Environmental DNA最新文献

{"title":"Detecting Fish Diversity in Urban-Impacted Ecosystems: A Comparative Approach of eDNA Metabarcoding and UVC","authors":"Arthur Chung,&nbsp;Y. C. Kam,&nbsp;Stanley K. H. Shea,&nbsp;Celia Schunter","doi":"10.1002/edn3.70048","DOIUrl":"https://doi.org/10.1002/edn3.70048","url":null,"abstract":"<p>Comprehensive assessments of coastal biodiversity in complex coral communities are crucial but challenging, particularly under unfavorable conditions such as poor underwater visibility in urbanized and eutrophic environments. Here we aim to examine the scope of underwater diversity detection and community shifts across habitat transitions spanning different geographic regions in Hong Kong SAR, a highly urbanized coastal city with limited underwater visibility of 3.93 ± 1.25 m during the sampling period. We employ and compare two methods: 12S rRNA eDNA metabarcoding coupled with custom built reference database and simultaneous extensive underwater visual census (UVC) surveys. eDNA detected a higher species richness per site. Yet, each survey method featured a distinct species profile with associated trophic guilds, where 98 (32.3%) species found exclusively by UVC and 120 (39.6%) species detected only by eDNA. eDNA featured species from diverse habitats and evolutionary distances, including cryptic and large mobile fishes, offering enhanced prediction on local ecosystem functions. eDNA also recorded 90 putative species that had never been recorded in additional seven yearlong UVC dataset, with seven prospective new occurrence records to the territorial waters. UVC on the other hand was more efficient in documenting reef-associated species. Both methods captured similar patterns of community spatial structure along the habitat transitions while only eDNA detected more large fish species in offshore compared to sheltered inshore environments, This may suggest inshore overfishing and incapability of UVC in surveying large mobile species in turbid environments. Considering the discrepancies between two methods, we highlight the importance of complementing both UVC and eDNA metabarcoding survey for a complete overview of local biodiversity under unfavored underwater conditions in an urbanized seascape.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70048","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142861299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using Gap Visualization to Navigate Multivariate Metabarcode Data, Select Primer Pairs, and Enhance Reference Data Quality","authors":"Xin-Yi Chua,&nbsp;Louise Ord,&nbsp;Stephen J. Bent,&nbsp;David Lovell,&nbsp;Annette McGrath","doi":"10.1002/edn3.597","DOIUrl":"https://doi.org/10.1002/edn3.597","url":null,"abstract":"<p>The success of amplicon sequencing studies of environmental DNA (eDNA) depends on the choice of primer pairs used to select taxa-specific regions of DNA for amplification then sequencing to characterize sample composition. This paper presents practical methods to visualize the extent to which different primer pairs can differentiate taxonomic groups, enabling researchers to assess which primers might be best suited for a study or environment of interest. These methods can also be used to review taxonomic annotations in genomic reference sequence databases. We apply the concept of DNA barcoding gaps to metabarcoding of multiple species in environmental DNA to leverage reference data on the amplicon sequences of previously characterized specimens. Since reference data sets are large and complex, we provide a simple and intuitive method to navigate subsets of reference sequence data containing conflicting or ambiguous relationships between genomic information and taxonomic classification. We demonstrate how to use gap visualization and taxonomic segmentation in comparing how well different primer pairs discriminate species of interest, and in detecting anomalies in reference sequence annotation. We show how these visualization methods can enable amplicon survey study design and make fundamental molecular resources more accessible to a wider research audience beyond bioinformaticians and data scientists.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.597","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142860562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Origin of the Matter Matters: The Influence of Terrestrial Inputs on Coastal Benthic Microeukaryote Communities Revealed by eDNA","authors":"Mathisse Meyneng,&nbsp;Raffaele Siano,&nbsp;Naïna Mouras,&nbsp;Dominique Ansquer,&nbsp;Christine Laporte-Magoni,&nbsp;Florence Antypas,&nbsp;Thomas Haize,&nbsp;Hugues Lemonnier","doi":"10.1002/edn3.70041","DOIUrl":"https://doi.org/10.1002/edn3.70041","url":null,"abstract":"<p>Estuaries are a key component of the land-sea continuum, and their microbial diversity depends on the connection with terrestrial ecosystems. This work aimed to demonstrate that the terrestrial matter carried by rivers influences the structuration of microeukaryote communities of superficial (0–3 cm) sediments collected at the interface between the land and marine coastal areas. To demonstrate this hypothesis, we have chosen the main island of New Caledonia as a study site, a French overseas territory located in the South West Pacific. Using amplicon sequencing of the 18S-V4 rDNA extracted from sediments, we analyzed microeukaryote community composition in relation to numerous environmental