Environmental DNA最新文献

Artificial reefs are widely deployed to restore marine biodiversity and ecosystem functions. Benthic meiofauna and macrofauna are key indicators of reef ecological performance, yet their small size and habitat complexity make traditional sampling methods inefficient. Environmental DNA (eDNA) metabarcoding offers a powerful alternative to characterize these communities comprehensively. In this study, we used benthic eDNA targeting the COI marker to investigate metazoan biodiversity, co-occurrence networks, and network stability in two artificial reef ecosystems: Wanshan (WR, shallow) and Miaowan (MR, deep), across 12 sites in both dry and wet seasons (n = 92 samples). Our results showed that artificial reef deployment can induce localized velocity changes (0.005–0.03 m/s), with mean water velocity during flood and ebb peaks significantly higher in shallow reef waters, 1.6 times higher than in deep reef waters (p < 0.001). Dissolved oxygen (DO) concentrations were consistently higher in WR than in MR across both dry and wet seasons (p < 0.05). Alpha diversity was significantly higher in the dry season but did not differ between sites. Community structure varied significantly across both spatial and temporal scales, with the lowest Bray–Curtis dissimilarity observed in MR during the wet season (p < 0.05). Co-occurrence network analysis revealed greater complexity in the dry season, whereas higher network stability in the wet season was likely driven by increased contributions of homogeneous selection. Notably, Rhopilema hispidum and Pseudorhombus oligodon were identified as indicator and keystone species in MR during the wet season, potentially contributing to network stability. Random forest analysis identified temperature, nitrite, and DO as the primary predictors of community variation. Overall, our findings highlight the importance of integrating both biodiversity and network stability when evaluating the ecological effects of artificial reefs, providing a framework for understanding their role in marine ecosystem restoration.

The white-clawed crayfish (Austropotamobius pallipes) is IUCN Red-Listed as globally endangered being in unfavorable (bad) status in both the UK and Ireland. Crayfish, and crayfish plague (Aphanomyces astaci) eDNA were sampled at 110 sites throughout Northern Ireland during 2024. Crayfish eDNA was detected at 45% of sites comparable to sightings and field signs at 44% of sites during the last survey in 2017. All samples were crayfish plague eDNA negative. Crayfish eDNA detection was unrelated to water levels preceding sampling, or the volume of water filtered, but declined throughout September and October reflecting the end of the survey season as crayfish are less active in cooler conditions. Future surveys should be restricted to late spring to mid-summer when crayfish are more active. Crayfish were detected more frequently at sites with past records, and those with more recent than old records, suggesting vulnerability to local extirpation. Crayfish distribution was restricted by calcareous bedrock, where calcium is necessary for shell growth, and occurrence was higher at rivers than lakes, in lowland grassland sites with boulder and cobble substrates. At rivers, occurrence was higher in wider channels and at lakes with rocky shores. Eighteen perceived pressures were recorded, notably, risk of siltation from adjacent plowing (49% of sites), pollution (47% of sites) mostly agricultural in origin (32% of sites) where livestock (mostly cattle) access to water (44% of sites) demonstrably lowered crayfish eDNA detection by −33%. This study suggested there has been no change in white-clawed crayfish conservation status in Northern Ireland which remains vulnerable to stochastic extirpation potentially driven by water quality deterioration principally associated with agriculture. Concerns are raised about the condition of white-clawed crayfish in Areas of Special Scientific Interest (ASSIs) especially four key sites with the species as their designated feature. Eighteen candidate conservation measures are identified.

