Environmental DNA最新文献

{"title":"Quantifying the Temporal Dynamics of Marine Biodiversity Under Anthropogenic Impacts Using eDNA Metabarcoding","authors":"Zhewei Si,&nbsp;Wu Han,&nbsp;Tsz Ying Chan,&nbsp;Gert-Jan Jeunen,&nbsp;Cheng Qian,&nbsp;Isis Guibert,&nbsp;Cheuk Fung Wong,&nbsp;David Baker,&nbsp;Mathew Seymour","doi":"10.1002/edn3.70113","DOIUrl":"https://doi.org/10.1002/edn3.70113","url":null,"abstract":"<p>Marine biodiversity is rapidly declining due to anthropogenic activities; however, the key causal agents of this decline remain largely elusive. Improving our understanding of anthropogenic impact on biodiversity dynamics requires fine-scale temporal observations, which are logistically challenging using traditional methods. Coral reef ecosystems are key biodiversity hotspots for a wide range of organisms, making them essential for wider marine ecosystem stability and important focal points for marine biodiversity dynamics research. The use of autonomous reef monitoring systems (ARMS) has been effective in assessing reef benthic biodiversity. However, it remains unknown how ARMS marine biodiversity changes over time or in response to anthropogenic activity. Here, we utilized eDNA and a full factorial experiment consisting of 12, 2,042 L mesocosms, seeded with ARMS previously colonized from natural reef habitats. A total of 240 eDNA samples were collected over 20 time points across 232 days to assess: (1) eDNA accumulation dynamics, (2) effects of anthropogenic activity on biodiversity dynamics and (3) eDNA degradation rates. Biological communities changed drastically over time, with 814 ASVs across 617 marine families identified over the course of the experiment. Arthropoda dominated during the accumulation phase, Mollusca during the treatment phase, and Platyhelminthes and Bacillariophyta during the degradation phase. Richness across all mesocosms increased to 110 ± 18 initially, then stabilized at 147 ± 31 during the treatment phase before declining rapidly to 49 ± 17 during the degradation phase. We found that fish feed had a significant negative effect on community composition over time (<i>p</i> &lt; 0.01). Additionally, we identified Lithodesmiaceae and Haminoeidae as potential bioindicator groups. eDNA decay rates across species groups showed faster declines for fish compared to algae and invertebrates. Overall, our findings demonstrate that eDNA metabarcoding offers a detailed assessment of biodiversity, allowing us to differentiate between spatiotemporal and anthropogenic impacts on community dynamics.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70113","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144135720","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":"Enhancing Environmental DNA Sampling Efficiency for Cetacean Detection on Whale Watching Tours","authors":"Lauren Kelly Rodriguez,&nbsp;Belén García Ovide,&nbsp;Eleonora Barbaccia,&nbsp;Jana Robertson,&nbsp;Taïme Smit Pellure,&nbsp;Ángela Ceballos-Caro,&nbsp;Caterina Lanfredi,&nbsp;Maddalena Jahoda,&nbsp;Enrico Villa,&nbsp;Arianna Azzellino,&nbsp;Marianne Helene Rasmussen,&nbsp;Michael Traugott,&nbsp;Bettina Thalinger","doi":"10.1002/edn3.70103","DOIUrl":"https://doi.org/10.1002/edn3.70103","url":null,"abstract":"<p>Monitoring cetaceans is essential for evaluating ecosystem health and informing the establishment of marine protected areas. Conventional cetacean monitoring techniques, such as photo-identification, acoustic surveys, and satellite tagging, are often resource-intensive, costly, and sometimes intrusive. Environmental DNA (eDNA)-based methods have emerged as non-invasive, cost-efficient complements based on the analysis of genetic material shed into the environment. However, eDNA research is still evolving, with ongoing efforts to optimize field sampling and laboratory protocols. Building on the challenges of conventional monitoring methods, this study sought to refine eDNA sampling parameters to offer a more efficient and scalable approach for cetacean research, leveraging citizen science platforms. From June to October 2023, eDNA samples were collected across three regions in the Northeast Atlantic Ocean and Mediterranean Sea aboard whale-watching vessels or monitoring platforms engaging citizen scientists. Samples were analyzed for total DNA concentration using Qubit fluorometry and target DNA concentration with quantitative polymerase chain reactions (qPCR). Key variables tested in the field included water volume (2, 5, and 10 L), sampling timing (immediately after a whale was present and at 5-, 10-, and 20-min intervals), and three filter