Environmental DNA最新文献

Reunion Island is in the South-West Indian Ocean (SWIO), where all freshwater fish species are diadromous. The ecological status assessments of freshwater in watersheds have revealed a continuing deterioration in these fish populations due to anthropic pressures. In this context, monitoring the fish's biological sustainability is crucial to ensure the health of these estuarine ecosystems. The aim of this study was to compare the efficacy of conventional electrofishing monitoring (EF) with the environmental DNA metabarcoding tool to evaluate fish biodiversity in the estuaries. We measured the diversity and structure of the fish community in three estuaries with various geographical, hydrological, and anthropogenic conditions over different seasons. To this end, fish were captured by EF, and we then isolated DNA from the water samples to perform bioinformatic analyses derived from eDNA, using the 12S marker. Statistical analyses were carried out to compare the results of these two methods. For all watersheds combined, a comparison of the results for measuring fish richness showed that eDNA performed significantly better than EF. Indeed, the eDNA detected 31 species, whereas the EF detected only 12 species. For both methods, we observed significant differences in community structure between watersheds, with a significant nestedness phenomenon where the fish assemblage obtained from EF captures is a sub-assemblage of that obtained from eDNA. Moreover, compared to EF, eDNA enabled the detection of endemic to the Mascarene region species (e.g., Cotylopus acutipinnis), introduced exotic species (e.g., Oreochromis niloticus), and species difficult to capture and identify due to their juvenile life stage through EF (e.g., Anguilla sp.). Our data confirm the effectiveness of eDNA to detect fish species, both taxonomically and in terms of species richness and proves to be an effective tool for monitoring fish diversity of the islands of the SWIO.

Environmental DNA (eDNA) offers an efficient approach to biodiversity monitoring and biosecurity surveillance in coastal ecosystems. Understanding eDNA dynamics in tidal areas is critical for guiding sampling strategy design and interpreting molecular detection results. In a field study conducted at Ōpua, Bay of Islands, Aotearoa, New Zealand, an international marina with a dynamic coastal environment, we investigated eDNA detection patterns across a local spatial and temporal gradient. Hourly samples were collected from six sampling stations around the marina, from artificial shore structures and a channel, over a 12-h tidal cycle. Detected eukaryotic communities were assessed using eDNA metabarcoding analysis of the small-subunit ribosomal RNA (18S rRNA) and mitochondrial Cytochrome C Oxidase subunit I (COI) genes. This core community was screened for marine nonindigenous species (NIS) using an online metabarcoding data screening app (ExPAT). Community composition varied significantly based on sampling location and time, with most of the core community captured around mid-tide. The NIS community exhibited inconsistent detection for some species (e.g., the amphipod Monocorophium acherusicum) across space and time, whereas other NIS (e.g., the mussel Arcuatula senhousia) were consistently detected and behaved similar to the core community. Overall, species-specific eDNA detection patterns may be linked to the biology and movement of the organism. The results indicated slightly higher NIS detection from artificial structures at the shore stations and within 2 h of low tide. For marine biosecurity applications, users may want to prioritize sampling near-shore during low tide, while samples collected during mid-tide may provide more comprehensive insights into the core community for biomonitoring. Further field studies across multiple tidal cycles and marinas may guide the standardization of molecular biomonitoring and biosurveillance sampling strategies and support their broader integration into marine biosecurity programs.

