Environmental DNA最新文献

{"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}

{"title":"Out in the Open: Investigating Passive Airborne eDNA Detection of Bats at Artificial Feeding Stations","authors":"Daniel E. Sanchez,&nbsp;Faith M. Walker,&nbsp;Savannah J. Marriott,&nbsp;Anna L. Riley,&nbsp;Sarah Stankavich,&nbsp;Amanda M. Adams,&nbsp;Donald Solick,&nbsp;Doug Bradley,&nbsp;Christian Newman","doi":"10.1002/edn3.70108","DOIUrl":"https://doi.org/10.1002/edn3.70108","url":null,"abstract":"<p>Environmental DNA (eDNA) is a valuable biomonitoring tool, but application in terrestrial settings remains challenging due to a lack of generalizable sampling approaches. With bat species needing urgent research attention, airborne eDNA may offer this generalizability, as current eDNA sampling for bats is mostly limited to conspicuous sources (e.g., guano). While previous studies detected bats from roosts and open-air sites using active air sampling, it remains uncertain whether bats can be readily detected from the open air using passive approaches. In central Texas, we used passive air sampling to determine if we could recover bat assemblages with metabarcoding and an imperiled focal species (tricolored bat, <i>Perimyotis subflavus</i>) with qPCR. Outside two cave locations, we positioned passive air samplers (two collection media per sampler; <i>n</i> = 24 media) near artificial prey patches, monitoring acoustically for bat activity and foraging. In the lab, we subjected the media to multiple eDNA extraction methods, direct DNA extraction, and two resuspension-concentration approaches (filtration and pelleting). Metabarcoding allowed the detection of two bat species within a single sample, while qPCR allowed detection of <i>P. subflavus</i> in two samples. Although the detections all came from direct extraction, pelleting substantially improved taxonomic recovery and sample success for vertebrates overall. Detection of bat eDNA from passive samplers establishes a lower bound possibility for open-air settings, and the low number of detections highlights the need for improved sampling strategies. We offer recommendations to enhance future efforts and introduce a qPCR assay for <i>P. subflavus</i> that can be used in a variety of eDNA contexts.</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/edn3.70108","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143925815","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":"CRISPR-Based Environmental Biosurveillance Assisted via Artificial Intelligence Design of Guide-RNAs","authors":"Benjamín Durán-Vinet,&nbsp;Jo-Ann L. Stanton,&nbsp;Gert-Jan Jeunen,&nbsp;Ulla von Ammon,&nbsp;Jackson Treece,&nbsp;Xavier Pochon,&nbsp;Anastasija Zaiko,&nbsp;Neil J. Gemmell","doi":"10.1002/edn3.70105","DOIUrl":"https://doi.org/10.1002/edn3.70105","url":null,"abstract":"<p>Environmental biosecurity challenges are intensifying as climate change and human activities accelerate the spread of invasive species, disrupting ecosystem composition, function, and essential services. Environmental DNA (eDNA) has transformed traditional biosurveillance by detecting trace DNA fragments left by organisms in their surroundings, primarily by applying quantitative polymerase chain reaction (qPCR) methods. However, qPCR presents challenges, including limited portability, reliance on precise thermal cycling, and susceptibility to inhibitors. To address these challenges and enable field-deployable monitoring, isothermal amplification techniques such as recombinase polymerase amplification (RPA) paired with clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) have been proposed as promising alternatives. CRISPR-Cas technology also presents challenges, including searching and optimizing a guide RNA (gRNA) that is highly sensitive and has no off-target interactions for use as an effective environmental biosurveillance tool. We present here the development of SENTINEL (<b>S</b>mart <b>E</b>nvironmental <b>N</b>ucleic-acid <b>T</b>racking using <b>I</b>nference from <b>N</b>eural-networks for <b>E</b>arly-warning <b>L</b>ocalization) that harnesses the programmability, specificity and sensitivity of a one-pot RPA-CRISPR-Cas13a reaction by integrating an accessible and pre-trained neural network to accelerate assay design for rapid deployment. We challenged SENTINEL with waterborne eDNA from two marine sites invaded by species not native to New Zealand as proof-of-concept fluorescence-based tests: <i>Sabella spallanzanii</i> (Mediterranean fanworm) and <i>Undaria pinnatifida</i> (Wakame). Off-target effects were explored by challenging the SENTINEL assays on gDNA from a suite of co-occurring species. SENTINEL presented a robust, streamlined method incorporating the trained neural network, achieving a sensitivity down to 10 attomolar using recombinant DNA and down to ~0.34 copies/μL for eDNA samples with 1 h, costing 3.5 USD per sample. There was a 100% agreement between SENTINEL results and qPCR-based analysis of the eDNA samples. SENTINEL displayed no off-target activity when challenged against 23 gDNA samples from co-occurring species. Thus, our study showcases SENTINEL's potential as a robust platform for eDNA screening applications.