Patterns in marine surface fish biodiversity and community composition detected by different eDNA metabarcoding sampling methods

Comparison of environmental DNA metabarcoding and bottom trawling for detecting seasonal fish communities and habitat preference in a highly disturbed estuary

It is difficult to understand the composition and diversity of biological communities in complex and heterogeneous environments using traditional sampling methods. Recently, developments in environmental DNA metabarcoding have emerged as a powerful, non-invasive method for comprehensive community characterization and biodiversity monitoring in different types of aquatic ecosystems. In this study, water eDNA targeting fish (wf-eDNA) and four traditional fish sampling methods (electrofishing, gill netting, seining, trawling) were compared to evaluate the reliability and efficiency of wf-eDNA (vertebrate mitochondrial 12S ribosomal RNA (rRNA) as an alternative approach to assess the diversity and composition of freshwater fish communities. The results of wf-eDNA showed a consistency between the traditional sampling methods regarding species detection. However, some fish species detected using wf-eDNA assay were not detected using traditional sampling methods and vice versa. Comparison of wf-eDNA and traditional sampling methods revealed spatial homogeneity in fish community composition in all reservoirs. Ordination analysis showed that the wf-eDNA approach covers all traditional sampling methods and occupies an intermediate position. In addition, based on the Shannon diversity index, we found that in one reservoir the wf-eDNA method yielded similar fish community diversity to traditional sampling methods. However, in other reservoirs, the calculated Shannon diversity index of the wf-eDNA method was significantly higher than traditional sampling methods. In general, significant positive correlations were found between the wf-eDNA method and almost all traditional sampling methods. We conclude that wf-eDNA seems to be a reliable and complementary approach for biomonitoring and ecosystem management of freshwater ichthyofauna.

Accurate assessments of fish species diversity and community composition are essential for understanding fish ecology and conservation management. Environmental DNA (eDNA) metabarcoding has become an integrated method for monitoring fish species. The accuracy and efficacy of eDNA metabarcoding rely heavily on the choice of primers used for PCR amplification. A wide selection of metabarcoding primers for fish has been developed; however, there exists no comprehensive and comparative evaluation of their amplification or taxonomic classification of a rich diversity of fish species, which hinders informed decisions regarding their suitability for different study systems. Here we reviewed the literature and compiled a list of 22 primer sets for eDNA‐based metabarcoding analysis of teleost fish, the performance of which was compared using in silico PCR, followed by in vitro metabarcoding analysis using eDNA from waterbodies in Beijing, which harbour a high number of freshwater fish species. We found that the primers showed considerable differences in the amplified taxonomic ranges and proportions, fish taxa richness, species discrimination power and fish community compositions, both in silico and in vitro. The number of fish taxa detected from eDNA by the primer sets varied from 0 to 66. Primers targeting the 12S rRNA gene generally detected greater fish diversity than those targeting the 16S rRNA or COI genes, while primers targeting the cytochrome b gene amplified the fewest fish taxa in vitro. Regarding target genes, 12S primers generally outperformed other primers in terms of amplified fish diversity. The results of in silico PCR and in vitro tests were not always in agreement, suggesting that primer choice for biodiversity surveys should not be based solely on in silico evaluation. The use of different primers can qualitatively and quantitatively affect the detected biodiversity and these effects should be considered in experimental design and data interpretation. These results will assist with primer selection for eDNA‐based fish surveys, and consequently support conservation of freshwater biodiversity.

ABSTRACTEnvironmental DNA (eDNA) metabarcoding has been widely used in freshwater systems, contributing to the advancements in the monitoring of fish diversity and community species composition. Nevertheless, the accuracy and reliability of eDNA metabarcoding in assessing functional structures and revealing the mechanisms underlying fish community assembly remain unclear. In this study, we combined a traditional survey method (electrofishing) and eDNA metabarcoding to conduct fish stock monitoring in the upper reaches of the Huishui stream. We assessed taxonomic and functional structures, as well as community assembly mechanisms, during dry and wet seasons. The results revealed that, compared with electrofishing surveys, eDNA metabarcoding detected a greater number of species and higher functional richness in both seasons. Despite significant differences in fish taxonomic composition between the seasons, both eDNA and traditional methods indicated that environmental filtering dominated the process of fish community assembly in both dry and wet seasons. We showed that eDNA metabarcoding is comparable to the electrofishing method in monitoring the community composition of stream fish and can accurately and reliably determine fish community assembly mechanisms. Combining functional traits and eDNA is a robust approach for monitoring stream fish community compared to taxonomic uncertainty.