Environmental DNA (eDNA) analysis is a powerful tool for quantifying and assessing the diversity of organisms in the environment. Unfortunately, isolating eDNA from aquatic environments is challenging due to the difficulties associated with water collection, preservation of samples during transportation, and onsite filtration. These processes are expensive and time-consuming and can lead to eDNA degradation. These difficulties can be addressed by preserving eDNA in the collected water. In this study, we assessed the effect of short- and long-term water storage using three different cationic surfactants on the half-life of zebrafish (Danio rerio) mitochondrial DNA (mtDNA) in mesocosm water. The surfactants used were benzalkonium chloride (BAC), cetylpyridinium chloride (CPC), and cetyltrimethylammonium bromide (CTAB). We observed that CPC and CTAB treatment extended the half-life of mtDNA by 3–5 times. Analysis by quantitative polymerase chain reaction (qPCR) demonstrated a mtDNA retention rate of 17.6%, 26.3%, and 2.2% for CPC, CTAB, and BAC, respectively, compared to 0.1% in untreated water after 30 days. The preservation of mtDNA by cationic surfactants was attributed to their bactericidal and cytotoxic properties as well as their electrostatic interaction with DNA molecules, as observed by spectrofluorometric analysis and subsequent precipitation. Our results demonstrated an inexpensive and convenient method to protect eDNA in water and improve its extraction.

Marine metazoan biodiversity is accretively being explored through environmental DNA (eDNA) metabarcoding of seawater. However, knowledge gaps in the use of eDNA to study changes in diversity resulting from changing abiotic conditions still do exist. In order to address these gaps, we analyzed patterns of marine invertebrate biodiversity based on eDNA from water and sediment samples along a decreasing salinity gradient from the North Sea toward the Baltic Sea. eDNA was collected from surface (SW) and bottom (BW) water, and from the uppermost sediment layer (SE). To supplement the eDNA approach, we conducted parallel zooplankton (ZP) metabarcoding and morphological identification. DNA was extracted from eDNA and ZP samples, amplified using two universal primers that target of the mitochondrial cytochrome c oxidase subunit 1 (COI) and the nuclear ribosomal 18S rRNA genes, and paired-end sequenced on Illumina Miseq. Metabarcoding detected 279 metazoan species (from 16 phyla) of which > 87% are known from the study area or adjacent regions. Communities identified in SW eDNA were a subset of communities identified in ZP metabarcoding. BW eDNA had additional benthic (mainly bivalve) species. Communities identified in SE eDNA were distinct from those in water eDNA and ZP metabarcoding, and mainly represented by in- and meiofauna. Out of all approaches, only ZP metabarcoding uncovered the expected decrease in species richness toward brackish conditions. Neither salinity nor spatial distance had a significant effect on species composition. All approaches revealed regional differences of which SE eDNA was least informative. The detection of holoplanktonic species from SE eDNA provided evidence for sinking of eDNA particles, dead organisms or the presence of resting eggs. Our study confirms the value of metabarcoding to identify the North Sea and Baltic Sea invertebrates and underscores the importance of combining multiple approaches to understand invertebrate biodiversity and its change in the marine realm.

Bats are a species-rich mammalian order that provide a host of ecosystem services, but presently face threats from habitat loss, disease, climate change, and insect declines. Bat species often co-occur with other ecologically similar bats, making them a suitable group in which to study niche overlap and partitioning. This study aimed to compare different non-invasive sources of data on wildlife populations, while examining dietary, temporal, and spatial partitioning patterns among sympatric bat species. We used two different methods to assess niche partitioning among insectivorous bats at a site in the San Francisco Bay Area, California: (1) eDNA sequencing of bat feces that were collected weekly from a bat roost, and (2) nightly acoustic recordings of ultrasonic bat calls from recorders at multiple sites. Both the eDNA and acoustic data were collected over the course of an entire roosting season in 2020. We hypothesized that the insectivorous bats at this site would rely on one or more niche partitioning mechanisms to promote interspecific coexistence and limit competition. We found evidence of fine-scale spatial partitioning of the broad community of bat species in our study area based on acoustic data, as well as temporal differences in activity of different species. The two species using the roosting site, Tadarida brasiliensis and Eptesicus fuscus, displayed some differences in the identities and relative abundances of prey species consumed, but both ultimately exhibited a strong reliance on dipterans and aquatic-dependent insects. We demonstrate differences between the acoustic data and eDNA data, which has implications for how such datasets may be interpreted in future research. The study finds evidence of some types of niche partitioning in this community and characterizes baseline interactions between species, providing a foundation for future efforts to non-invasively monitor for unexpected biological change in local ecosystems.

