Interaction between phytoplankton and heterotrophic bacteria in Arctic fjords during the glacial melting season as revealed by eDNA metabarcoding

The hydrographic variability in the fjords of Svalbard significantly influences water mass properties, causing distinct patterns of microbial diversity and community composition between surface and subsurface layers. However, surveys on the phytoplankton-associated bacterial communities, pivotal to ecosystem functioning in Arctic fjords, are limited. This study investigated the interactions between phytoplankton and heterotrophic bacterial communities in Svalbard fjord waters through comprehensive eDNA metabarcoding with 16S and 18S rRNA genes. The 16S rRNA sequencing results revealed a homogenous community composition including a few dominant heterotrophic bacteria across fjord waters, whereas 18S rRNA results suggested a spatially diverse eukaryotic plankton distribution. The relative abundances of heterotrophic bacteria showed a depth-wise distribution. By contrast, the dominant phytoplankton populations exhibited variable distributions in surface waters. In the network model, the linkage of phytoplankton (Prasinophytae and Dinophyceae) to heterotrophic bacteria, particularly Actinobacteria, suggested the direct or indirect influence of bacterial contributions on the fate of phytoplankton-derived organic matter. Our prediction of the metabolic pathways for bacterial activity related to phytoplankton-derived organic matter suggested competitive advantages and symbiotic relationships between phytoplankton and heterotrophic bacteria. Our findings provide valuable insights into the response of phytoplankton-bacterial interactions to environmental changes in Arctic fjords.

Revolutionizing early-stage green tide monitoring: eDNA metabarcoding insights into Ulva prolifera and microecology in the South Yellow Sea

Green tides, characterized by excessive Ulva prolifera blooms, pose significant ecological and economic challenges, especially in the South Yellow Sea. We successfully employed 18S environmental DNA (eDNA) metabarcoding to detect Ulva prolifera micropropagules, confirming the technique's reliability and introducing a rapid green tide monitoring method. Our investigation revealed notable disparities in the eukaryotic microbial community composition within Ulva prolifera habitats across different regions. Particularly, during the early stages of the South Yellow Sea green tide outbreak, potential interactions emerged between Ulva prolifera micropropagules and certain previously undocumented microorganisms from neighboring waters. These findings enhance our comprehension of early-stage green tide ecosystem dynamics, underscoring the value of merging advanced molecular techniques with conventional ecological methods to gain a comprehensive understanding of the impact of green tide on the local ecosystem. Overall, our study advances our understanding of green tide dynamics, offering novel avenues for control, ecological restoration, and essential scientific support for sustainable marine conservation and management.

Environmental DNA metabarcoding reveals the effect of environmental selection on phytoplankton community structure along a subtropical river

The Dongjiang River, a major tributary of the Pearl River system that supplies water to more than 40 million people in Guangdong Province and neighboring regions of China, harbors rich biodiversity, including many endemic and endangered species. However, human activities such as urbanization, agriculture, and industrialization have posed serious threats to its water quality and biodiversity. To assess the status and drivers of phytoplankton diversity, which is a key indicator of aquatic ecosystem health, this study used Environmental DNA (eDNA) metabarcoding combined with machine learning methods to explore spatial variations in the composition and structure of phytoplankton communities along the Dongjiang River, including its estuary. The results showed that phytoplankton diversity exhibited spatial distribution patterns, with higher community structure similarity and lower network complexity in the upstream than in the downstream regions. Environmental selection was the main mechanism shaping phytoplankton community composition, with natural factors driving the dominance of Pyrrophyta, Ochrophyta, and Cryptophyta in the upstream regions and estuaries. In contrast, the downstream regions was influenced by high concentrations of pollutants, resulting in increased abundance of Cryptophyta. The random forest model identified temperature, dissolved oxygen, chlorophyll a, NO2-, and NH4+ as the main factors influencing the primary phytoplankton communities and could be used to predict changes during wet periods. This study provides valuable insights into the factors influencing phytoplankton diversity and community composition in the Dongjiang River, and demonstrates the application value of eDNA metabarcoding technique in large-scale, long-distance river biodiversity monitoring.

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.

Using environmental DNA to better inform decision making around decommissioning alternatives for offshore oil and gas infrastructure

Artificial reefs are being utilised globally to aid in natural resource management, conservation, restoration or the creation of unique marine habitats. There is discussion around the optimal construction materials and designs for artificial reefs, the influences these have on biological communities, and the resulting ecological and social benefits. This discussion also includes the ecological value of repurposed marine infrastructure, such as decommissioned oil and gas platforms. Platforms often have an operational life spanning multiple decades, over which time they can develop extensive and unique community assemblages. The creation of artificial reefs by repurposing oil and gas platforms can have ecological, economic and sociological merit. However, with >12,000 platforms requiring decommissioning globally, there is the need for holistic assessment of biological communities associated with these platforms to inform the potential outcomes of different decommissioning options. We use environmental DNA metabarcoding (eDNA) of water, bio-foul and sediment samples to census broad eukaryotic diversity at eight platforms in the Gulf of Thailand (GoT) and five nearby soft sediment habitat locations. We sampled three target depths at sites (shallow, mid, deep) and detected 430 taxa at platforms, with higher diversity in shallow (near-surface) samples (313 taxa), compared to mid (30 m collection depth; 261 taxa) and deep (50 m; 273 taxa). Three percent of taxa were shared among all depths at platforms with distinct assembles at each depth. Introduced species are an ongoing risk for platforms, however the eDNA detected no known introduced species. While the eDNA data provide broad taxon coverage and significant assemblage patterns, ongoing sampling innovation, assay design and local reference material still require development to obtain the maximum benefit of the technique. This study highlights the versatility and scalability of eDNA metabarcoding to holistically census marine infrastructure and inform the management and potential conservation of extant communities.