parameters. Samples were collected in five bays influenced by riverine inputs and corresponding to distinct geological features of the watersheds, as revealed by high variations in metal concentrations released from specific minerals in the sediment. Particularly, the influence of ultramafic soils was highlighted by higher nickel concentration (correlated to Co, Cr, Mn, and Fe). Diatoms were the dominant taxonomic group, especially the classes of Bacillariophyceae and Mediophyceae. Then Apicomplexa, Ciliophora, Dinoflagellata, and Cercozoa followed. The metallic composition of the sediment explained 18.46% of the community spatial variability. The selection of ASVs based on their contribution to beta diversity and their correlation with metallic concentrations enabled us to identify spatial patterns. This information could lead to identifying microeukaryote bioindicators of terrestrial influences, particularly of ultramafic origin. We hypothesized that the association between microeukaryotes and metallic compositions is linked to selection processes, given the resistance of some microeukaryotes to some high metallic concentrations. In vitro experiments are needed to confirm this hypothesis. Our results emphasized the role of terrestrial inputs in shaping estuarine diversity and the need to consider the entire land–sea continuum for studying these ecosystems.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70041","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142860345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hydrodynamics and Aquatic Vegetation Drive Spatial Patterns of Environmental DNA in Ponds","authors":"Sandra R. Mayne,&nbsp;Jeffrey A. Manning,&nbsp;Stephen M. Henderson,&nbsp;Meghan B. Parsley,&nbsp;Katherine M. Strickler,&nbsp;Jeffrey R. Nielson,&nbsp;Caren S. Goldberg","doi":"10.1002/edn3.70036","DOIUrl":"https://doi.org/10.1002/edn3.70036","url":null,"abstract":"<p>Environmental DNA (eDNA) sampling is a powerful method for detecting aquatic species at low densities. However, eDNA may remain close to the source in lentic systems, decreasing the effectiveness of eDNA surveys. We conducted cage experiments with salamanders and simultaneous detailed hydrologic and wind measurements to investigate the influence of the physical environment on detection patterns of eDNA in ponds. We found much higher detection rates in the surface layer than at depth, and that aquatic vegetation reduced detection of eDNA produced in open water by 80%–94%. Within the surface mixed layer, detection rates were highest close to the source in the direction of water flow in the bottom half of the layer, and detections farthest from the source occurred when velocities in this sublayer were high. Detections were near zero even close to the source when this sublayer was flowing fast and away from the sampling point. The direction of water flow in this lower half of the surface mixed layer was negatively correlated with wind direction for most of the study. These spatial and temporal dynamics indicate that eDNA transport processes in ponds are highly complex. Sampling away from aquatic vegetation, in the surface mixed layer, and upwind of potential sources, in addition to sampling at many locations within a pond and considering temporal patterns, may improve detection of rare pond species. This work contributes to a growing body of literature characterizing the variability of eDNA detection in lentic systems.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142860344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Monitoring of Endangered Freshwater Mussels in Sweden Using Digital PCR","authors":"Per Sundberg,&nbsp;Alizz Axberg,&nbsp;Nauras Daragmeh,&nbsp;Niklas Wengström,&nbsp;Marina Panova","doi":"10.1002/edn3.70046","DOIUrl":"https://doi.org/10.1002/edn3.70046","url":null,"abstract":"<p>Freshwater mussels are traditionally monitored by visual observations which is time-consuming and can be difficult depending on water conditions. Environmental DNA (eDNA) is an attractive alternative since it can detect a species in the water without visual observations. Furthermore, since the DNA can potentially travel downstream in the river systems, presence of a species can be detected even away from the population of mussels. In this paper, we evaluate and describe how dPCR (digital PCR) technique can be used to efficiently monitor four freshwater mussel species: the freshwater pearl mussel <i>Margaritifera margaritifera</i> from Margaritiferidae family and three species from Unionidae family: the depressed river mussel <i>Pseudanodonta complanata</i>, the painter's mussel <i>Unio pictorum</i>, and the thick shelled river mussel <i>Unio crassus</i>, which are all regarded endangered in many regions worldwide. dPCR assays for the four mussel species were developed and tested in silico before conducting field surveys. The verification step in the field was carried out in two Swedish rivers with confirmed populations of the freshwater pearl mussel (<i>M. margaritifera</i>). Furthermore, two other rivers with unknown presence of the endangered freshwater mussels were surveyed for occurrence of the four mussel species, using the capacity to multiplex several species simultaneously in a dPCR reaction. We furthermore showed that the target DNA concentrations probably depend on the season and water level, which may largely affect the detection probability and interpretation of the results in terms of population size.