eDNA Techniques Research Articles

A preliminary study on detecting human DNA in aquatic environments: Potential of eDNA in forensics

Human environmental DNA (eDNA) application have not been fully applied or adequately considered in the fields of eDNA and forensics. Nonetheless, this technique holds great potential as a complementary tool for detecting human DNA in aquatic environments, particularly in cases involving crimes connect to such environments. However, the detectability or stability of eDNA can vary depending on several factors. Therefore, this preliminary study investigates the detection and degradation rates of human eDNA, as well as the recovery of nuclear short tandem repeat (STR) profiles and mitochondrial DNA (mtDNA) sequencing, using water samples from both saltwater and freshwater sources. To conduct the experiment, whole human blood was spiked into the water samples. Water samples were then filtered using a 5 µm pore size filter, and samples were collected at various time intervals up to 23 days. A human specific qPCR assay targeting HV1 region of human mtDNA was used to detect human eDNA. Results demonstrated that human eDNA remains detectable for up to 36 hours in freshwater samples and up 84 hours in saltwater samples. The limit of detection (LOD) of human eDNA, (205 copies/µl), was achieved after 60 hours in freshwater and 180 hours in saltwater samples. Partial STR profiles could be recovered up to 24 hours for freshwater and saltwater. Results from mtDNA sequencing indicate that full mtDNA profiles could be recovered from freshwater samples up to 48 hours and remained detectable up to 72 hours in saltwater. Overall, the findings of this study underscore the importance of considering and incorporating human eDNA analysis as a valuable tool in forensic practice. By harnessing the power of eDNA, law enforcement agencies can enhance their investigation capabilities, improve the accuracy of forensic reconstructions, and ultimately contribute to the resolution of cases involving aquatic environments. Further research and validation are needed to optimize and expand the utilization of eDNA techniques in forensic investigations.

Rapid Monitoring of Aquatic Organism Biodiversity Based on Environmental DNA in a Medium-Sized Reservoir

Environmental DNA (eDNA) has emerged as a highly sensitive and efficient tool for the biomonitoring of aquatic ecosystems. In this study, we investigated fish and benthic species communities using eDNA techniques in a medium-sized reservoir (about 3 square kilometers) in Anhui, China. A total of 12 water samples and 11 sediment samples were analyzed by 12S and 18S primers, respectively. We analyzed the composition of species diversity and the effect of seven environmental factors using the Mantel test. A total of 42 fish taxa were present in the water samples, and 188 benthic taxa in the sediment samples. Species composition was different in disparate stations. We found that water temperature and salinity are pivotal factors influencing the composition of fish communities, while chlorophyll-a is a primary environmental determinant for benthic species assembly structures across different zones. Biodiversity information generated by eDNA techniques can be used to reflect the resource status of this reservoir. The relevant results will provide important scientific reference information for the development and exploitation of medium-sized reservoirs.

Complete mitochondrial genomes and phylogenetic analysis of native and non-native fishes in a national key wetland of China

Fish are considered objective indicators of environmental health and ecosystem stability. Establishing regional reference databases of mitochondrial genome sequences from local fish communities can significantly enhance fish monitoring using environmental DNA (eDNA) analysis. For non-native species, the eDNA technique provides early detection and rapid monitoring. It is also crucial to include fundamental genetic information for both native and non-native species in genetic databases. This study presents the complete mitochondrial genomes of 17 fish species inhabiting the Baiyangdian Basin, a national key wetland in China. The mitochondrial DNA of these fish was analyzed to investigate their characteristics, and their phylogeny was determined using maximum likelihood (ML) methods. Various analyses were performed, including the examination of nucleotide composition, evaluation of AT-skew and GC-skew, analysis of codon frequency, and determination of relative synonymous codon usage (RSCU) values, and assessment of selection pressure on protein-coding genes (PCGs). The analysis showed that all PCGs in all fish underwent purifying selection. Using Xenocyprididae as a representative, this study investigated the genetic selection tendencies of native and non-native fish species in the Baiyangdian Basin. Significant differences were found in five of the 13 PCGs: COI, COII, COIII, Cytb, and ATP8. Except for ATP8, the findings indicated that the genes of non-native species underwent stronger purifying selection during evolution compared to native species. Additionally, comparing the population ω values of non-native species to those of native species showed that the Cytb and COIII genes exhibited greater differential purification selection than COI and COII. These differences may be the result of the evolution of non-native species to migrate and adapt to the Baiyangdian Basin, thereby affecting the evolution of related genes.