Supervised machine learning improves general applicability of eDNA metabarcoding for reservoir health monitoring

Effective and standardized monitoring methodologies are vital for successful reservoir restoration and management. Environmental DNA (eDNA) metabarcoding sequencing offers a promising alternative for biomonitoring and can overcome many limitations of traditional morphological bioassessment. Recent attempts have even shown that supervised machine learning (SML) can directly infer biotic indices (BI) from eDNA metabarcoding data, bypassing the cumbersome calculation process of BI regardless of the taxonomic assignment of eDNA sequences. However, questions surrounding the general applicability of this taxonomy-free approach to monitoring reservoir health remain unclear, including model stability, feature selection, algorithm choice, and multi-season biomonitoring. Here, we firstly developed a novel biological integrity index (Me-IBI) that integrates multitrophic interactions and environmental information, based on taxonomy-assigned eDNA metabarcoding data. The Me-IBI can better distinguish the actual health status of the Three Gorges Reservoir (TGR) than physicochemical assessments and have a clear response to human activity. Then, taking this reliable Me-IBI as a supervised label, we compared the impact of selecting different numbers of features and SML algorithms on the stability and predictive performance of the model for predicting ecological conditions in multiple seasons using taxonomy-free eDNA metabarcoding data. We discovered that even with a small number of features, different SML algorithms can establish a stable model and obtain excellent predictive performance. Finally, we proposed a four-step strategy for standardized routine biomonitoring using SML tools. Our study firstly explores the general applicability problem of the taxonomy-free eDNA-SML approach and establishes a solid foundation for the large-scale and standardized biomonitoring application.

First pelagic fish biodiversity assessment of Cosmonaut Sea based on environmental DNA

The Cosmonaut Sea is a typical marginal sea in East Antarctica that has not yet been greatly impacted by climate change. As one of the least explored areas in the Southern Ocean, our knowledge regarding its fish taxonomy and diversity has been sparse. eDNA metabarcoding, as an emerging and promising tool for marine biodiversity research and monitoring, has been widely used across taxa and habitats. During the 38th Chinese Antarctic Research Expedition (CHINARE-38), we collected seawater and surface sediment samples from 38 stations in the Cosmonaut Sea and performed the first, to our knowledge, eDNA analysis of fish biodiversity in the Southern Ocean based on the molecular markers of 12S rRNA and 16S rRNA. There were 48 fish species detected by the two markers in total, with 30 and 34 species detected by the 12S rRNA and 16S rRNA marker, respectively. This was more than the trawling results (19 species) and historical survey records (16 species, "BROKE-West" cruise). With some nonsignificant differences between the Gunnerus Ridge and the Oceanic Area of Enderby Land, the Cosmonaut Sea had a richer fish biodiversity in this research compared with previous studies, and its overall composition and distribution patterns were consistent with what we know in East Antarctica. We also found that the eDNA composition of fish in the Cosmonaut Sea might be related to some environmental factors. Our study demonstrated that the use of the eDNA technique for Antarctic fish biodiversity research is likely to yield more information with less sampling effort than traditional methods. In the context of climate change, the eDNA approach will provide a novel and powerful tool that is complementary to traditional methods for polar ecology research.

eDNA Metabarcoding- and Microscopic Analysis for Diet Determination in Waterfowl, a Comparative Study in Vejlerne, Denmark

Understanding diets and structural food webs are keys to the apprehension of ecological communities, upon which conservation and management biology are based. The understanding of grazing and habitat choice for waterfowl is one of the most important topics for avian ecologists today and can, to some degree, be answered by dietary analysis. Droppings collected from four waterfowl, the Eurasian wigeon (Anas penelope), Greylag goose (Anser anser), pink-footed goose (Anser brachyrhynchus) and Barnacle goose (Branta leucopsis) in Vejlerne (Denmark), were analysed microscopically and through eDNA metabarcoding with the use of next generation sequencing (NGS) to accumulate knowledge about the diet of these waterfowl. In total, 120 dropping samples were microscopically analysed, of which the eDNA metabarcoding analysis was done on 79 samples. The prey items were identified according to the taxonomic level of species, and a qualitative method, frequency of occurrence (FO) and FO calculated as a percentage, was used in order to compare the results from the two methods. As neither of the methods was able to encompass all species discovered when combining the two methods, it was concluded in this study that the two methods can support each other in a dietary analysis of waterfowl, but not replace one another.

Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary

Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam Corbicula fluminea to examine biodiversity within estuarine ecosystem. Field sampling was conducted at three points in the Nakdong River Estuary, which is characterised by closed estuarine features resulting from the presence of an estuarine barrage. The collected C. fluminea samples were dissected to separate the gut contents, and the extracted eDNA was amplified using 18S V9 primer targeting all eukaryote-derived DNA. The amplified DNA was sequenced using a next-generation sequencing (NGS) technique, and a BLASTn search was performed based on the National Centre for Biotechnology Information (NCBI) database for taxa identification. We obtained 23 unique operational taxonomic units (OTUs), including fish (approximately 8.70%), copepods (approximately 17.39%), and green algae (approximately 21.74%), representing a wide range of habitats. Furthermore, 8 out of the 20 families were identified through comparisons with reference data from conventional field surveys, and the OTUs of elusive migratory fish were detected. The results support the application of C. fluminea as an eDNA sampler for supplementary biodiversity monitoring.

Biodiversity exploration of Formosa Ridge cold seep in the South China Sea using an eDNA metabarcoding approach

The Formosa Ridge, also named Site F, is an active cold seep marine ecosystem site that has been studied since it was discovered on the continental slope of the northeast South China Sea (SCS). However, few studies have focused on the eukaryotic diversity at Site F. Environmental DNA (eDNA) technology is a non-invasive method applied in biodiversity surveys with a high species detection probability. In the present study, we identified multi-trophic biodiversity using eDNA metabarcoding combined with multiple ribosomal RNA gene (rDNA) markers. We detected 142 phytoplankton, 90 invertebrates, and 64 fish species by amplifying the 18S rRNA gene V4 region, the 18S rRNA gene V9 region, and the 12S rRNA gene. The results elucidated dissimilar trends of different assemblages with depth. The diversity of phytoplankton and invertebrate assemblages markedly decreased with depth, whereas little change was observed within the fish assemblage. We comprehensively assessed the relationship between the three assemblages and environmental factors (temperature, salinity, depth, dissolved oxygen, and chlorophyll a). These factors strongly impacted on phytoplankton and invertebrates, but only slightly on fish. We inferred the finding might be due to fish having a strong migration capacity and wide distribution. This study indicates that eDNA metabarcoding with multiple markers is a powerful tool for marine biodiversity research that is able to provide technical support and knowledge for resource management and biodiversity protection efforts.

Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects

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

Comparing quantile regression spline analyses and supervised machine learning for environmental quality assessment at coastal marine aquaculture installations

Organic enrichment associated with marine finfish aquaculture is a local stressor of marine coastal ecosystems. To maintain ecosystem services, the implementation of biomonitoring programs focusing on benthic diversity is required. Traditionally, impact-indices are determined by extracting and identifying benthic macroinvertebrates from samples. However, this is a time-consuming and expensive method with low upscaling potential. A more rapid, inexpensive, and robust method to infer the environmental quality of marine environments is eDNA metabarcoding of bacterial communities. To infer the environmental quality of coastal habitats from metabarcoding data, two taxonomy-free approaches have been successfully applied for different geographical regions and monitoring goals, namely quantile regression splines (QRS) and supervised machine learning (SML). However, their comparative performance remains untested for monitoring the impact of organic enrichment introduced by aquaculture on marine coastal environments. We compared the performance of QRS and SML using bacterial metabarcoding data to infer the environmental quality of 230 aquaculture samples collected from seven farms in Norway and seven farms in Scotland along an organic enrichment gradient. As a measure of environmental quality, we used the Infaunal Quality Index (IQI) calculated from benthic macrofauna data (reference index). The QRS analysis plotted the abundance of amplicon sequence variants (ASVs) as a function to the IQI from which the ASVs with a defined abundance peak were assigned to eco-groups and a molecular IQI was subsequently calculated. In contrast, the SML approach built a random forest model to directly predict the macrofauna-based IQI. Our results show that both QRS and SML perform well in inferring the environmental quality with 89% and 90% accuracy, respectively. For both geographic regions, there was high correspondence between the reference IQI and both the inferred molecular IQIs (p < 0.001), with the SML model showing a higher coefficient of determination compared to QRS. Among the 20 most important ASVs identified by the SML approach, 15 were congruent with the good quality spline ASV indicators identified via QRS for both Norwegian and Scottish salmon farms. More research on the response of the ASVs to organic enrichment and the co-influence of other environmental parameters is necessary to eventually select the most powerful stressor-specific indicators. Even though both approaches are promising to infer environmental quality based on metabarcoding data, SML showed to be more powerful in handling the natural variability. For the improvement of the SML model, addition of new samples is still required, as background noise introduced by high spatio-temporal variability can be reduced. Overall, we recommend the development of a powerful SML approach that will be onwards applied for monitoring the impact of aquaculture on marine ecosystems based on eDNA metabarcoding data.

eDNA metabarcoding reveals shifts in sediment eukaryote communities in a metal contaminated estuary

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

Investigations of Fish Assemblages Using Two Methods in Three Terminal Reservoirs of the East Route of South-to-North Water Transfer Project, China

The terminal reservoirs of water transfer projects directly supply water for domestic, agricultural, and industrial applications, and the water quality of these reservoirs produce crucial effects on the achievement of project targets. Typically, fish assemblages are monitored as indicators of reservoir water quality, and can also be regulated for its improvement. In the present study, we compared traditional fish landing (TFL) and environmental DNA (eDNA) metabarcoding methods for monitoring fish assemblages in three terminal reservoirs of the East Route of the South-to-North Water Transfer Project, China. Results of TFL and eDNA showed similar assemblage structures and patterns of diversity and spatial distribution with obvious differences in fish composition across three examined reservoirs. Demersal and small fish were dominant in all reservoirs. In addition, a strong association between water transfer distance and assemblages and distribution of non-native fish was found. Our findings highlight the necessity of the fish assemblage monitoring and managing for water quality and revealed the impact of water diversion distance on the structure of fish assemblages and dispersal of alien species along the water transfer project.

Contrasting seasonal patterns in diet and dung-associated invertebrates of feral cattle and horses in a rewilding area

Trophic rewilding is increasingly applied in restoration efforts, with the aim of reintroducing the ecological functions provided by large-bodied mammals and thereby promote self-regulating, biodiverse ecosystems. However, empirical evidence for the effects of megafauna introductions on the abundance and richness of other organisms such as plants and invertebrates, and the mechanisms involved still need strengthening. In this study, we use environmental DNA (eDNA) metabarcoding of dung from co-existing feral cattle and horses to assess the seasonal variation in plant diet and dung-associated arthropods and nematodes. We found consistently high diet richness of horses, with low seasonal variability, while the generally lower dietary diversity of cattle increased substantially during summer. Intriguingly, season-specific diets differed, with a greater proportion of trees in the horses' diet during winter, where cattle relied more on shrubs. Graminoids were predominantly found in the diet of horses, but were generally underrepresented compared to previous studies, possibly due to the high prevalence of forbs in the study area. Dung-associated arthropod richness was higher for cattle, largely due to a high richness of flies during summer. Several species of dung-associated arthropods were found primarily in dung from one of the two herbivores, and our data confirmed known patterns of seasonal activity. Nematode richness was constantly higher for horses, and nematode communities were markedly different between the two species. Our results demonstrate complementary effects of cattle and horses through diet differences and dung-associated invertebrate communities, enhancing our understanding of large herbivore effects on vegetation and associated biodiversity. These results are directly applicable for decision-making in rewilding projects, suggesting biodiversity-benefits by inclusion of functionally different herbivores.

Profiling Analysis of Filter Feeder Polypedilum (Chironomidae) Gut Contents Using eDNA Metabarcoding Following Contrasting Habitat Types-Weir and Stream

We analyzed the dietary composition of Polypedilum larvae among two contrasting habitats (river and weir). Our approach was (i) to apply eDNA-based sampling to reveal the gut content of the chironomid larvae, (ii) the diversity of gut contents in the two aquatic habitats, and (iii) assessment of habitat sediment condition with the food sources in the gut. The most abundant food was Chlorophyta in the gut of the river (20%) and weir (39%) chironomids. The average ratio of fungi, protozoa, and zooplankton in river chironomids gut was 5.9%, 7.2%, and 3.8%, while it was found decreased to 1.2%, 2.5%, and 0.1% in weir chironomids. Aerobic fungi in river midge guts were 3.6% and 10.34% in SC and IS, while they were in the range of 0.34-2.58% in weir midges. The hierarchical clustering analysis showed a relationship of environmental factors with food contents. Abiotic factors (e.g., pH) in the river and weir habitats correlated the clustered pattern with phytoplankton and minor groups of fungi. This study could help understand the food source diversity in the chironomid and habitat environmental conditions by using eDNA metabarcoding as an effective tool to determine dietary composition.