Traditional approaches for studying potential interactions in marine ecosystems often struggle to fully capture all taxa in a community, especially rare species. This issue is particularly challenging in coastal waters with high biodiversity and spatiotemporal dynamics. In this study, we employed environmental DNA (eDNA) metabarcoding, utilizing multiple marker genes, to comprehensively investigate interspecific interactions across various domains in the subtropical coastal waters of Hong Kong. The southern and eastern regions of Hong Kong waters exhibit distinct environmental seasonality, and our investigation focused on comparing the potential interaction networks and the keystone taxa between these two regions. The putative species interaction networks across various groups (i.e., bacteria, protists, and metazoans) were revealed by using weighted correlation network analysis (WGCNA). Our results showed that primary consumers, mainly dinoflagellates and ciliates, were the dominant actors within the interaction networks, although their distributions varied between the two regions. Bacterial taxa from the Pseudomonadota groups primarily constituted saprobes in the southern region, while exhibiting an even distribution in the eastern region. The interaction network in the southern region was larger but less stable compared to the eastern region. This could be attributed to the stronger responses of keystone taxa to environmental variations and the relatively higher number of connectors (e.g., Akashiwo and Protoperidinium within Dinophyceae) in the eastern region. Our findings highlight the versatility of eDNA metabarcoding for studying potential species interactions, providing critical insights into ecosystem structure and stability, and offering suggestions for marine biodiversity conservation.

Ecosystems in coastal waters of Gulf of Maine (GOM) are undergoing environmental challenges in response to climate change and anthropogenic stressors. eDNA metabarcoding, a powerful tool for assessing the fish community structure, was used to identify fish communities in three types of GOM aquatic environments (sand, macroalgae, and eelgrass) in Maine and New Hampshire, USA. The available 12S rRNA fish universal primer analysis system (MiFish and 12S-V5) was modified using nested polymerase chain reaction (PCR) to improve targeting of fish products and reduce non-target products. The nested PCR strategy allowed successful amplification of 12S rRNA genes in fishes without production of non-target products and identified 28 fish groups at the genus level. Presence/Absence data and Relative Abundance showed significant differences among locales but not among habitats. Myoxocephalus sp. were found at all sampling sites. Relative Abundance data revealed that Menidia menidia and Brevoortia sp. were statistical indicator species in Goosefare, Maine, and New castle, New Hampshire, respectively. Although beta diversity indicated that fish communities were not different across habitats, statistical analysis found that Pholis sp. and Ammodytes sp. were dominant species in macroalgae and sand, respectively. To our knowledge, this is the first metabarcoding study to assess fish communities in the Western Atlantic region using the MiFish primer set, and the study suggests that metabarcoding is useful for mapping geographic and temporal marine fish diversity.

Marine biodiversity worldwide is rapidly declining, and nowhere is this more evident than in coastal ecosystems where the impacts of climate change and anthropogenic activities concentrate. The ongoing biodiversity crisis affects all components of the marine food web, but data required to monitor biodiversity shifts at continental scales are scarce and taxonomically and spatially heterogeneous. The application of environmental DNA metabarcoding can complement traditional approaches to monitoring marine biodiversity, but its efficiency in detecting large-scale biogeographic breaks remains to be tested. Using 86 coastal surface water samples collected during the Canada C3 expedition in the summer of 2017, we investigated metazoan biodiversity across Canada's three oceans—North Pacific, Arctic and North Atlantic—using multi-marker eDNA metabarcoding. The resulting dataset, combining information from seven separate amplicons, identified 1477 unique species ranging from zooplankton to marine mammals. We found that marine coastal biodiversity around Canada separated into four clusters that overlapped with known marine ecoregions, indicating a higher connectivity between the Arctic and Atlantic than between the Arctic and Pacific clusters. However, the detection of Pacific salmon eDNA in the Canadian Arctic suggests that these species may be extending their Pacific distribution range poleward. By comparing the distribution of eDNA with species occurrence recorded in the Ocean Biodiversity Information System (OBIS) for Canada and Alaska coastal waters, we identified 324 “unexpected” species. These results demonstrate the importance of primer selection for species-specific applications of eDNA metabarcoding and provide a benchmark for further work aimed at validating species identification and map species distribution at large spatial scale. Our results showed that eDNA metabarcoding is a powerful method for monitoring biodiversity shifts at an interoceanic scale. Integrating eDNA into monitoring programs can provide valuable insights into biodiversity changes associated with climate change and contribute to filling gaps in the distribution of species-at-risk.