Environment DNA Reveals Fish Diversity in a Canyon River within the Upper Pearl River Drainage.

Investigating fish diversity in canyon rivers through conventional fish surveys is challenging due to precipitous conditions, including steep slopes, rapid water flow, and complex habitats. Additionally, intensive construction of dams has further complicated the understanding of contemporary fish diversity in these rivers. In this study, we used the environmental DNA (eDNA) technique to assess fish diversity and examine the effects of dams on fish diversity in the Mabiehe River, a canyon river in the upper reaches of the Pearl River drainage. Water samples from 15 sampling sites were collected, yielding 9,356,148 valid sequences. Utilizing the NCBI public database, a total of 60 freshwater fish species were identified, with Carassius auratus, Cyprinus carpio, and Pelteobagrus fulvidraco being the most dominant species in the Mabiehe River. We also detected one nationally protected fish species, three provincially protected fish species, and six exotic species in this river. Furthermore, eDNA analyses demonstrated that the lotic river sections harbor more species and greater diversity than dammed sections, suggesting that dams might exert significant impacts on local fish diversity. Overall, this study supports the effectiveness of the eDNA technique as a complementary tool to traditional field surveys for monitoring fish biodiversity in canyon rivers.

Contribution of environmental DNA toward fungal Red Listing

In navigating the biodiversity crisis, a major uncertainty is the conservation status of inconspicuous, yet megadiverse and functionally crucial, soil organisms. Massive datasets on soil biota are accumulating through molecular sampling approaches, but to date these datasets have provided only limited input into conservation planning and management. We investigated how environmental DNA (eDNA) data of soil macrofungi contribute to regional Red List assessments, which are currently based on fruiting bodies (hereafter, fruit‐bodies). In our test region of Estonia (northern Europe), which contained ~15,000 fruit‐body records for 1583 assessed species, an average soil sample increased the range estimates of Threatened and Near Threatened fungal species by 0.18%. Five hundred soil samples almost doubled their known localities and added 19% previously unrecorded species. However, even after accumulating >1000 soil samples, about half of the Threatened and Near Threatened species known by fruit‐bodies remained undetected through eDNA techniques. Effective conservation assessment of soil fungi thus requires both fruit‐body and eDNA data; therefore, special efforts are needed to make these data available to conservationists.

Monitoring estuarine fish communities – environmental DNA (eDNA) metabarcoding as a complement to beach seining

Environmental DNA (eDNA) metabarcoding offers advantages over physical capture for identifying and quantifying animals in monitoring programs. In this study, the fish community was sampled at three stations (inner, middle, and outer estuary) in three estuaries in August 2020, and four estuaries in June and August 2021 (Prince Edward Island, Canada) using both beach seining and eDNA metabarcoding. Two 12S primer sets, 12S-160 and 12S-248F, with different amplicon lengths, yielded similar results. eDNA metabarcoding consistently detected species captured by 186 co-located beach seines and revealed additional species. It also detected monthly (June-August), interannual (2020-2021), and spatial shifts in the fish community, distinguishing stations separated by as little as 0.4 km. Positive correlations existed between eDNA metabarcoding species reads and beach seining captures. These findings suggest eDNA metabarcoding complements physical capture methods for characterising nearshore fish communities in Prince Edward Island’s estuaries. While eDNA techniques lack certain population parameter information provided by physical methods, such as size, sex, and age structure, they offer a more comprehensive diversity assessment and presence-abundance insights, especially in inaccessible environments.