</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/edn3.70105","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143925816","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":"A Time- and Cost-Effective eDNA Protocol to Survey Freshwater Mussels (Bivalvia: Unionida) in Tropical Rivers","authors":"Alexandra Zieritz,&nbsp;Tabitha Richmond,&nbsp;Florian Melzer,&nbsp;Khairul Adha A. Rahim,&nbsp;John-James Wilson,&nbsp;Hazeeqah Filzah binti Kassim,&nbsp;Hanna Hartikainen","doi":"10.1002/edn3.70099","DOIUrl":"https://doi.org/10.1002/edn3.70099","url":null,"abstract":"<p>Tropical freshwater mussels (Bivalvia: Unionida) are one of the most endangered groups of animals globally, but conservation is hindered by a lack of species distribution data. Traditional hand-sampling is time- and cost-intensive and not always possible, for example, because of the presence of crocodiles. Surveying freshwater mussel populations by environmental DNA (eDNA) could potentially rapidly increase data availability, but no published study and protocols targeted towards tropical freshwater mussels are available to date. We aimed to develop a reliable and cost-efficient eDNA protocol for surveying tropical freshwater mussels. We first developed and validated a qPCR primer-probe assay within the cytochrome <i>c</i> oxidase subunit 1 (COI) gene for <i>Rectidens sumatrensis</i>. We applied this assay in a controlled laboratory setting on eDNA collected from lake and river water, respectively, at two different <i>R. sumatrensis</i> densities in order to test a set of 18 different protocols for capturing, preserving, and extracting freshwater mussel eDNA. All protocols use equipment that is readily available and reusable. Our results revealed that samples stored in Longmire's buffer (at 4°C) yielded more mussel DNA than when stored in absolute ethanol (at −20°C), with &lt; 1% of ethanol- and 78% of buffer-preserved samples fulfilling the criteria for positive <i>R. sumatrensis</i> eDNA detection (i.e., amplifying above the limit of detection in at least four out of five qPCR replicates). Across buffer-preserved samples, eDNA detection and amplification success rates were higher and quantification cycle values were lower for eDNA captured without pre-filtration and with filter membrane pore sizes &gt; 0.45 μm, and eDNA extracted with the Qiagen DNeasy Blood &amp; Tissue Kit rather than the PowerSoil ProKit (albeit latter exhibiting fewer instances of amplification in negative controls). The assay detailed here was capable of detecting down to <i>R. sumatrensis</i> eDNA concentrations of 6.38 × 10⁻⁷ ng/μL and reflected the difference in stocking density.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70099","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143926011","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 Impact of Flow Velocity on Environmental DNA Detectability for the Application in River Systems","authors":"Jelle A. Dercksen,&nbsp;Jan Willem Foppen,&nbsp;Astrid Blom,&nbsp;Krijn B. Trimbos,&nbsp;Julia Gebert,&nbsp;Thom A. Bogaard,&nbsp;Laura Maria Stancanelli","doi":"10.1002/edn3.70111","DOIUrl":"https://doi.org/10.1002/edn3.70111","url":null,"abstract":"<p>Organisms perpetually release genetic material in their surroundings, referred to as environmental DNA (eDNA), which can be captured and subsequently analyzed to detect biodiversity across the tree of life. In lotic, dynamic environments, little is known about the specific factors that affect the concentration of eDNA between release by the host and its dissemination into the environment. This gap in knowledge introduces significant uncertainty when applying eDNA as a monitoring tool. Our objective is to provide insight on the factors that affect the eDNA concentrations in ecosystems representative of rivers and streams. To this end, we conducted a series of laboratory experiments in a rotating circular (annular) flume, which allows for extended degradation experiments under conditions of flow. Here, we show that flow velocity impacts the observed eDNA concentration over time. Our results suggest that flow-induced transport keeps eDNA in suspension, reducing eDNA removal from the water column, which increased the observed concentration of eDNA. We observed a temporary increase in eDNA concentration over the early phase of the flume experiment with the highest flow velocity. This increase in eDNA concentration seems to be due to a combination of low eDNA degradation rates and high shear stress, which fragment and subsequently homogenize eDNA particles over the water column. The results of our study show the importance of better understanding and assessing the detection probability of eDNA, both in controlled laboratory and larger-scale environmental conditions.