types (pore sizes of 1.2, 0.8, and 0.45 μm). Our results illustrate that larger water volumes (10 L), sampling immediately after a whale breach or fluking behavior, and Smith-Root eDNA filters (1.2 μm pore size) significantly increased eDNA detection probability and signal strength. However, the combination of certain filter types with different water volumes had a significant impact on detection probability, with smaller pore sizes more effectively yielding detections with a lower water volume. These findings provide guidance for future cetacean research initiatives and highlight the potential of eDNA methods in enhancing research and conservation efforts through scalable citizen science-based initiatives.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70103","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126019","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":"Environmental Gradients, Not Geographic Boundaries, Structure Meiofaunal Communities in Siberian Seas","authors":"Adele Maciute,&nbsp;Elias Broman,&nbsp;Francisco J. A. Nascimento,&nbsp;Tommaso Tesi,&nbsp;Evgeniy Yakushev,&nbsp;Birgit Wild,&nbsp;Elena Kirillova,&nbsp;Igor Semiletov,&nbsp;Örjan Gustafsson,&nbsp;Stefano Bonaglia","doi":"10.1002/edn3.70124","DOIUrl":"https://doi.org/10.1002/edn3.70124","url":null,"abstract":"<p>Meiofauna (all invertebrates smaller than 1 mm) are not only sensitive to environmental changes but also contribute significantly to nutrient cycling and energy transfer to higher trophic levels. Despite their importance, meiofauna distribution and ecology in the Siberian seas remain understudied. Here, we employ sediment environmental DNA metabarcoding to characterize meiofauna diversity across the unexplored Siberian seas. We show that meiofauna community structure is primarily driven by river discharge and coastal erosion, which are heavily influenced by climate change, rather than geographical distinctions between the seas. We observed higher meiofauna diversity in nearshore areas where river plumes promoted colonizer nematode communities that are resilient to disturbances. Yet, their dominance may lead to decreased ecosystem stability in the future. This study provides a valuable baseline for meiofauna diversity in remote Siberian seas undergoing rapid environmental change, which will be useful for assessing the future direction and pace of benthic ecological trajectories.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70124","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126017","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":"Promoting Community-Led Monitoring of Taonga (Treasured) Species and Freshwater Health Through eDNA Metabarcoding","authors":"Amy A. Gault,&nbsp;Susan A. Welsh,&nbsp;Arapera Paewai,&nbsp;Penelope Drysdale,&nbsp;Shaun P. Wilkinson,&nbsp;Hone Morris,&nbsp;Erana Mōtū,&nbsp;Hineatatu Dorset,&nbsp;Rose Collis,&nbsp;Adrian Cookson","doi":"10.1002/edn3.70098","DOIUrl":"https://doi.org/10.1002/edn3.70098","url":null,"abstract":"<p>In response to intensified agricultural impacts on Aotearoa New Zealand's river systems, our study sought to demonstrate a novel approach for assessing freshwater quality through environmental DNA (eDNA) and promote a holistic understanding of ecological health. Employing 13 eDNA tree-of-life metabarcoding assays alongside 11 standard physicochemical attributes, we generated a comprehensive temporal and spatial dataset along a 3.5 km section of an upper river catchment. The study catchment moves from a culturally significant native bush area, through sheep and beef farming, to an organic dairy farm, capturing the transition through varying land uses. Our analysis focused on the detections of key culturally significant taonga (treasured) species, known animal sources of fecal contamination, and the taxon-independent community index (TICI) as a measure of ecological health. We identified 479 species including whīo/native blue duck, long and short finned tuna/eels, kaharore bully/cockabully, kōkopu/dwarf galaxias, and kōura/freshwater crayfish. Although <i>Escherichia coli</i> (<i>E. coli</i>) levels did not significantly vary across sites, eDNA sequence counts of cattle and deer were significant predictors of a site's <i>E. coli</i> levels, suggesting that eDNA could be a valuable indicator of fecal contamination sources. TICI scores were strongly correlated with changes in water quality attributes (Adj-<i>R</i>² = 0.92) and consistently detected subtle declines driven by increased pastoral land use. Community leadership was central to our methodology, enabling local stakeholders, including mana whenua and farmers, to actively participate in water monitoring and data interpretation. This approach not only fulfilled regulatory requirements but also fostered a deep connection with the river, enhancing community-led conservation efforts. By enhancing the mauri (life force) of the community through active participation and capacity building, this approach exemplifies sustainable, collaborative efforts in environmental management and revitalization.