Diatom eDNA metabarcoding and morphological methods for bioassessment of karstic river

Karst ecosystems play a unique role as exceptional natural habitats in sustaining biodiversity. This study focuses on diatoms, a diverse group of microeukaryotes in the periphytic community of a karstic river. In a multi-microhabitat study along the Krka River (Croatia), our goal was to obtain a detailed overview of diatom diversity and community structure using morphological and molecular approaches, and to assess the applicability of eDNA metabarcoding as a reliable tool for biomonitoring assessment. The results revealed a relatively low agreement in the diatom community composition between the two approaches, but also provided complementary information, with no differences in beta diversity detected between microhabitats. The SIMPER analysis underlined the importance of the molecular approach in identifying diatom community composition, due to errors in distinguishing between deposited diatom cells that occurred in the morphological analysis. In contrast, the morphological approach indicated a clear diatom community separation along the river with a strong location effect. Despite certain differences, both approaches provided a feasible assessment of the ecological status according to the relationship to environmental pressures, classifying the Krka River as High (morphological approach) or Good (molecular approach) throughout the most of its course. Moreover, diatom diversity based on both approaches provides a reliable dataset applicable in routine monitoring assessment and offers a deeper understanding of the presented ecological status. The incompleteness of a reference database presents one major drawback of the molecular approach, which needs further updating in order to improve routine diatom metabarcoding.

Complementary molecular and visual sampling of fish on oil and gas platforms provides superior biodiversity characterisation

Offshore oil and gas platforms have the potential to provide complex refugia for fish and benthic colonisers. We compare two methods of biodiversity assessment for fish and elasmobranchs at seven decommissioned oil and gas platforms as well as five sediment sites, located 5 km from platforms, in the Gulf of Thailand. Using surveys from stereo-video ROV transects, and data from Environmental DNA (eDNA) water-column samples, we detected fish and elasmobranch taxa from 39 families and 66 genera across both platform and sediment sites with eDNA, compared with 18 families and 29 genera by stereo-ROV with platforms yielding significantly greater species richness. This study demonstrates that the combination of stereo-video ROV and eDNA provide effective, non-extractive and complementary methods to enhance data capture. This approach sets new benchmarks for evaluating fish assemblages surrounding platforms and will enhance measurements of biota to inform decisions on the fate of oil/gas infrastructure.

Diverse Host Plants of the First Instars of the Invasive Lycorma delicatula: Insights from eDNA Metabarcoding

Identification of host plants of the invasive spotted lanternfly, Lycorma delicatula (Hemiptera: Fulgoridae), has been the focus of many studies. While the adults and late nymphs are relatively easy to observe on plants and to use for molecular gut-content analysis, studying the early instars is more challenging. This study is the continuation of our ongoing efforts to determine the host range for each developmental stage of L. delicatula. In the present study, we focused exclusively on the first nymphal instars, and we used a novel approach, utilizing "bulk" DNA extracts for DNA metabarcoding of nymphal gut contents, to identify all the detectable plants that the nymphs had ingested prior to being collected. We were able to obtain high-quality amplicons (up to 406 bp) of a portion of the rbcL gene and detect 27 unique ingested plant species belonging to 17 families. Both native and introduced plants with the prevalence of trees and grasses were present among the ingested plants. We also identified 13 novel host plants that have not been previously reported for L. delicatula on the U.S. territory. The results from our study have important applications for developing effective programs on early monitoring of invasive L. delicatula.

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.

Biodiversity exploration in autumn using environmental DNA in the South China sea

The South China Sea (SCS) is an important part of the Indo-Pacific convergence zone, with high biodiversity and abundant marine resources. Traditional methods are primarily used to monitor biodiversity. However, a few studies have used environmental DNA (eDNA) metabarcoding to research the assemblage structure of the SCS. This study used eDNA metabarcoding to survey the SCS assemblage and its relationship with environmental factors over a month-long time-series (August 30th to September 30th, 2020) of seawater samples from the central part of the SCS (9°-20°86' N, 113°-118°47' E). 32 stations were divided into six groups (A, B, C, D, E, F) according to longitude. We collected water samples, extracted eDNA, and amplified 18S rRNA gene V4 region (18S V4), 18S rRNA gene V9 region (18S V9), and 12S rRNA gene (12S). Krona diagrams were used to show species composition. We identified 192 phytoplankton, 104 invertebrate, and 61 fish species from 18S V4, 18S V9, and 12S, respectively. Generally, the three assemblage structures exhibited an increase in species diversity with increasing longitude. Group E had the highest fish diversity. Groups F and C had the highest phytoplankton and invertebrate diversity, respectively. Canonical correspondence analysis showed that four factors (chlorophyll a, depth, salinity, and temperature) were correlated with assemblage structure. Chlorophyll a was the main environmental factor that affected fish, phytoplankton, and invertebrate assemblage structures; salinity was strongly correlated with fish and invertebrate assemblage structures; temperature was a key factor that impacted fish and invertebrate assemblage structures; and depth was strongly correlated with invertebrate assemblage structure. Our results revealed that eDNA metabarcoding is a powerful tool for improving detection rate and using multiple markers is an effective approach for monitoring biodiversity. This study provided information that can be used to enhance biodiversity protection efforts in the SCS.

eDNA biomonitoring revealed the ecological effects of water diversion projects between Yangtze River and Tai Lake

Water diversion has been widely used to address water shortages and security issues. However, its long-term ecological impacts, particularly on the biodiversity and structure of the local community, have often been neglected due to limitations of conventional biomonitoring. Taking the water diversion projects from Yangtze River to Tai Lake (WDYT) as examples, environmental DNA (eDNA) metabarcoding was used to investigate the potential ecological impact of water diversion on the connected basins. Firstly, 136 phytoplankton genera/species, including 31 cyanobacteria and 105 eukaryotic phytoplankton (Euk-phytoplankton), were identified from 26 sites by metabarcoding of 16S rDNA V3 and 18S rDNA V9 regions. eDNA metabarcoding showed an obvious advantage in detecting nano/pico-plankton (< 20 μm in size) compared with the morphological approach. Secondly, more shared taxa and higher similarity of community composition were observed in Gonghu Bay/Zhushan Bay with its connected river than with the center of Tai Lake, indicating that water diversions were accelerating the biotic homogenization between different waterbodies. Skeletonema potamos, the native species of Yangtze River (4.04% of the total Euk-phytoplankton reads) was detected in different connecting regions of Tai Lake (0.03%-0.54% of the total Euk-phytoplankton reads), where its relative abundance was consistent with the influence of water diversion from Yangtze River. Furthermore, the introduction of S. potamos significantly affected the local community compositions of phytoplankton in Tai Lake. Finally, the ecological effect (e.g., taxa richness, community composition and species invasion) of the WDYT on phytoplankton in the west of Tai Lake was more significant than that in the east, which was consistent with the scale (volume and duration) of the water diversion projects. Overall, this study highlights the value of eDNA biomonitoring in the ecological impact assessment of water transfer projects.