Environmental DNA (eDNA) metabarcoding offers an effective solution to determine fish species compositions in communities across diverse environments. However, it is not clear how different metabarcoding primers perform in terms of recovering fish species and community diversity in the Indo-Pacific bioregion. In this study, we compared the relative performance of five metabarcoding primers (Berry 16S, Riaz 12S, MiFish E 12S, MiFish U 12S, and Leray CO1) in recovering Indo-Pacific fish taxa. We tested the primers using template DNA from three different environments: (1) a controlled mock community composed of tissue-based DNA extractions from 96 species, (2) a semi-controlled Indo-Pacific reef fish community from a public aquarium tank, and (3) a natural tropical coral reef lagoon. In the mock community sample, each primer recovered a distinct subset of the community, and no single primer recovered all taxa. Of the 65 distinct genera included in the mock community, all but six were recovered by at least one primer, representing 91% of genera. Fifty-nine of the 96 included species (61%) were identified to species level using at least one primer set. From the aquarium community, 17 of the 20 known genera were recovered (85%), and 13 out of 24 (54%) censused species were identified by at least one primer. In the coral reef lagoon, 48 genera were identified, and 47 species-level identifications were made, including 87% endemic and established species. Overall, we find Riaz 12S performed better than other fish-specific markers, although there were differences in the specific fish taxa recovered. While all markers performed well in the mock community in terms of the relative proportion of fish sequences recovered, this did not accurately predict how they would perform under natural conditions. Caution is therefore urged in using a mock community alone to evaluate metabarcoding primer performance for studies in natural environments.

The East Asian–Australasian Flyway (EAAF) is experiencing notable population declines in its migratory waterbird species. Understanding the foraging ecology of these waterbirds, including ducks, is crucial for monitoring and safeguarding their food sources and wetland habitats. Here, we used a DNA metabarcoding approach to analyze fecal DNA from duck species to elucidate their dietary composition during the wintering period in a subtropical East Asian wetland. By employing multiple markers (18S, COI, and trnL) targeting different taxonomic groups and levels, we offered a comprehensive dietary analysis for omnivores that consume both plants and animals. We revealed the dietary compositions of common migratory duck species and their intraspecific and interspecific dietary variations. While ducks are generally known to be omnivorous, Anas crecca (green-winged teal) had a more specialized diet and was primarily herbivorous throughout winter. In contrast, the sympatric Mareca penelope (Eurasian wigeon) and Spatula clypeata (northern shoveler) exhibited more omnivorous foraging behaviors. Moreover, A. crecca displayed less dietary variation among samples, while samples of M. penelope and S. clypeata were highly variable in their compositions. Comparing our results with those of studies conducted in different regions, we found that the dietary compositions of these duck species varied to different degrees across geographic locations. This variation underscores the flexibility of these duck species in their diets and their adaptable foraging strategies. Our findings also indicate that grasslands rich in herbaceous plants and aquatic environments abundant with small aquatic invertebrates are vital foraging habitats for duck species during their winter period.

Environmental DNA (eDNA) preserved in sediments (sed-eDNA) holds promise for improving our understanding of historical species occurrences and contemporary biomonitoring. However, uneven DNA distribution, DNA fragmentation, and polymerase chain reaction (PCR) inhibition present challenges to species detection. Herein, we evaluate the efficacy of sed-eDNA methods to detect the presence of a patchily distributed marine mammal in a coastal marine ecosystem. We developed a targeted quantitative PCR (qPCR)-based assay for the detection of sea otter (Enhydra lutris ) DNA. This assay successfully amplified target DNA from aquaria occupied by sea otters and from two of eight seawater samples from areas where sea otters are often present. Additionally, we conducted an experiment to examine the utility of our assay in detecting sea otter DNA in sediment. We compared four sed-eDNA extraction techniques and two DNA cleaning protocols in surface sediment samples taken from areas with varying sea otter occupancy. To test for DNA extraction efficiency, we used fish and chloroplast as endogenous controls. DNA quantity varied between the different extraction protocols and between the different DNA sample types. Sea otter DNA was detected at lower yields than expected, considering the presence of sea otters at the sampled sites. Furthermore, sediment cleaning protocols further reduced sed-eDNA yield. Among the extraction methods tested, the Qiagen Powersoil Pro kit was most effective, yielding higher rates of target species detection with smaller input sediment amounts and no need for cleaning to remove PCR inhibitors. The present study lays the groundwork for large-scale monitoring of marine mammals using sed-eDNA and advances the use of sed-eDNA detection as a valuable tool for reconstructing the temporal and spatial patterns of marine mammal presence. Importantly, we identify the need for a better understanding of the effects of marine sediment composition, mammal eDNA shedding rates, and DNA fragment size on detecting target sed-eDNA.