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70098","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144091639","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":"In Vitro Passive eDNA Sampling Provides a Cost-Effective Alternative for Large Scale Sample Collection","authors":"Samuel Thompson,&nbsp;Simon Jarman,&nbsp;Kingsley Griffin,&nbsp;Matthew Heydenrych,&nbsp;Julian Partridge,&nbsp;Tim Langlois","doi":"10.1002/edn3.70101","DOIUrl":"https://doi.org/10.1002/edn3.70101","url":null,"abstract":"<p>Passive sampling is an emerging method for environmental DNA (eDNA) sampling in aquatic environments. Passive eDNA collection methods are time efficient, inexpensive, and require minimal equipment, making them suited to high-density sampling, especially in remote locations. Here we trial new passive eDNA sampling methods, which we term ‘in vitro passive eDNA sampling’; where a water aliquot is collected at a sampling location and passively sampled in a microcosm experiment, allowing for high-density sampling while the researcher moves to other areas. Furthermore, we test whether agitating in vitro passive samples improves DNA yield and biodiversity estimations. We show that at a species level, in vitro passive sampling methods can return comparable species richness estimates to conventional filtration at both estuarine and inshore marine locations when analyzed as detections per unit of time taken to process the sample. In addition, agitating our in vitro passive samples improved DNA yields by an average of 2.2×as opposed to in vitro passive sampling without agitation, though both were significantly lower than filtration. These in vitro approaches to eDNA sampling will suit cost- and time-sensitive biological surveys, where access to equipment is restricted and the need to complete high-density sampling over large spatial scales is paramount.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70101","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144091636","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-Based Detection of Invasive Crayfish and Crayfish Plague in Estonia","authors":"Michael Oliewo Aluma,&nbsp;Katrin Kaldre,&nbsp;David A. Strand,&nbsp;Margo Hurt,&nbsp;Lilian Pukk","doi":"10.1002/edn3.70107","DOIUrl":"https://doi.org/10.1002/edn3.70107","url":null,"abstract":"<p>In Estonia, three invasive North American crayfish species—<i>Pacifastacus leniusculus</i>, <i>Faxonius limosus</i>, and <i>Procambarus virginalis</i>—have been detected through the annual monitoring program. To protect <i>Astacus astacus</i>, the only native freshwater crayfish species in Estonia, rapid and effective conservation-based management actions are necessary. Recently, the environmental DNA (eDNA) approach has been increasingly used in Europe to detect crayfish species and the crayfish plague pathogen <i>Aphanomyces astaci</i>. Our study explored the potential of integrating the eDNA approach into ongoing annual monitoring programs for invasive crayfish species and <i>A. astaci</i>. We also evaluated the relationship between eDNA concentration and signal crayfish population density at a single location. We filtered 139 eDNA samples from 16 water bodies and screened them for <i>A. astacus</i>, <i>P. leniusculus</i>, and <i>A. astaci</i> using singleplex qPCR assays. A subset of the samples was also screened for <i>P. virginalis</i> and <i>F. limosus</i>. Crayfish eDNA was detected in nine out of 14 water bodies where presence was confirmed by trapping, resulting in a 64% detection efficiency. Detection of <i>P. virginalis</i> was only observed in samples with amplifications below the limit of detection, and <i>A. astaci</i> eDNA was found in only one water body hosting invasive crayfish species. Although we could not establish a convincing quantitative correlation between the estimated <i>P. leniusculus</i> eDNA concentration and crayfish population density, we conclude that the eDNA approach is promising and, with further optimization, it can be integrated into routine monitoring of crayfish and crayfish plague pathogen as a supplement to traditional trapping methods.