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70046","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142860412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fishy Business—Assessing the Efficacy of Active and Passive eDNA to Describe the Fish Assemblage of a River in Southwestern Western Australia to Support Effective Monitoring","authors":"Emma R. Stevens,&nbsp;Josephine Hyde,&nbsp;Leah S. Beesley,&nbsp;Daniel C. Gwinn,&nbsp;Suzanne Thompson,&nbsp;Lenore Morris,&nbsp;Paige R. Wilson,&nbsp;Deirdre B. Gleeson","doi":"10.1002/edn3.70040","DOIUrl":"https://doi.org/10.1002/edn3.70040","url":null,"abstract":"<p>Worldwide, freshwater vertebrate populations are declining with increasing pressure on rivers due to numerous environmental and climatic threats. Environmental DNA (eDNA) could potentially provide a more efficient and non-invasive mechanism to monitor freshwater systems, either as a complement or in replacement to traditional methods to accurately assess species' distributions. Here, we utilize a hierarchical multispecies N-mixture model to compare three fish sampling methods: traditional fyke netting and active and passive environmental DNA sampling along a 30 km stretch of the Canning River in Western Australia. We used the fitted model to compare capture probabilities among sampling methods and reveal the sampling effort required to describe the species assemblage. Results indicated that while all methods could detect fish, combined eDNA methodologies detected one more fish species than those caught by fyke netting. In addition, active eDNA sampling produced the highest capture probabilities and more consistently described the entire fish assemblage at any given site. Fyke netting and passive eDNA did not show significant differences in their average capture probabilities, and both methods had lower abilities to capture individual species than active eDNA. Active eDNA also required fewer replicate samples to detect the expected observed richness, and fyke netting required the most replicates. Additionally, a hierarchical multispecies abundance model showed that active environmental DNA (eDNA) sampling is the most effective method for monitoring freshwater fish populations. This study contributes to our understanding of eDNA in aquatic systems and demonstrates that, at least under current conditions, active sampling is still the preferred method in freshwater systems with low flow compared to both passive sampling and fyke netting.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70040","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142860367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"eDNA Metabarcoding, a Promising Tool for Monitoring Aquatic Biodiversity in the Estuaries of Reunion Island (South-West Indian Ocean)","authors":"Lou-Anne Jannel,&nbsp;François Guilhaumon,&nbsp;Pierre Valade,&nbsp;Pascale Chabanet,&nbsp;Guillaume Borie,&nbsp;Henri Grondin,&nbsp;Philippe Jourand","doi":"10.1002/edn3.70044","DOIUrl":"https://doi.org/10.1002/edn3.70044","url":null,"abstract":"<p>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., <i>Cotylopus acutipinnis</i>), introduced exotic species (e.g., <i>Oreochromis niloticus</i>), and species difficult to capture and identify due to their juvenile life stage through EF (e.g., <i>Anguilla</i> 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.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ebbs and Flows of Marine Biodiversity: Navigating Spatiotemporal Patterns of Environmental DNA in a Coastal Tidal Ecosystem","authors":"Michelle Scriver,&nbsp;Ulla von Ammon,&nbsp;Xavier Pochon,&nbsp;Martin Zirngibl,&nbsp;Francois Audrezet,&nbsp;Kaeden Leonard,&nbsp;Kylie Pedersen,&nbsp;Nick Bamford,&nbsp;Ngairo Tahere,&nbsp;Jo-Ann L. Stanton,&nbsp;Neil J. Gemmell,&nbsp;Anastasija Zaiko","doi":"10.1002/edn3.70039","DOIUrl":"https://doi.org/10.1002/edn3.70039","url":null,"abstract":"<p>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 <i>Cytochrome C Oxidase subunit</i> 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 <i>Monocorophium acherusicum</i>) across space and time, whereas other NIS (e.g., the mussel <i>Arcuatula senhousia</i>) 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.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70039","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142763963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preservation of Aquatic Environmental DNA Using Cationic Detergents","authors":"Viresh Thamke,&nbsp;Yared H. Bezabhe,&nbsp;Jana Jass,&nbsp;Per-Erik Olsson","doi":"10.1002/edn3.70038","DOIUrl":"https://doi.org/10.1002/edn3.70038","url":null,"abstract":"<p>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 (<i>Danio rerio</i>) 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.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70038","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Roaming the Seas—Assessing Marine Invertebrate Biodiversity Along Salinity Gradients With Zooplankton and eDNA Metabarcoding","authors":"Alica Ohnesorge,&nbsp;Uwe John,&nbsp;Lucie Kuczynski,&nbsp;Stefan Neuhaus,&nbsp;Kingsly Chuo Beng,&nbsp;Bernd Krock,&nbsp;Silke Laakmann","doi":"10.1002/edn3.70037","DOIUrl":"https://doi.org/10.1002/edn3.70037","url":null,"abstract":"<p>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 &gt; 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.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}