Detection of environmental DNA of finless porpoise (Neophocaena asiaeorientalis) in Osaka Bay, Japan

Finless porpoises (Neophocaena asiaeorientalis) currently face population decline caused by significant human activities and are categorized as endangered on the International Union for Conservation of Nature (IUCN) Red List; however, information on their habitats is currently insufficient. Although conducting visual surveys to determine the distribution of cetaceans is common, visual observation of finless porpoises is challenging owing to their specific morphological and ecological characteristics. In this study, we developed an environmental DNA (eDNA) assay for species-specific detection of finless porpoises. To test the utility of the assay, we conducted a visual survey in parallel with an eDNA survey by collecting water samples from 50 sites throughout Osaka Bay. We visually found a finless porpoise at one location and detected eDNA at nine sites, including sites near the visual observation site and those with rare sightings of finless porpoises. Therefore, in this study, we suggest that the use of eDNA analysis for distribution surveys of finless porpoises will enable more efficient surveys. The proposed eDNA technique can not only be applied to the distribution surveys finless porpoises but also to those of other cetacean species.

A circumpolar study of surface zooplankton biodiversity of the Southern Ocean based on eDNA metabarcoding

Under pressure from climate change and fishing, the Southern Ocean ecosystems have been changing. Zooplankton plays a vital role in the food web of the Southern Ocean and is crucial for maintaining ecosystem stability. Investigating the circumpolar-scale species composition and biodiversity of zooplankton is crucial for ensuring ecosystem-based conservation and management of the Southern Ocean in a changing climate. Here, we utilized eDNA metabarcoding to assess the biodiversity of zooplankton in the surface seawater surrounding the Antarctica based on samples collected during two expeditions spanning from 2021 to 2022. The main purpose of this paper is to provide more baseline information about circumpolar zooplankton biodiversity based on the emerging eDNA metabarcoding tool. This comprehensive approach led to the identification of over 300 distinct zooplankton species, forming a diverse community dominated by Jellyfish, Mollusca and Polychaete. Surprisingly, common dominant taxonomic groups such as krill and copepods in the Southern Ocean did not show high relative abundance (reads) in surface seawater. The results of redundancy analysis (RDA) and correlation analysis highlighted that water temperature and chlorophyll a had the most significant impact on the reads and diversity of zooplankton. Notably, the influence of water temperature on zooplankton seemed to be primarily indirect, potentially mediated by its effects on primary productivity. Increasing in primary production might lead to lower zooplankton biodiversity in the Southern Ocean in future. This research underscores the effectiveness of eDNA metabarcoding as a valuable tool for monitoring zooplankton diversity in open seas. Given the ongoing changes in temperature, sea ice extent and their impact on primary production, our findings lay a crucial foundation for using eDNA techniques to establish long-term biodiversity monitoring programs across extensive marine ecosystems in the future.

Using eDNA to play whack-a-mole with invasive species in green yard waste.

As large cities begin to overrun their landfill capacities, they begin to look for alternative locations to handle the waste stream. Seeing an opportunity to bring in revenue, rural communities offer to handle municipal waste in their landfills. However, many rural communities are also places of agricultural production, which are vulnerable to attacks by invasive insect species, which could be present in green yard waste, the component of municipal waste most likely to contain agriculturally harmful insect species. We used environmental DNA (eDNA) to determine whether green yard waste could be a pathway for invasive insect species to enter and establish in the landfill-receiving agricultural community. We identified several target species that could be in green yard waste coming from Vancouver, BC, Canada, to Central Washington State, USA. We sampled green yard waste from 3 sites every 2 weeks from June to October in 2019 and 2020. DNA was extracted from the nearly 400 samples and subjected to amplification with COI barcoding primers followed by sequencing to identify target insects in the samples. Sequence analyses identified 3 species from the target list: 2 species that are pests of deciduous tree fruits and a generalist root-feeding crop pest. This eDNA technique was useful in identifying potential invasive species in green yard waste and may prove to be an important tool informing policy on the movement of biological material across borders and stemming the spread of invasive species.