Mapping differences in mammalian distributions and diversity using environmental DNA from rivers

Finding more efficient ways to monitor and estimate the diversity of mammalian communities is a major step towards their management and conservation. Environmental DNA (eDNA) from river water has recently been shown to be a viable method for biomonitoring mammalian communities. Most of the studies to date have focused on the potential for eDNA to detect individual species, with little focus on describing patterns of community diversity and structure. Here, we first focus on the sampling effort required to reliably map the diversity and distribution of semi-aquatic and terrestrial mammals and allow inferences of community structure surrounding two rivers in southeastern England. Community diversity and composition was then assessed based on species richness and β-diversity, with differences between communities partitioned into nestedness and turnover, and the sampling effort required to rapidly detect semi-aquatic and terrestrial species was evaluated based on species accumulation curves and occupancy modelling. eDNA metabarcoding detected 25 wild mammal species from five orders, representing the vast majority (82%) of the species expected in the area. The required sampling effort varied between orders, with common species (generally rodents, deer and lagomorphs) more readily detected, with carnivores detected less frequently. Measures of species richness differed between rivers (both overall and within each mammalian order) and patterns of β-diversity revealed the importance of species replacement in sites within each river, against a pattern of species loss between the two rivers. eDNA metabarcoding demonstrated its capability to rapidly detect mammal species, allowing inferences of community composition that will better inform future sampling strategies for this Class. Importantly, this study highlights the potential use of eDNA data for investigating mammalian community dynamics over different spatial scales.

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.

eDNA metabarcoding revealed differential structures of aquatic communities in a dynamic freshwater ecosystem shaped by habitat heterogeneity

Freshwater ecosystems have been threatened by complicated disturbances from both natural and anthropogenic variables, especially in dynamic and complex river basins. The environmental DNA (eDNA)-based approach provides a broader spectrum and higher throughput way of biomonitoring for biodiversity assessment compared with traditional morphological survey. Most eDNA metabarcoding studies have been limited to a few specific taxa/groups and habitat scopes. Here we applied the eDNA metabarcoding to characterize the structures and spatial variations of zooplankton and fish communities among different habitat types in a highly dynamic and complex freshwater ecosystem of the Daqing River basin (DRB). The results showed that varied species spectra of zooplankton and fish communities were identified and unique dominant species occurred across habitats. Additionally, markedly spatial distributions of biotic community structures were observed in areas with different habitat characteristics. Natural variables, including geographic distances and gradient ratio, as well as anthropogenic factors of chemical oxygen demand (COD) and organic chemicals demonstrated significant effects but different outcomes on the structures of zooplankton and fish communities. Moreover, the relative abundances of specific aquatic taxa were associated with the gradient of particular environmental variables. This case study verified the distribution patterns and differentiation mechanisms of biotic communities under habitat heterogeneity could be captured by application of eDNA biomonitoring. And habitat-specific and even species-specific environmental stressors would be diagnosed for improving management of complex river basins.

Validation of an Effective Protocol for Culicoides Latreille (Diptera: Ceratopogonidae) Detection Using eDNA Metabarcoding

Simple Summary

All organisms shed genetic material into the environment, which is known as environmental DNA. Current molecular technologies allow for sequencing molecular markers in complex environmental samples. The use of these methods permits an effective identification and monitoring of flighted insects such as Culicoides species. These biting midges are agricultural pests of significant economic concern. This study identified Culicoides species using a novel molecular-based approach for this group and compared these results to morphological identifications of the specimens collected. There were forty-two Culicoides specimens collected in total, using a saturated salt solution as a collection fluid. Molecular identification detected four species. Using morphological identification, we identified two out of these four taxonomic ranks at the species level and one at the subgenus level. The inconsistency in identifying Culicoides specimens to the species level indicates the need for curated DNA reference libraries for molecular-based identification. The saturated salt solution used in the traps preserved the morphological characteristics and the organisms’ environmental DNA, which is an essential contribution of this study.

Abstract

eDNA metabarcoding is an effective molecular-based identification method for the biosurveillance of flighted insects. An eDNA surveillance approach maintains specimens for secondary morphological identification useful for regulatory applications. This study identified Culicoides species using eDNA metabarcoding and compared these results to morphological identifications of trapped specimens. Insects were collected using ultraviolet (UV) lighted fan traps containing a saturated salt (NaCl) solution from two locations in Guelph, Ontario, Canada. There were forty-two Culicoides specimens collected in total. Molecular identification detected four species, C. biguttatus, C. stellifer, C. obsoletus, and C. mulrennani. Using morphological identification, two out of these four taxonomic ranks were confirmed at the species level (C. biguttatus and C. stellifer) and one was confirmed at the subgenus level (Avaritia [C. obsoletus]). No molecular detection of Culicoides species occurred in traps with an abundance of less than three individuals per taxon. The inconsistency in identifying Culicoides specimens to the species level punctuates the need for curated DNA reference libraries for Culicoides. In conclusion, the saturated salt (NaCl) solution preserved the Culicoides’ morphological characteristics and the eDNA.

Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot

Marine biodiversity can be surveyed using underwater visual censuses and recently with eDNA metabarcoding. Although a promising tool, eDNA studies have shown contrasting results related to its detection scale and the number of species identified compared to other survey methods. Also, its accuracy relies on complete reference databases used for taxonomic assignment and, as other survey methods, species detection may show false-negative and false-positive errors. Here, we compared results from underwater visual censuses and simultaneous eDNA metabarcoding fish surveys in terms of observed species and community composition. We also assess the effect of a custom reference database in the taxonomic assignment, and evaluate occupancy, capture and detection probabilities, as well as error rates of eDNA survey data. We amplified a 12S rRNA fish barcode from 24 sampling sites in the gulf of California. More species were detected with eDNA metabarcoding than with UVC. Because each survey method largely detected different sets of species, the combined approach doubled the number of species registered. Both survey methods recovered a known biodiversity gradient and a biogeographic break, but eDNA captured diversity over a broader geographic and bathymetric scale. Furthermore, the use of a modest-sized custom reference database significantly increased taxonomic assignment. In a subset of species, occupancy models revealed eDNA surveys provided similar or higher detection probabilities compared to UVC. The occupancy value of each species had a large influence on eDNA detectability, and in the false positive and negative error. Overall, these results highlight the potential of eDNA metabarcoding in complementing other established ecological methods for studies of marine fishes.