Invasive species present considerable threats to native biodiversity by disrupting ecosystem processes. The gill louse Salmincola californiensis is a copepod that parasitizes Oncorhynchus species, which includes ecologically, commercially, and recreationally important fishes. As S. californiensis expands its geographic range, there are concerns that conservation efforts focused on Rocky Mountain cutthroat trout Oncorhynchus virginalis may be thwarted. To address these concerns, we (1) assessed upstream range expansions of S. californiensis from known infected waters; (2) compared the efficacy of environmental DNA (eDNA) sampling to traditional sampling methods in detecting S. californiensis; (3) evaluated S. californiensis population genetic structure using DNA barcoding; and (4) assessed gill lice occupancy and detection probabilities using occupancy modeling. We compared the success of detecting S. californiensis using electrofishing versus eDNA sampling methods at 48 sites throughout the state of Colorado. We detected gill lice at 17 sites via electrofishing, and at 10 sites using eDNA. For DNA barcoding, we collected 58 lice at 11 sampling localities and sequenced the mitochondrial cytochrome c oxidase subunit 1 for species identification, to assess genetic diversity across Colorado, and to estimate divergence times. Salmincola californiensis was the only species of gill lice we detected. Divergence time estimates show that it is possible that the highly divergent gill lice lineages originally co-invaded with cutthroat trout. However, the presence of the most widespread parasite haplotypes across multiple drainages presents a phylogeographic pattern consistent with fish stocking facilitating its range expansion. Occupancy modeling suggests that fluvial processes, temperature, and UV impact gill lice detection using eDNA. We conclude that eDNA is effective at detecting gill lice presence in a system, perhaps best used in conjunction with electrofishing methods for early detection, that gill lice continue to expand their range in Colorado, and that continued monitoring will be an important component of future management efforts.

Analysis of environmental DNA (eDNA) through DNA metabarcoding has become an important technique for environmental science as it allows precise reconstructions of species communities in a fast, cheap and non-invasive way. In this study, we scrutinize how environmental reconstructions derived from metabarcoding data may be affected by a process in which sample specific labels (tags), added to sequences for identification of individual samples, are changed unintentionally during adapter ligation causing translocation of sequences between samples (‘tag jumping’). We compare animal and plant communities reconstructed using sedimentary eDNA records processed according two different protocols: (i) a twin-tagging approach (control) where all amplicons received the same tag on both sides (N = 102); and (ii) a combinatorial tagging protocol (affected by tag jumps) where each amplicon received a unique combination, but where some tags on each side were reused to form new combinations (N = 102). We analyzed six different sediment matrices and observed higher average number of taxa in the combinatorial tagging dataset in comparison to our twin-tagged dataset serving as a reference for results unaffected by tag jumps. In the control dataset with twin tagged amplicons, reconstructed animal communities were statistically different in 14 out of 15 pairwise comparisons, while only 8 out of 15 of the comparisons were different when samples were analyzed using the combinatorial tagging protocol. All of the inferred plant communities were statistically different when analyzed with a twin-tagging approach, while 20% of these plant communities were not different in our combinatorial tagged dataset. Our results clearly show that tag jumps added species to samples where they were not originally present and affects interpretations of species diversity and time-trends for whole communities. We conclude that tag jumping, being rarely discussed in metabarcoding studies, constitutes a concern in parity with direct sample contamination.