Application of environmental DNA metabarcoding to identify fish community characteristics in subtropical river systems

AbstractFish are vital in river ecosystems; however, traditional investigations of fish usually cause ecological damage. Extracting DNA from aquatic environments and identifying DNA sequences offer an alternative, noninvasive approach for detecting fish species. In this study, the effects of environmental DNA (eDNA), coupled with PCR and next‐generation sequencing, and electrofishing for identifying fish community composition and diversity were compared. In three subtropical rivers of southern China, fish specimens and eDNA in water were collected along the longitudinal (upstream–downstream) gradient of the rivers. Both fish population parameters, including species abundance and biomass, and eDNA OTU richness grouped 38 sampling sites into eight spatial zones with significant differences in local fish community composition. Compared with order‐/family‐level grouping, genus‐/species‐level grouping could more accurately reveal the differences between upstream zones I−III, midstream zones IV−V, and downstream zones VI–VIII. From the headwaters to the estuary, two environmental gradients significantly influenced the longitudinal distribution of the fish species, including the first gradient composed of habitat and physical water parameters and the second gradient composed of chemical water parameters. The high regression coefficient of alpha diversity between eDNA and electrofishing methods as well as the accurate identification of dominant, alien, and biomarker species in each spatial zone indicated that eDNA could characterize fish community attributes at a level similar to that of traditional approaches. Overall, our results demonstrated that eDNA metabarcoding can be used as an effective tool for revealing fish composition and diversity, which is important for using the eDNA technique in aquatic field monitoring.

Cuvier's beaked whale (Ziphius cavirostris) detection through surface-sourced eDNA: A promising approach for monitoring deep-diving cetaceans

Among cetaceans, the Cuvier’s beaked whale is considered an extreme diver, thus not one of the easiest cetacean species to be studied due to its elusive behaviour and a preference for deep offshore waters. Although dedicated cetacean surveys have increased our knowledge on the distribution of Cuvier’s beaked whales in the Mediterranean Sea, knowledge gaps still remain where the study effort is non-existent. In this context, the use of new molecular methodologies capable of intercepting small traces of DNA left in the environment (eDNA) by marine organisms represents a valid approach to infer species’ occurrence. Moreover, the collection of water from the superficial layer is suitable for targeting marine mammals, as the constraints imposed by their nature implies periodic and frequent surfacing in order to breathe, releasing exhalants rich in their epithelial cells. Therefore, we designed and tested a taxon-specific primer set to infer Cuvier’s beaked whale presence, with the aims of 1) examining the effectiveness of the eDNA technique to detect the presence of a deep-diving cetacean in open waters, using the Cuvier’s beaked whale as case study; 2) providing data on the occurrence of this species within the Canyon of Caprera over a six-months study period and 3) assessing the species presence in adjacent waters in the central northern Mediterranean Sea based on the analysis of samples collected in a Citizen Science campaign. Results from this study demonstrated that superficial waters may retain biological traces of this cetacean despite the fact that it mostly inhabits deep waters. Specifically, this study provides evidence of the regular presence of Cuvier’s beaked whale in the Canyon of Caprera, with a preference for bathymetry in the range of 700–1000 m. Molecular traces’ distribution suggests a potential inshore movement of this species during Fall, which might be related to migration of its cephalopod prey or a shift in prey preferences, although this aspect requires further investigation. Overall, this study showed that the stronger positive signals were recorded in sampling stations located on surfaces above submarine canyon systems, demonstrating the importance of these areas as elective habitats for the Cuvier’s beaked whale, thus the pivotal priority to their conservation.