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70107","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144091638","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":"Improving the Understanding of Detections From iDNA Surveys in Malaysian Borneo With Multiscale Occupancy Models: A Case-Study Using Leech Blood Meals","authors":"Rosie Drinkwater,&nbsp;Elizabeth L. Clare,&nbsp;Stephen J. Rossiter","doi":"10.1002/edn3.70121","DOIUrl":"https://doi.org/10.1002/edn3.70121","url":null,"abstract":"<p>Invertebrate-derived DNA (iDNA) has been successfully utilized for surveying mammalian biodiversity in several ecosystems. Yet, as with all sampling methods, this approach suffers from potential biases, including those introduced by the choice of invertebrate sampler, as well as the stochasticity of DNA amplification during PCR. Occupancy modeling is a statistical framework that can help account for imperfect detections in sampling and can be used to improve iDNA surveys. Using a case study based on the DNA screened from the blood meals of leeches, we demonstrate how multiscale occupancy models can be applied to the molecular detection of vertebrates to reveal the nuances in iDNA detections. Leeches were collected across a habitat degradation gradient in Sabah, Malaysian Borneo, in 2015 and 2016. We estimated three probabilities describing the occupancy, availability, and detection of three abundant mammals (bearded pig, muntjac and sambar deer) and compared how these values were impacted by environmental and technical covariates. For 2015, we found that null models without covariates revealed no clear differences in each of the three probabilities across taxa. However, in 2016, although the taxa have comparable occupancy, deviations occurred in the other two probabilities, with the sambar deer showing the lowest availability and muntjac with the lowest detection probability. Univariate models constructed for each taxon and year revealed differential impacts of the covariates; for example, a strong positive effect of DNA concentration on the detection of sambar deer and bearded pig was seen in 2016 only. Finally, our estimation of the minimum numbers of biological and technical replicates highlights the important trade-off between achieving high probabilities of availability and detection and realistic amounts of sampling. Our results showcase the use of occupancy models for leech-iDNA biodiversity surveys but highlight the potential effects of sample type, methodological design, and sample size.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70121","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144085197","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":"Detection of Non-Native Pink Salmon (Oncorhynchus gorbuscha) in Swedish Rivers Using eDNA","authors":"Thomas A. B. Staveley,&nbsp;Micaela Hellström,&nbsp;Viktor Birgersson,&nbsp;Patrick Hernvall,&nbsp;Hans Schibli,&nbsp;Erika Axelsson,&nbsp;Linus Larliander,&nbsp;Lars Molander,&nbsp;Eva B. Thorstad,&nbsp;Henrik H. Berntsen,&nbsp;Ida Ahlbeck Bergendahl","doi":"10.1002/edn3.70117","DOIUrl":"https://doi.org/10.1002/edn3.70117","url":null,"abstract":"<p>Biological invasions are increasing on a worldwide scale and can have severe ecological and economic consequences. Pink salmon (<i>Oncorhynchus gorbuscha</i>) have a native range in the Pacific Ocean but have been introduced and are now spreading in the Arctic and North Atlantic Oceans, including Sweden. A comprehensive eDNA sampling scheme was conducted in 27 river systems in south-western Sweden in 2023, with the aim to detect adult spawning pink salmon. We applied qPCR and dPCR analysis on aquatic eDNA samples. Results indicated the presence of pink salmon at 24 sites across 11 river systems. Pink salmon were not detected in any of the sampled rivers that drain into the Baltic Sea. However, pink salmon were present in a river only 35 km from the entrance to the Baltic Sea, which means there is a high risk pink salmon will spread into the Baltic Sea in the coming years. Catch reporting is generally low and camera fish counters are few across these systems; therefore, the strength of incorporating eDNA methods is beneficial for the development of pink salmon monitoring programs and aquatic invasive species management.