Nearshore fish diversity changes with sampling method and human disturbance: Comparing eDNA metabarcoding and seine netting along the Upper St. Lawrence River

Understanding biodiversity in aquatic systems is critical to ecological research and conservation efforts, but accurately measuring species richness using traditional methods can be challenging. Environmental DNA (eDNA) metabarcoding, which uses high‐throughput sequencing and universal primers to amplify DNA from multiple species present in an environmental sample, has shown great promise for augmenting results from traditional sampling to characterize fish communities in aquatic systems. Few studies, however, have compared exhaustive traditional sampling with eDNA metabarcoding of corresponding water samples at a small spatial scale. We intensively sampled Boardman Lake (1.4 km2) in Michigan, USA, from May to June in 2019 using gill and fyke nets and paired each net set with lake water samples collected in triplicate. We analyzed water samples using eDNA metabarcoding with 12S and 16S fish‐specific primers and compared estimates of fish diversity among methods. In total, we set 60 nets and analyzed 180 1 L lake water samples. We captured a total of 12 fish species in our traditional gear and detected 40 taxa in the eDNA water samples, which included all the species observed in nets. The 12S and 16S assays detected a comparable number of taxa, but taxonomic resolution varied between the two genes. In our traditional gear, there was a clear difference in the species selectivity between the two net types, and there were several species commonly detected in the eDNA samples that were not captured in nets. Finally, we detected spatial heterogeneity in fish community composition across relatively small scales in Boardman Lake with eDNA metabarcoding, but not with traditional sampling. Our results demonstrated that eDNA metabarcoding was substantially more efficient than traditional gear for estimating community composition, highlighting the utility of eDNA metabarcoding for assessing species diversity and informing management and conservation.

Recent developments in environmental DNA (eDNA) metabarcoding suggest that eDNA-based representation of ecological communities can be a promising tool in both fundamental ecological research and environmental assessment. However, it is less known, how eDNA performs in characterising ecological communities and community-environment relationships at the regional scale compared with traditional sampling methods. Here, we used electrofishing (EF), gillnetting (GN) and eDNA-based surveys to compare their congruency in characterising the taxonomic and trait-based structure of (oxbow) lake fish communities and their structuring mechanisms. eDNA proved to be more effective in detecting taxa in the total samples and by traits than EF and GN. Principal coordinate analysis and multiple factor analysis showed a moderate separation of communities according to sampling methods for the taxon and the trait-based structures, respectively, but eDNA samples were always located in intermediate position in the ordination plots. Procrustes analyses indicated significant among-method congruency in community structure. However, in general, eDNA-based community patterns always showed higher correlation with either the EF or the GN-based community patterns, than the two traditional methods to each other. Variance partitioning in redundancy analyses indicated large differences among the sampling methods in the importance of environmental and spatial variables in shaping metacommunity structure. These results thus suggest that the sampling method can largely influence the identified mechanisms which govern fish metacommunity organisation. Our results suggest, that eDNA metabarcoding can be the best universal method for understanding the taxonomic and trait-based organisation of lake fish metacommunities.

The 1997/1998 Mass Mortality of Corals: Effects on Fish Communities on a Tanzanian Coral Reef

Unraveling fish diversity and assembly patterns in a temperate river: Evidence from environmental DNA metabarcoding and morphological data

Exploring fish communities in the mud volcano polluted river using environmental DNA metabarcoding

Comparing diversity and structure of freshwater fish assemblages using environmental DNA and gillnetting methods: A case study of a large deep reservoir in East China