Optimization and validation of a cost-effective protocol for biosurveillance of invasive alien species

Environmental DNA (eDNA) metabarcoding has revolutionized biodiversity monitoring and invasive pest biosurveillance programs. The introduction of insect pests considered invasive alien species (IAS) into a non-native range poses a threat to native plant health. The early detection of IAS can allow for prompt actions by regulating authorities, thereby mitigating their impacts. In the present study, we optimized and validated a fast and cost-effective eDNA metabarcoding protocol for biosurveillance of IAS and characterization of insect and microorganism diversity. Forty-eight traps were placed, following the CFIA's annual forest insect trapping survey, at four locations in southern Ontario that are high risk for forest IAS. We collected insects and eDNA samples using Lindgren funnel traps that contained a saturated salt (NaCl) solution in the collection jar. Using cytochrome c oxidase I (COI) as a molecular marker, a modified Illumina protocol effectively identified 2,535 Barcode Index Numbers (BINs). BINs were distributed among 57 Orders and 304 Families, with the vast majority being arthropods. Two IAS (Agrilus planipennis and Lymantria dispar) are regulated by the Canadian Food Inspection Agency (CFIA) as plant health pests, are known to occur in the study area, and were identified through eDNA in collected traps. Similarly, using 16S ribosomal RNA and nuclear ribosomal internal transcribed spacer (ITS), five bacterial and three fungal genera, which contain species of regulatory concern across several Canadian jurisdictions, were recovered from all sampling locations. Our study results reaffirm the effectiveness and importance of integrating eDNA metabarcoding as part of identification protocols in biosurveillance programs.

Seasonal dynamics of riverine fish communities using eDNA

As fish communities are a major concern in rivers ecosystems, we investigated if their environmental (e)DNA signals vary according to the sampling period or hydromorphological conditions. Three rivers were studied over a year using eDNA metabarcoding approach. The majority of the species (c. 80%) were detected all year round in two rivers having similar hydromorphological conditions, whereas in the river affected by an upstream lake waterflow, more species were detected sporadically (42%). For all the rivers, in more than 98% of the occasional detections, the reads abundance represented <0.4% of the total reads per site and per sampling session. Even if the majority of the fish communities remained similar over the year for each of the three rivers, specific seasonal patterns were observed. We studied if the waterflow or the reproduction period had an effect on the observed dynamics. Waterflow, which influences eDNA downstream transportation, had a global influence in taxonomic richness, while the fishes' reproductive period had only an influence on certain species. Our results may help selecting the best sampling strategy according to research objectives. To study fish communities at local scale, seasons of low waterflow periods are recommended. This particularly helps to restraint effects of external eDNA coming from connections with other aquatic environment (tributaries, lakes, wetlands, sewage effluents, etc.). To obtain a more integrative overview of the fish community living in a river basin, high waterflow or breeding seasons are preferable for enhancing species detection probability, especially for rare species.

Benthic monitoring of oil and gas offshore platforms in the North Sea using environmental DNA metabarcoding

Since 2010, considerable efforts have been undertaken to monitor the environmental status of European marine waters and ensuring the development of methodological standards for the evaluation of this status. However, the current routine biomonitoring implicates time-consuming and costly manual sorting and morphological identification of benthic macrofauna. Environmental DNA (eDNA) metabarcoding represents an alternative to the traditional monitoring method with very promising results. Here, we tested it further by performing eDNA metabarcoding of benthic eukaryotic communities in the vicinity of two offshore oil and gas platforms in the North Sea. Three different genetic markers (18S V1V2, 18S V9 and COI) were used to assess the environmental pressures induced by the platforms. All markers showed patterns of alpha and beta diversity consistent with morphology-based macrofauna analyses. In particular, the communities' structure inferred from metabarcoding and morphological data significantly changed along distance gradients from the platforms. The impact of the operational discharges was also detected by the variation of biotic index values, AMBI index showing the best correlation between morphological and eDNA data sets. Finally, the sediment physicochemical parameters were used to build a local de novo pressure index that served as benchmark to test the potential of a taxonomy-free approach. Our study demonstrates that metabarcoding approach outperforms morphology-based approach and can be used as a cost and time-saving alternative solution to the traditional morphology-based monitoring in order to monitor more efficiently the impact of industrial activities on marine biodiversity.

Effects of soil preservation for biodiversity monitoring using environmental DNA

Environmental DNA (eDNA) metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa such as soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guideline for best practices so far. Here, we assessed the impact of four methods of soil sample preservation that can be conveniently used also in metabarcoding studies targeting remote or difficult to access areas. Tested methods include: preservation at room temperature for 6 hr, preservation at 4°C for 3 days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6 hr at room temperature and preservation for 21 days. For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under ideal conditions (i.e., extraction of eDNA immediately after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in molecular operational taxonomic units (MOTU) richness of bacteria, fungi and eukaryotes across treatments, but MOTU richness was similar across preservation methods if rare taxa were not considered. All the approaches were able to identify differences in community structure among habitats, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.

Assessment of fish biodiversity in four Korean rivers using environmental DNA metabarcoding

Environmental DNA (eDNA) metabarcoding is a cost-effective novel approach to estimate biodiversity in an ecosystem. In this study, the MiFish pipeline was employed to test if the system methodology is sufficiently reliable to estimate fish biodiversity in Korean rivers. A total of 125 unique haplotypes and 73 species were identified at the species level from 16 water samples collected from a single survey in four Korean rivers (Hyeongsan, Taehwa, Seomjin, and Nakdong). Among the four rivers, the highest species richness was recorded in the Seomjin River (52 species), followed by the Taehwa (42 species) and Hyeongsan (40 species) rivers. The Nakdong River (26 species) presented the lowest species richness and number of endemic species, presumably due to its metropolitan location and anthropogenic impacts, such as dams or weirs. We were also able to detect that five exotic species (Carassius cuvieri, Cyprinus carpio, Cyprinus megalophthalmus, Lepomis macrochirus, and Micropterus salmoides) are widely distributed in all surveyed rivers, a situation that might be problematic in terms of conservation. Our findings indicate that the eDNA metabarcoding technique is one of the most cost-effective scientific tools available for the management and conservation of the freshwater fish resources available in Korea. However, the low number of 12S sequences of endemic species in the database and low resolution of the MiFish region for differentiating several taxa should be upgraded for their wide use.

