 54 species. The largest number of fish species were cypriniformes, accounting for 64.81% of the total number of fish species. Overall, the composition of fish species was mainly carnivorous fish, demersal fish, resident fish, and viscous egg fish. According to the relative importance index, there were eight dominant species (including Coilia brachygnathus and Megalobrama mantschuricus). Fish species was more abundant and community structure was more complex during the flood period and in the downstream area. The regional differences in the fish community in the river–lake transitional zone of Poyang Lake were significant, whereas seasonal differences were not significant. Our analysis showed that the water level and flow correlated significantly with the Margalef richness index and Shannon–Wiener diversity index. Redundancy analysis showed that pH, oxidation–reduction potential, dissolved oxygen, and the water level were key environmental factors affecting the spatiotemporal variation of fish species composition and community structure. This led to the conclusion that high water levels in the flood period and in the downstream area are important factors affecting the river–lake transitional zone of Poyang Lake. Taken together, the results of this study support the protection and management of fish resources in the river–lake transitional zone of Poyang Lake.

Aim Our goal was to use eDNA metabarcoding to characterize fish community diversity, detect aquatic invasive species (AIS) and assess how measures of community (or AIS) diversity are influenced by lake physical and environmental covariates, measures of hydrological connectivity and human accessibility. Location Michigan, USA. Methods eDNA samples collected from 22 lakes were sequenced using two mitochondrial gene regions (12S and 16S rRNA). Metabarcoding data were compared to traditional fisheries survey data for a subset of lakes, and data from all 22 lakes were combined with environmental information to identify significant associations with community diversity and AIS relative abundance. Results Occupancy modelling indicated that detection probabilities were generally higher with eDNA than traditional fisheries gear. Measures of connectivity with upstream aquatic habitats were positively associated with both AIS relative abundance and fish species diversity. We also demonstrate the use of spatial interpolation methods to map distributions of species diversity and AIS relative abundance within lakes. Main conclusions eDNA metabarcoding methods provided information on the composition and diversity of fish assemblages and the presence of AIS in freshwater lakes that varied greatly in drainage connectivity and anthropogenic development. Our case study identified associations between environmental covariates and fish diversity or AIS relative abundance across lakes. This information is of particular importance given increasing anthropogenic disturbance, invasive species spread and associated declines in aquatic biodiversity. Incorporating eDNA metabarcoding as a supplement to traditional fisheries surveys will permit managers to identify greater numbers of taxa, including early detection of AIS, with less field effort and fish mortality. Further, eDNA methods may more accurately identify physical and biological features that correlate with diversity and abundance and allow agencies to more effectively direct AIS management activities.

Using unregulated tributaries to compensate fish habitat loss in dammed mainstreams has recently been suggested as a promising strategy for river ecological restoration. One critical prerequisite is to find potential tributaries as alternative habitat, which depends on precise fish community surveys. In this study, both eDNA metabarcoding and electrofishing were used to characterise fish community compositions in the dammed lower Jinsha river and its tributaries (Heishui, Pudu, and Xiaojiang rivers) in China. The fish community composition detected by eDNA metabarcoding was consistent with that detected by the conventional method. Besides, metabarcoding has the advantage of detecting the presence of rare species with relatively low abundances. The non-metric multidimensional scaling showed that there was no significant difference in fish community composition between the mainstream and the Heishui river, while there was large difference in the fish community composition between the mainstream and other tributaries. The effectiveness of using the Heishui river as alternative fish habitat was verified by comparing the changes in fish communities before and after the impoundment of the mainstream. Taken together, this study indicates that eDNA metabarcoding is a viable method to identify the suitable tributaries which at least partly compensate for fish habitat loss in the dammed mainstream.

Aim: Chronic anthropogenic stressors are increasing in intensity, making ecosystems more vulnerable to acute disturbances. Recovery processes are not always well understood due to the complexity of ecosystems and the lack of appropriate indicators. Temporal synchrony is a valuable metric for assessing whether fluctuations in abundance of different species are homogeneous or heterogeneous over time. Theoretically, a great diversity of responses by species facing disturbances is associated with a stable ecosystem, with species turnover guaranteeing the persistence of key ecological processes. We analysed the fluctuations of synchrony of a fish community to assess its resilience in an ecosystem exposed to various disturbances.Location: Moorea (French Polynesia).Methods: Using one of the longest time series available for coral reefs (ca. 35 years), we examined the variations in substrate cover, and the abundance, synchrony and composition of different fish trophic guilds. Multivariate analyses involving synchrony were used to determine the stability of trophic guilds.Results: Changes in fish community composition indicated incomplete taxonomic resilience. However, community synchrony was lower during periods of low coral cover, indicating greater response diversity, while total fish abundance remained fairly stable. Synchrony drop was due to relationships with coral cover that differed by trophic guild, or the differences in species responses within guilds. Some guilds such as sessile invertebrate feeders exhibited a strong homogeneity of response over time, indicating a greater vulnerability. We also highlighted that various types of disturbances had different effects on the synchrony of particular guilds.Main conclusions: The fish community appeared functionally resilient, with stability of total abundance and most trophic guilds. This could be a factor explaining the rapid recovery of Moorea's coral reefs from disturbances. However, the homogeneous responses of some fish groups to disturbances may compromise the reef recovery potential on the long term if disturbances become more frequent.