Evaluating the effectiveness of the eRNA technique in monitoring fish biodiversity – A case study in the Qingdao offshore, China

With the continuous intensification of human activities, fish biodiversity has been reduced in the Yellow Sea. Therefore, accurate monitoring methods are crucial for determining fish biodiversity in the target area. The environmental DNA (eDNA) technique has emerged as a promising non-invasive method, but it is prone to false positives. The rapid degradation of environmental RNA (eRNA) has the potential to reduce false positives in the eDNA technique; however, there is limited research on using the eRNA technique to study fish biodiversity. This study aimed to explore a suitable sampling method for extracting sufficient eRNA from seawater samples. Furthermore, we performed a case study in Qingdao offshore, China, to survey fish species and community composition based on the eRNA and eDNA techniques in November 2022 using seawater samples collected from 19 sampling sites. We compared the results with data obtained through traditional field survey (TFS) methods and examined the relationship between fish species and environmental factors. The results revealed a significant overlap between fish species detected by the eRNA and eDNA techniques, with the eRNA technique demonstrating higher sensitivity and positive predictivity, and fewer false positives compared to those of eDNA. Our study highlighted the potential of the eRNA technique as a powerful tool for improving the detection rate of fish species in marine ecosystems.

Advancing fish diversity monitor in degraded marine ecosystem with environmental DNA approach: Unveiling hidden riches

Comprehending fish diversity through multiple dimensions is a crucial aspect in advancing our understanding of fish populations and promoting sustainable fisheries as well as diversity conservation. Traditional research on fish diversity has been limited to non-genetic methods. The advent of environmental DNA (eDNA) technology enables simultaneous examination of both non-genetic and genetic aspects of fish diversity. In this study, we evaluated the ability of eDNA to capture multidimensional fish diversity in the northern South China Sea, with emphasis on phylogenetic diversity. The effect of environmental change and geographical location on multidimensional fish diversity across different seasons was also investigated. The analysis of species accumulation curves revealed that the observed species richness approached an asymptote, achieving 94.7% and 89.5% of the predicted values during the summer and winter, respectively. Alpha diversity of taxonomic (species, 225 vs. species, 102), functional (FRic, 0.51 vs. FRic, 0.19), and phylogenetic (PD, 26.27 vs. PD, 15.81) dimensions were found to be higher in summer compared to winter, with environmental factors significantly influencing these diversities across seasons. Regarding the three dimensions of beta diversity, replacement made a greater relative contribution to total taxonomic, functional, and phylogenetic beta diversity than richness difference. These effects were primarily influenced by water environment factors (e.g., NO2−, SiO32−, surface temperature) during the summer and geographical factors (e.g., longitude and latitude) during the winter. This study provides evidence supporting the feasibility of utilizing eDNA techniques to uncover fish diversity in multiple dimensions, with a specific emphasis on its intrinsic genetic characteristics, which hold substantial value for the protection of diversity and the scientific administration of fishery resources.

Bridging the gap: The integration of eDNA techniques and traditional sampling in fish diversity analysis

IntroductionBiodiversity loss poses a significant environmental challenge, particularly in aquatic ecosystems. The advent of environmental DNA (eDNA) sampling technology offers a promising tool for monitoring biological communities with purported high efficiency. Yet, its efficacy compared to traditional sampling methods remains underexplored, especially in fish diversity research.MethodsThis study conducted a comparative analysis of fish diversity and distribution across 29 sampling points within the rivers of the Changqing Nature Reserve, Central China, employing both eDNA techniques and traditional sampling methods.ResultsA total of 46 unique fish species were identified through this comprehensive approach. eDNA sampling detected 34 species, surpassing the 22 species identified by traditional methods. Interestingly, 10 species were detected by both methods, while traditional methods exclusively identified 12 species not detected by eDNA, and eDNA uniquely identified an additional 24 species. Despite eDNA's broader species detection range, traditional sampling methods typically yielded higher Shannon diversity index values. Both β-diversity indices (Bray-Curtis and Jaccard) and multivariate analyses (NMDS and PCoA) were applied, revealing no significant statistical differences in biodiversity measurement between the two sampling methods.DiscussionThe findings suggest that while eDNA sampling excels in identifying a wider range of species, it does not significantly outperform traditional methods in overall biodiversity assessment. By integrating both methodologies, this study demonstrates a more comprehensive and precise assessment of riverine biodiversity, underscoring the benefits of a synergistic approach for enhancing species detection and understanding distribution patterns. The combined methodology notably improves alpha diversity evaluations, particularly regarding Shannon diversity and Berger-Parker dominance. This integrated approach advocates for the amalgamation of data from both eDNA and conventional methods, fostering a robust and accurate biodiversity appraisal.