Estuarine habitats serve as critical feeding and nursery grounds for many aquatic species and support fisheries. However, monitoring these complex ecosystems using conventional trawling methods is destructive, costly, and labor-intensive. This study compared trawling and a multi-marker environmental DNA (eDNA) metabarcoding approach to monitor marine vertebrate and crustacean communities in an estuarine environment in subtropical Hong Kong. We analyzed 16 bottom trawl samples and the eDNA from 32 two-liter water samples using primer sets specific to fishes and mammals (MiFish-U, 12S-V5, and Berry-Fish) and decapod crustaceans (MiDeca). We found that the eDNA approach detected more pelagic and demersal fishes (237 vs. 106 in trawling) and elasmobranchs (6 vs. 3) than trawling. The eDNA approach was also more effective than trawling in detecting threatened vertebrates (16 vs. 4), including the Indo-Pacific Finless Porpoise and the critically endangered Large Yellow Croaker. Among the detected fish at species level, 70 species were detected by both approaches, 32 species were detected by trawling only, and 142 species were detected by the eDNA approach only. Regarding crustaceans, the eDNA approach detected slightly fewer decapods (61 vs. 77) and stomatopods (5 vs. 8) than trawl surveys. However, the eDNA approach could be enhanced through the development of suitable decapod-specific primers and the expansion of the local reference database. In addition, multivariate analyses of the eDNA data revealed spatial patterns of fish and crustacean assemblages that might be associated with sediment loading, oxygen, and nutrient levels. Furthermore, there was a positive correlation between eDNA read counts and trawl catch, but their correlation coefficient was low. We conclude that eDNA metabarcoding can provide high-resolution detection of species, composition, and unravel community–environment relationships in estuarine ecosystems. Overall, integrating the non-destructive eDNA approach can complement the conventional trawling method for better-informed sustainable fishery management and conservation.

Environmental DNA (eDNA) has significant potential to improve the efficiency of biological sampling and detect species that pose challenges for traditional sampling methods. However, a key obstacle in utilizing eDNA data for ecosystem management is uncertainty surrounding the ability to estimate abundance or biomass of multiple species simultaneously. In this study, we use experimental trials with known biomasses of multiple species to explore the feasibility of (1) estimating species proportions from eDNA metabarcoding data and (2) estimating absolute eDNA concentrations of multiple species by scaling metabarcoding proportions with eDNA concentrations of a single species obtained from qPCR. The focal species for this study were three gadid fishes that are key components of marine ecosystems in Alaska and vary in their distribution and habitat use: Walleye pollock (Gadus chalcogrammus), Pacific cod (Gadus macrocephalus), and Arctic cod (Boreogadus saida). After designing gadid-specific metabarcoding primers and accounting for PCR biases in the metabarcoding data, we found corrected read proportions closely approximated the true biomass proportions of species. Furthermore, we found strong positive relationships between absolute eDNA concentration and absolute biomass for Arctic cod and Pacific cod using quantitative metabarcoding data combined with estimates of Walleye pollock eDNA concentration derived from qPCR. These findings suggest that it is possible to accurately quantify species compositions and estimate metrics of biomass for gadids in real-world scenarios. Furthermore, this work provides a framework for developing primers and analytical approaches that can be applied to other species to improve the quantitative utility of eDNA.