Efficient and scalable methods for monitoring marine biodiversity are critical for understanding ecological change in coastal environments, given the limited resources available. Environmental DNA (eDNA) metabarcoding shows promise for monitoring coastal taxa, but its ability to differentiate communities from different locations remains insufficiently understood, particularly in dynamic marine environments. Here, we evaluate the effectiveness and resolution capacity of eDNA metabarcoding in detecting rocky intertidal taxa across three spatial scales—national, regional, and local—in the United Kingdom. Onshore surface-water samples were collected from 32 sites across five UK Regional Seas from rockpools in high and low shore zones, as well as directly from the sea. We detected 1026 target taxa within 442 families and 19 phyla using two established markers targeting invertebrates (COI) and macroalgae (18S). Distinct eDNA signals were found at all spatial scales, indicating local discreteness even between vertical shore heights within the same sites. Communities were more discrete at larger scales (i.e., between regions) than at smaller scales (i.e., between shore heights). eDNA signals were more strongly structured by geographical location than by vertical shore height as a probable consequence of greater DNA homogenization over the tidal cycle at smaller spatial scales. Established ecological zonation patterns were reflected in eDNA signals, with higher richness at lower shore heights, reflecting abiotic stress gradients. Detections of cold-affinity boreal species increased with latitude, while warm-affinity lusitanian species declined with latitude. Our work supports the utility of eDNA metabarcoding for multiscale biodiversity monitoring in dynamic marine environments and for detections beyond this study's target taxa. We recommend the adoption of scale-appropriate sampling protocols to optimize the benefits of eDNA, such as prioritizing open water sampling at high tide for broad-scale assessments and rockpool sampling at low tide for capturing local-scale patterns. Future work should validate detections through direct visual comparisons.

The European green toad (Bufotes viridis) is currently in decline and considered endangered across the northern extent of its native range, with large investments in ongoing conservation and translocation efforts. To assist conservation efforts, survey methods must be established that are cost-effective, non-invasive, and rapidly deployable. Here we evaluated the effectiveness of eDNA metabarcoding for amphibian conservation across three objectives: (1) Test B. viridis probability of detection before and after translocation efforts in 3 ponds in Öland, Sweden. (2) Assess pond biodiversity and biotic interactions across Öland and Kalmar using eDNA metabarcoding. (3) Determine which surveyed sites are suitable for future translocation efforts. We found that the detection probability of B. viridis increased 100% 24 h after the translocation was initiated, whereby they were undetected prior to release. Additionally, we detected 11 fish species, 14 bird species, 9 mammal species, and 4 amphibian species across the translocated sites. The results from the 37 pond eDNA surveys resulted in the detection of 15 fish species, 38 bird species, 8 amphibian species, and 17 mammal species. Species richness of the surveyed ponds ranged from 1 to 24, with an average richness of 8. Co-occurrence analysis found significant associations between several species, including a significant negative association between amphibian occurrence and cattle and gray heron and positive associations with duck and common crane. Multi-Criteria Decision Analysis (MCDA) suggests 6 sites had consistent lower site rankings, indicating them as more favorable locations for future amphibian translocation efforts. Overall, these findings showcase eDNA high-throughput sequencing as a viable means to non-invasively assess European green toads and simultaneously assess wider community dynamics that may help evaluate the sustainability of reintroduced and endemic populations.

Plant–animal interactions (PAIs) are critical in natural and agricultural ecosystems, mediating energy flow with both positive and negative interactions. Traditional methods of tracking PAIs, such as morphological identification and camera trapping, are limited in speed and scalability, posing challenges for comprehensive biodiversity monitoring. Recently, environmental DNA (eDNA) metabarcoding has emerged as a promising technique for detecting species interactions non-destructively. This pilot study explores the application of eDNA metabarcoding to investigate frugivorous interactions involving 18 partially consumed and three intact fruits of each Carica papaya and Ananas comosus. Metabarcoding of mitochondrial COI gene fragments generated 796,234 paired-end reads representing 117 ASVs spanning diverse taxonomic groups, including Metazoans, Protozoans, Algae, Fungi, and Bacteria. After filtering for animal taxa, 41 ASVs were retained, dominated by Arthropoda (~97%). Major frugivores included Drosophila, Zaprionus, and Bactrocera species. Additional detections included beetles, ants, parasitoid wasps, and vertebrates such as Acridotheres javanicus, Callosciurus erythraeus, and Bandicota indica. Moreover, consumed fruits showed high insect (~90%–95%) and mammal (~4%–5%) DNA, while intact fruits were dominated by rotifers (~75%–80%). Distinct communities were found between pineapple and papaya, with 15 and 11 unique ASVs, respectively, and only one ASV was unique to intact fruits. Alpha and beta diversity analyses confirmed the differences in community structure between fruit types. Despite the limited sample size, our findings demonstrate the potential of fruit-surface eDNA to monitor frugivory and species interactions. Future studies should scale this approach across seasons and crop types to assess its potential in long-term biodiversity and pest management monitoring.