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143939035","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 Replicates, Polymerase and Amplicon Size Impact Inference of Richness Across Habitats","authors":"Jarl Andreas Anmarkrud,&nbsp;Fabricio dos Anjos Santa Rosa,&nbsp;Lisbeth Thorbek,&nbsp;Audun Schrøder-Nielsen,&nbsp;Silvana Melo Sviggum,&nbsp;Jonathan Stuart Ready,&nbsp;Hugo J. de Boer,&nbsp;Quentin Mauvisseau","doi":"10.1002/edn3.70095","DOIUrl":"https://doi.org/10.1002/edn3.70095","url":null,"abstract":"<p>Environmental DNA-based monitoring has been increasingly used in the last decade to monitor biodiversity in aquatic and terrestrial systems. Molecular-based surveys now allow quick and reliable production of baseline knowledge of species community composition on a large scale, allowing a better understanding of ecosystem function and mitigation of stressors linked to anthropogenic activities. Despite this, technical hurdles often remain, and the impact of replicates, PCR polymerases, and amplicon size on the recovered species richness is still poorly understood. Here, we conducted a large controlled experiment, with bulk samples collected from terrestrial, marine, and freshwater environments to assess the impact of natural and technical replicates, PCR polymerases with different degrees of fidelity or proofreading activity, as well as amplicon size on species richness recovery across habitats. In this study, we consistently found variations in sample species richness depending on PCR polymerase choice. We further demonstrate the dissimilar impacts between natural and technical replicates on species richness recovery and the necessity of increasing natural replications in eDNA-based surveys. We highlight the benefits and limitations of replication strategies, polymerase choice, and amplicon size across terrestrial, marine, and freshwater habitats, and provide recommendations to increase the reliability of future eDNA-based metabarcoding studies.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70095","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143925940","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":"DNA Extraction Methodology has a Limited Impact on Multitaxa Riverine Benthic Metabarcoding Community Profiles","authors":"Lindsay K. Newbold,&nbsp;Joe D. Taylor,&nbsp;Amy C. Thorpe,&nbsp;Jonathan Warren,&nbsp;Kerry Walsh,&nbsp;Daniel S. Read","doi":"10.1002/edn3.70102","DOIUrl":"https://doi.org/10.1002/edn3.70102","url":null,"abstract":"<p>There is an expanding body of evidence that environmental DNA (eDNA) can serve as a reliable alternative to traditional assessments of biodiversity and ecological quality. Riverine benthic ecosystems represent one such habitat, holding significant promise for ecological health evaluations using eDNA. Diatoms have typically been assessed in these environmental biofilms through both molecular and conventional methods. However, a wide diversity of life has not been targeted previously, which may serve as important indicators of water quality. To be fully integrated into existing monitoring programs, it is essential to demonstrate the reliability of eDNA-based assessments. This entails developing unbiased methodologies that capture total DNA across the entire community. DNA extraction from environmental samples is critical in analyzing microbial communities; nevertheless, current workflows often focus on individual kingdoms or communities. In this study, we investigated how extraction methodologies can bias the analysis of microbial community composition using amplicon sequencing at a cross-kingdom level in river phytobenthos samples. We tested four commercially available DNA extraction methodologies on 23 freshwater benthic biofilm samples collected across a pH and conductivity gradient. Quantitative PCR and metabarcoding of four amplicons (16S, 18S, ITS, and rbcL), targeting bacterial, eukaryotic, fungal, and phototrophic communities, were employed to assess the impact of the DNA extraction kits on community evaluation. This study revealed a high level of similarity between methods incorporating mechanical lysis, which exhibited higher PCR and sequencing success rates as well as increased cross-kingdom richness and differential abundance compared to chemical and enzymatic lysis alone. However, the origin of the samples, rather than the extraction methodology, emerged as the most significant factor linking them. We recommend utilizing mechanical lysis to optimize cross-kingdom recovery from environmental samples. Nonetheless, the strong correlation between sample origin and extraction method implies that existing data gathered through alternative methodologies remain valid for informing future monitoring practices.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70102","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143925939","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}