Identifying error and accurately interpreting environmental DNA metabarcoding results: A case study to detect vertebrates at arid zone waterholes

Environmental DNA (eDNA) metabarcoding surveys enable rapid, noninvasive identification of taxa from trace samples with wide-ranging applications from characterizing local biodiversity to identifying food-web interactions. However, the technique is prone to error from two major sources: (a) contamination through foreign DNA entering the workflow, and (b) misidentification of DNA within the workflow. Both types of error have the potential to obscure true taxon presence or to increase taxonomic richness by incorrectly identifying taxa as present at sample sites, but multiple error sources can remain unaccounted for in metabarcoding studies. Here, we use data from an eDNA metabarcoding study designed to detect vertebrate species at waterholes in Australia's arid zone to illustrate where and how in the workflow errors can arise, and how to mitigate those errors. We detected the DNA of 36 taxa spanning 34 families, 19 orders and five vertebrate classes in water samples from waterholes, demonstrating the potential for eDNA metabarcoding surveys to provide rapid, noninvasive detection in remote locations, and to widely sample taxonomic diversity from aquatic through to terrestrial taxa. However, we initially identified 152 taxa in the samples, meaning there were many false positive detections. We identified the sources of these errors, allowing us to design a stepwise process to detect and remove error, and provide a template to minimize similar errors that are likely to arise in other metabarcoding studies. Our findings suggest eDNA metabarcoding surveys need to be carefully conducted and screened for errors to ensure their accuracy.

Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle

Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict (R² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.

Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol

Automated species identification based on data produced with metabarcoding offers an alternative for assessing biodiversity of bulk insect samples obtained with traps. We used a standard two-step PCR approach to amplify a 313 bp fragment of the barcoding region of the mitochondrial COI gene. The PCR products were sequenced on an Illumina MiSeq platform, and the OTUs production and taxonomic identifications were performed with a customized pipeline and database. The DNA used in the PCR procedures was extracted directly from the preservative ethanol of bulk insect samples obtained with automatic light traps in 12 sampling areas located in different biomes of Brazil, during wet and dry seasons. Agricultural field and forest edge habitats were collected for all sampling areas. A total of 119 insect OTUs and nine additional OTUs assigned to other arthropod taxa were obtained at a ≥97% sequence similarity level. The alpha and beta diversity analyses comparing biomes, habitats, and seasons were mostly inconclusive, except for a significant difference in beta diversity between biomes. In this study, we were able to metabarcode and HTS adult insects from their preservative medium. Notwithstanding, our results underrepresent the true magnitude of insect diversity expected from samples obtained with automatic light traps in Brazil. Although biological and technical factors might have impacted our results, measures to optimize and standardize eDNA HTS should be in place to improve taxonomic coverage of samples of unknown diversity and stored in suboptimal conditions, which is the case of most eDNA samples.

Holistic pelagic biodiversity monitoring of the Black Sea via eDNA metabarcoding approach: From bacteria to marine mammals

As the largest semi-closed marine ecosystem in the world, the Black Sea has been heavily affected by human activities for a long time. Describing the biodiversity of multi-trophic biota in pelagic zone of the Black Sea and identifying the dominant environmental factors are prerequisites for protecting the sustainability of ecosystems. However, up to now, the taxonomic and distributional information about the Black Sea biota is not clear. Here, we employed a Tree-of-Life metabarcoding to analyze the biodiversity of eight communities in the Black Sea, investigated their biogeographical distribution, and further analyzed the influence of biological and abiotic factors on biota on large scales. We found that, (1) Over 8900 OTUs were detected in the Black Sea, of which 630 species were identified, covering the holistic biota from single-celled (bacteria 5620 OTUs 141 species; algae 1096 OTUs 185 species; protozoa 546 OTUs 146 species) to multicellular organisms (invertebrate metazoans 150 OTUs 34 species; fishes 1369 OTUs 76 species; large marine mammals 39 OTUs 5 species). (2) Higher trophic organisms (fishes and large mammals) distributed more evenly in space than the lower (microorganisms, protozoa and invertebrates). For lower trophic organisms, the vertical stratification was more obvious than the horizontal stratification (vertical p < 0.02, horizontal p < 0.05). (3) The bottom trophic organisms (bacteria and algae) of the food web significantly affected the distribution and composition of the others through biological interactions (Mantel p < 0.05). (4) At the level of abiotic factors, the effect of local species sorting on the composition of communities was 15% higher than that of mass dispersal effect. For the first time, this study monitored and profiled the holistic biodiversity in the pelagic zone of the Black Sea, and provided technological advances and preliminary knowledge for the ongoing Black Sea ecosystem protection efforts.

Assessment of fish communities using environmental DNA: Effect of spatial sampling design in lentic systems of different sizes

Freshwater fish biodiversity is quickly decreasing and requires effective monitoring and conservation. Environmental DNA (eDNA)-based methods have been shown to be highly sensitive and cost-efficient for aquatic biodiversity surveys, but few studies have systematically investigated how spatial sampling design affects eDNA-detected fish communities across lentic systems of different sizes. We compared the spatial patterns of fish diversity determined using eDNA in three lakes of small (SL; 3 ha), medium (ML; 122 ha) and large (LL; 4,343 ha) size using a spatially explicit grid sampling method. A total of 100 water samples (including nine, 17 and 18 shoreline samples and six, 14 and 36 interior samples from SL, ML and LL, respectively) were collected, and fish communities were analysed using eDNA metabarcoding of the mitochondrial 12S region. Together, 30, 35 and 41 fish taxa were detected in samples from SL, ML, and LL, respectively. We observed that eDNA from shoreline samples effectively captured the majority of the fish diversity of entire waterbodies, and pooled samples recovered fewer species than individually processed samples. Significant spatial autocorrelations between fish communities within 250 m and 2 km of each other were detected in ML and LL, respectively. Additionally, the relative sequence abundances of many fish species exhibited spatial distribution patterns that correlated with their typical habitat occupation. Overall, our results support the validity of a shoreline sampling strategy for eDNA-based fish community surveys in lentic systems but also suggest that a spatially comprehensive sampling design can reveal finer distribution patterns of individual species.

Multi-marker eDNA metabarcoding survey to assess the environmental impact of three offshore gas platforms in the North Adriatic Sea (Italy)

The environmental DNA (eDNA) metabarcoding represents a new promising tool for biomonitoring and environmental impact assessment. One of the main advantages of eDNA metabarcoding, compared to the traditional morphotaxonomy-based methods, is to provide a more holistic biodiversity information that includes inconspicuous morphologically non-identifiable taxa. Here, we use eDNA metabarcoding to survey marine biodiversity in the vicinity of the three offshore gas platforms in North Adriatic Sea (Italy). We isolated eDNA from 576 water and sediment samples collected at 32 sampling sites situated along four axes at increasing distances from the gas platforms. We obtained about 46 million eDNA sequences for 5 markers from nuclear 18S V1V2, 18S V4, 18S 37F and mitochondrial 16S and COI genes that cover a wide diversity of benthic and planktonic eukaryotes. Our results showed some impact of platform activities on benthic and pelagic communities at very close distance (<50 m), while communities for intermediate (125 m, 250 m, 500 m) and reference (1000 m, 2000 m) sites did not show any particular biodiversity changes that could be related to platforms activities. The most significant community change along the distance gradient was obtained with the 18S V1V2 marker targeting benthic eukaryotes, even though other markers showed similar trends, but to a lesser extent. These results were congruent with the AMBI index inferred from the eDNA sequences assigned to benthic macrofauna. We finally explored the relation between various physicochemical parameters, including hydrocarbons, on benthic community in the case of one of the platforms. Our results showed that these communities were not significantly impacted by most of hydrocarbons, but rather by macro-elements and sediment texture.

SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data

Background

High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) has become a routine tool for biodiversity survey and ecological studies. By including sample-specific tags in the primers prior PCR amplification, it is possible to multiplex hundreds of samples in a single sequencing run. The analysis of millions of sequences spread into hundreds to thousands of samples prompts for efficient, automated yet flexible analysis pipelines. Various algorithms and software have been developed to perform one or multiple processing steps, such as paired-end reads assembly, chimera filtering, Operational Taxonomic Unit (OTU) clustering and taxonomic assignment. Some of these software are now well established and widely used by scientists as part of their workflow. Wrappers that are capable to process metabarcoding data from raw sequencing data to annotated OTU-to-sample matrix were also developed to facilitate the analysis for non-specialist users. Yet, most of them require basic bioinformatic or command-line knowledge, which can limit the accessibility to such integrative toolkits. Furthermore, for flexibility reasons, these tools have adopted a step-by-step approach, which can prevent an easy automation of the workflow, and hence hamper the analysis reproducibility.

Results

We introduce SLIM, an open-source web application that simplifies the creation and execution of metabarcoding data processing pipelines through an intuitive Graphic User Interface (GUI). The GUI interact with well-established software and their associated parameters, so that the processing steps are performed seamlessly from the raw sequencing data to an annotated OTU-to-sample matrix. Thanks to a module-centered organization, SLIM can be used for a wide range of metabarcoding cases, and can also be extended by developers for custom needs or for the integration of new software. The pipeline configuration (i.e. the modules chaining and all their parameters) is stored in a file that can be used for reproducing the same analysis.

Conclusion

This web application has been designed to be user-friendly for non-specialists yet flexible with advanced settings and extensibility for advanced users and bioinformaticians. The source code along with full documentation is available on the GitHub repository (https://github.com/yoann-dufresne/SLIM) and a demonstration server is accessible through the application website (https://trtcrd.github.io/SLIM/).

eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity

Because significant global changes are currently underway in the Arctic, creating a large-scale standardized database for Arctic marine biodiversity is particularly pressing. This study evaluates the potential of aquatic environmental DNA (eDNA) metabarcoding to detect Arctic coastal biodiversity changes and characterizes the local spatio-temporal distribution of eDNA in two locations. We extracted and amplified eDNA using two COI primer pairs from ~80 water samples that were collected across two Canadian Arctic ports, Churchill and Iqaluit, based on optimized sampling and preservation methods for remote regions surveys. Results demonstrate that aquatic eDNA surveys have the potential to document large-scale Arctic biodiversity change by providing a rapid overview of coastal metazoan biodiversity, detecting nonindigenous species, and allowing sampling in both open water and under the ice cover by local northern-based communities. We show that DNA sequences of ~50% of known Canadian Arctic species and potential invaders are currently present in public databases. A similar proportion of operational taxonomic units was identified at the species level with eDNA metabarcoding, for a total of 181 species identified at both sites. Despite the cold and well-mixed coastal environment, species composition was vertically heterogeneous, in part due to river inflow in the estuarine ecosystem, and differed between the water column and tide pools. Thus, COI-based eDNA metabarcoding may quickly improve large-scale Arctic biomonitoring using eDNA, but we caution that aquatic eDNA sampling needs to be standardized over space and time to accurately evaluate community structure changes.

Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds

PREMISE OF THE STUDY

The detection of environmental DNA (eDNA) using high-throughput sequencing has rapidly emerged as a method to detect organisms from environmental samples. However, eDNA studies of aquatic biomes have focused on surveillance of animal species with less emphasis on plants. Pondweeds are important bioindicators of freshwater ecosystems, although their diversity is underestimated due to difficulties in morphological identification and monitoring.

METHODS

A protocol was developed to detect pondweeds in water samples using atpB-rbcL and ITS2 markers. The water samples were collected from the Grand River within the rare Charitable Research Reserve, Ontario (RARE). Short fragments were amplified using primers targeting pondweeds, sequenced on an Ion Torrent Personal Genome Machine, and assigned to the taxonomy using a local DNA reference library and GenBank.

RESULTS

We detected two species earlier documented at the experimental site during ecological surveys (Potamogeton crispus and Stuckenia pectinata) and three species new to the RARE checklist (P. foliosus, S. filiformis, and Zannichellia palustris).

DISCUSSION

Our targeted approach to track the species composition of pondweeds in freshwater ecosystems revealed underestimation of their diversity. This result suggests that eDNA is an effective tool for monitoring plant diversity in aquatic habitats.

Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture

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

Improving herpetological surveys in eastern North America using the environmental DNA method

Among vertebrates, herpetofauna has the highest proportion of declining species. Detection of environmental DNA (eDNA) is a promising method towards significantly increasing large-scale herpetological conservation efforts. However, the integration of eDNA results within a management framework requires an evaluation of the efficiency of the method in large natural environments and the calibration of eDNA surveys with the quantitative monitoring tools currently used by conservation biologists. Towards this end, we first developed species-specific primers to detect the wood turtle (Glyptemys insculpta) a species at risk in Canada, by quantitative PCR (qPCR). The rate of eDNA detection obtained by qPCR was also compared to the relative abundance of this species in nine rivers obtained by standardized visual surveys in the Province of Québec (Canada). Second, we developed multi-species primers to detect North American amphibian and reptile species using eDNA metabarcoding analysis. An occurrence index based on the distribution range and habitat type was compared with the eDNA metabarcoding dataset from samples collected in seven lakes and five rivers. Our results empirically support the effectiveness of eDNA metabarcoding to characterize herpetological species distributions. Moreover, detection rates provided similar results to standardized visual surveys currently used to develop conservation strategies for the wood turtle. We conclude that eDNA detection rates may provide an effective semiquantitative survey tool, provided that assay calibration and standardization is performed.