The aquatic environments of main stems in large rivers and their connected lakes exhibit significant disparities under human activities. Fish are crucial for sustaining the structure and function of aquatic ecosystems as high-level predators. This study investigated fish communities in 192 samples from lakes and rivers across the Yangtze river (YR) basin utilizing environmental DNA (eDNA) technology. Additionally, the environmental variable impact on fish biodiversity in these two aquatic environments was uncovered. Herein, we identified approximately 230 fish taxa in this basin, with lakes and rivers comprising both prevalent and habitat-specific species. Water quality played different roles in affecting fish diversity in these two water systems. The geography traits, including Longitude, Latitude, and Altitude, as well as the water traits conductivity (CD), demonstrated the variance in fish diversity and community composition in both rivers and lakes. The human activity factors, including permanganate index (PMI), chlorophyll-a (CHLA), and SiO2, elucidated much more variance in fish diversity and community composition in lakes. These findings suggested that human activity factors exert a more significant influence on fish diversity within lakes compared to rivers. Our outcomes document the complex impacts of water quality on fish diversity in different aquatic habitats of the YR basin and emphasize the distinctive considerations required to protect aquatic biodiversity in this basin. However, it should be noted that eDNA technology provides only a single snapshot of community composition. This method possesses limitations common to all approaches (e.g., detection gaps for certain taxa) as well as inherent biases (such as the difficulty in accurately reflecting the abundance and demographic structure of detected species).

The ecological consequences of the construction and operation of the Three Gorges Reservoir, particularly its unique operation strategy of storing clear water and releasing turbid water, exerts a profound influence on the composition and dynamics of local fish communities. To date, detailed and comprehensive research on seasonal changes in the fish community across the entire reservoir remains scarce. This study aims to fill this research gap by systematically investigating fish diversity through a comprehensive assessment of six main river reaches and eight major tributaries. The investigation employs environmental DNA (eDNA) technology across three critical life-cycle stages: breeding, feeding, and overwintering periods. A total of 124 fish species were recorded, comprising 10 orders, 20 families, and 80 genera. The comparative analyses of historical data suggest a significant decline in lotic and endemic fish populations, accompanied by a concurrent increase in lentic, eurytopic, and non-native fish species. Notably, the composition of fish communities exhibited similarities between breeding and overwintering periods. This study highlights the occurrence of significant seasonal fluctuations in the fish communities, showing a preference for reservoir tails and tributaries as optimal habitats. Water temperature has a predominant influence on structuring fish communities within aquatic ecosystems. This study investigates variations in the biodiversity of fish communities using historical data, with a focus on changes linked to reservoir operations and water impoundment activities. By integrating historical data, this research examines changes in fish diversity that are associated with water storage processes. It provides foundational data on the current composition and diversity of fish communities within the watershed, elucidating the spatiotemporal variations in fish diversity and the mechanisms by which environmental factors influence these communities. Furthermore, the current study serves as a valuable reference for understanding the changes in fish communities within other large reservoirs.

Environmental DNA unveiling the fish community structure and diversity features in the Yangtze River basin

Fish diversity plays a critical role in maintaining the balance of water ecosystems, especially in the Chongqing section of the National Nature Reserve for Rare and Endemic Fishes in the upper Yangtze River, which serves as an important habitat for rare and endemic fish, as well as an important channel for the replenishment of fishery resources in the Three Gorges Reservoir. Under a 10‐year ban on fishing in the Yangtze River basin, we investigate fish diversity and seasonal variation in the Reserve by using environmental DNA (eDNA) metabarcoding. We found fishes belonging to 85 genera, 24 families, and 8 orders in the Reserve. A comparison of eDNA metabarcoding results with the diversity of a recent fish catch revealed that eDNA metabarcoding not only enables rapid and efficient fish monitoring but also has a high sensitivity. Furthermore, the study demonstrates that eDNA metabarcoding can be used as a tool for monitoring seasonal variations of fish composition in freshwater ecosystems. The alpha and beta diversity analysis both showed compositional differences in the fish community in accordance with seasonal variations. In addition, changes in eDNA relative sequence abundance and the detection of fish species at different sampling sites may reflect shifts in habitat use and distribution. Thus, we provide detailed seasonal data on fish diversity in the Chongqing section of the Reserve. This will contribute to conservation and to the understanding of fish diversity and community dynamics in the Chongqing section of the Reserve.