Exploring freshwater snail diversity and community structure in china's largest lake using eDNA technology

Freshwater snails are a crucial benthic animal group that plays a pivotal role in algae regulation and ecosystems while serving as intermediate hosts for certain parasites. Environmental DNA (eDNA) technology offers numerous advantages for biodiversity assessment. However, the utilization of eDNA techniques for freshwater snail monitoring remains limited. In this study, we screened primers for assessing freshwater snail diversity using eDNA technology and constructed a comprehensive database for Poyang Lake. Using eDNA technology, a total of 21 species of snails were detected in Poyang Lake, while traditional methods detected only 11 species. Notably, all species collected by traditional methods were also detected by eDNA technology. Additionally, environmental DNA methods detected the invasive snail Pomacea canaliculata, while traditional methods did not. In this study, eleven intermediate host snail species for parasitic disease were identified using eDNA methods, while six were detected through traditional sampling techniques. The eDNA metabarcoding analysis showed that the α and β diversity levels of snails in Poyang Lake did not vary significantly, indicating that results obtained by eDNA sampling are not influenced by the season in which samples were collected. The correlation analysis between the community structure of snails and environmental factors in Poyang Lake revealed significant impacts of total nitrogen, chlorophyll a, water depth, and water temperature on the snail community structure. These results confirm that eDNA technology can be exploited to monitor freshwater snail biodiversity.

Assessing mesopelagic fish diversity and diel vertical migration with environmental DNA

Mesopelagic fishes are an important component of the world’s oceans in terms of their abundance, biomass, and ecosystem function. These fishes are important contributors to the biological carbon pump via their feeding and behaviors, whereby they facilitate the transfer of carbon from shallow waters to the deep sea. Several species undertake diel vertical migration, feeding in shallower waters at night and moving to deeper waters during the day. This process actively expedites the downward flux of carbon. However, carbon budgets and climate models require accurate information regarding the depth distributions and migration patterns of these fishes, and environmental DNA (eDNA) analyses can provide this information. Here, we utilize eDNA approaches, generating taxonomically-informative COI and 12S reference barcodes for 80 species of mesopelagic fishes, which can be used for species-level identification of eDNA sequences. Using these, along with a publicly available barcodes database, we compare results from eDNA analysis with traditional net sampling, and explore the ability of eDNA techniques to detect diel vertical migration in fishes from samples collected in Northwest Atlantic Slope Water. We found that eDNA and net samples often resulted in different species identifications, demonstrating that eDNA can detect species that would otherwise be missed with traditional methods. In our eDNA samples, we also detected more species (12) in our shallowest depth category (0 - 100 m) from night samples than from day samples (3). This is consistent with increased diversity in shallow waters at night due to diel vertical migration. Based on the variability observed in sample duplicates, we suggest that future mesopelagic eDNA studies incorporate larger sample volumes and scaled-up sampling efforts. We also note the potential applications of eDNA analysis in addressing ecological questions related to predator-prey relationships identification of foraging hotspots, and carbon flow through the ocean’s midwaters.