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70111","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143919320","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":"Capture—Incubate—Release: An Animal-Friendly Approach to Assess Local Aquatic Macroinvertebrate Species Diversity Through Environmental DNA Metabarcoding","authors":"Mandy Sander,&nbsp;Arne J. Beermann,&nbsp;Dominik Buchner,&nbsp;Martina Weiss,&nbsp;Marie-Thérése Werner,&nbsp;Florian Leese","doi":"10.1002/edn3.70112","DOIUrl":"https://doi.org/10.1002/edn3.70112","url":null,"abstract":"<p>Metabarcoding of environmental DNA (eDNA) from water samples has become an important tool for aquatic biodiversity assessment because it is minimally invasive, time-efficient, and generates comprehensive taxa lists. Nevertheless, species lists differ noticeably from those obtained via bulk metabarcoding of the local benthic community because of eDNA traces transported in the water column. However, it is important for several assessments to capture local biodiversity signals. Our goal was to test whether we can combine the advantages of both methods, that is, obtaining a local signal and being minimally invasive. Therefore, our developed method includes capturing local benthic invertebrates, incubating them in a water container for eDNA enrichment and analysis, and releasing them back to their habitat. We first quantified eDNA release over time for 10 invertebrate species in a laboratory setting using qPCR. We found that a 5-min incubation is sufficient to successfully detect 50% of the replicates for six of the 10 species. Three of the species showed a significant increase in eDNA molecules over time. However, the experiment showed a species-specific eDNA release pattern that was not directly linked to body sclerotization nor biomass. As a second experiment, we sampled bulk samples at three field sites and incubated the bulk samples for 0, 20, 40, and 80 min in containers filled with stream water to compare taxa lists obtained via metabarcoding of bulk and the enriched eDNA samples. Our results showed a much higher overlap between bulk and enriched eDNA metabarcoding (55%–60%) in comparison to reported overlaps between bulk and stream eDNA metabarcoding from other studies (often &lt; 20%). This overlap did not change with incubation time. Thus, our study demonstrates that it is possible to detect most locally occurring species via eDNA metabarcoding after shortly incubating them in water. Therefore, this approach has great potential for point-sample eDNA analysis of macroinvertebrates without compromising animal welfare.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70112","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904894","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":"Harnessing eDNA Metabarcoding to Monitor Species Diversity in Restoration Sites: Insights From Laikipia, Kenya","authors":"Cornelius Okello,&nbsp;Nina Wambiji,&nbsp;Susana W. Kihia,&nbsp;Nehemiah Ongeso,&nbsp;Samuel Mwakisha Mwamburi,&nbsp;Anthony Wandera,&nbsp;Marie-Estelle Demory,&nbsp;Margaret Awuor Owuor","doi":"10.1002/edn3.70110","DOIUrl":"https://doi.org/10.1002/edn3.70110","url":null,"abstract":"<p>Restoration of degraded arid and semi-arid lands (ASALs) dryland ecosystems gained traction globally with the enactment of the Bonn Challenge and UN Decade of Restoration. This has been domesticated in Kenya's context by The Forest and Landscape Restoration Implementation Plan (FOLAREP). However, effectively monitoring restored ecosystems is crucial but challenging because of data gaps and technical hurdles, highlighting the need for innovative approaches to assess and restore biodiversity. This study aimed to pilot soil environmental DNA (eDNA) metabarcoding to detect species compositions rapidly, evaluate population structures and abundances, and characterize taxonomic groups. The results from this study serve as a foundational step toward monitoring the impact of water bunds, a restoration approach on biodiversity conservation, in Lower Naibunga Community Conservancy in Laikipia County, Kenya. This study used 16S rDNA and rbCL metabarcoding to assess prokaryotic and plant diversity. Plant growth-promoting rhizobacteria species attributed to enhancing nutrient availability and improving plant resilience to abiotic stress were prevalent across all six sites: Lorubai (Site 1), Burtany (Site 2), Nkirashi (Site 3), Losopukia (Site 4), Munushoi (Site 5), and Loika (Site 6). Plant species attributed to drought tolerance and rangeland rehabilitation were also identified. The study demonstrates the potential of eDNA metabarcoding as an effective tool for monitoring nature-based solutions (NbS) interventions to enhance biodiversity and ecosystem restoration in ASALs.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70110","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904992","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}