Environmental DNA Detects Remaining Populations of Endangered Stream Salmon (Sichuan Taimen: Hucho bleekeri Kimura Salmonidae) in the Qinling Mountains

Sichuan taimen (Hucho bleekeri Salmonidae) populations are declining, and the status of remnant populations in the Qinling Mountains is poorly known. In this study, eDNA and creel netting were used to estimate the distributions of Sichuan taimen in two upper tributaries of the Hanjiang River. A qPCR assay was applied to detect the eDNA of H. bleekeri, and the presence of Sichuan taimen in the Taibai River, but not in the Xushui River, was confirmed. Sampling during summer achieved a relatively higher detection rate. The utility of eDNA techniques for detecting low-density Sichuan taimen was demonstrated in intricate stream ecosystems. The eDNA method can increase the efficiency of the management of endangered freshwater species, such as Sichuan taimen, by providing reliable distribution data.

Integration of environmental DNA metabarcoding technique to reinforce fish biodiversity assessments in seagrass ecosystems: A case study of Gazi bay seagrass meadows

AbstractAssessing biodiversity in marine nearshore ecosystems is crucial for effective management, especially in the context of climate change and overexploitation of marine resources. Conventional methods often fall short in providing comprehensive information for managing seagrass ecosystems. However, the emergence of environmental DNA (eDNA) techniques has transformed the field by enabling noninvasive surveys that are cost effective and provide detailed information with high resolution. In this study, we utilized eDNA to assess fish diversity and compared its effectiveness to conventional techniques such as catch assessment surveys and underwater surveys. We sampled three habitats (A: mangrove‐seagrass, B: seagrass only, and C: coral‐seagrass) with 4 replicates. Site A recorded 8 fish species, site B had 16 species, and site C, characterized by coral and seagrass habitats, exhibited the highest fish diversity with 45 species (mean H′ index = 2.455), underscoring its ecological importance. To ensure accurate taxonomic identification, we utilized an updated MiFish reference database containing a larger number of fish species compared to the initial library. This expanded reference database with 9569 fish species, facilitated more precise identification and enhanced the reliability of our findings. Notably, the eDNA technique outperformed conventional methods by detecting 23 additional fish species that went undetected using traditional surveys. Moreover, our study documented five fish species previously unknown to occur within the study region, further emphasizing the value of eDNA analysis in uncovering hidden biodiversity. These findings strongly advocate for integrating eDNA techniques into the monitoring and assessment of biodiversity in shallow tropical habitats of the Western Indian Ocean. By leveraging eDNA surveys, we can gain valuable insights into fish diversity, discover hidden species, and make informed decisions for the conservation and management of these ecologically significant areas.

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.

Can honey bees be used to detect rare plants? Taking an eDNA approach to find the last plants in a weed eradication program

AbstractThe detection of rare taxa, crucial to conservation and biosecurity, presents many challenges that emerging technologies have the potential to address or avoid. Analysis of environmental DNA (eDNA) is a promising tool for the detection of rare species, especially when applied in a way that exploits natural processes to accumulate biological material (natural aggregation). This study investigated the potential of using honey bees as aggregators of pollen eDNA to detect Chrysanthemoides monilifera subsp. monilifera (boneseed), an introduced species targeted for eradication in Western Australia. We developed a species‐specific polymerase chain reaction (PCR)‐based assay that detected boneseed pollen at levels as low as 70 grains per million in a constructed pollen mixture. The assay was successfully used on wild‐caught bees from large boneseed populations, confirming they collect boneseed pollen. However, our results did not detect boneseed DNA in honey bee pollen collected from hive pollen traps near isolated boneseed plants. We hypothesize that a combination of low abundance of boneseed individuals, vast alternative flower resources at the time of boneseed flowering, and honey bee behavior and ecology may have led to lack of detection. We propose ways in which future work using honey bees to detect rare species can be improved. We also outline how other eDNA substrates (e.g., air and water samples) could be used with the PCR assay we have developed. More broadly, our work highlights the potential of eDNA techniques to detect rare species in biosecurity and conservation contexts and contributes to the development of pollinator‐based detection.