Environmental DNA最新文献

{"title":"Targeting Terrestrial Vertebrates With eDNA: Trends, Perspectives, and Considerations for Sampling","authors":"Joshua P. Newton,&nbsp;Morten E. Allentoft,&nbsp;Philip W. Bateman,&nbsp;Mieke van der Heyde,&nbsp;Paul Nevill","doi":"10.1002/edn3.70056","DOIUrl":"https://doi.org/10.1002/edn3.70056","url":null,"abstract":"<p>Terrestrial vertebrates are experiencing worldwide population declines and species extinctions. To effectively conserve remaining populations and species, rapid, cost-effective, and scalable methods are needed to complement longstanding monitoring methods. Increasingly, environmental DNA (eDNA)-based approaches are being used for terrestrial vertebrate biomonitoring within a range of environments. However, as we move eDNA biomonitoring onto land, we are presented with a new set of challenges. This necessitates the development of “best-practice” eDNA sample collection guidelines for terrestrial systems with the purpose of detecting terrestrial vertebrates. To address these needs, we conducted a systematic literature review of 143 peer-reviewed papers applying eDNA to terrestrial vertebrate monitoring (excluding Lissamphibia) that were published between 2012 and 2023. We summarize the use of eDNA for terrestrial vertebrate biomonitoring, focusing on study design and field techniques. Over the decade we observe a steady growth in the annual number of publications, with 3 in 2012 and 33 in 2023. The majority of the reviewed studies targeted terrestrial mammals within temperate forest regions. While an equal number of studies focused on a metabarcoding approach to assess community taxon composition and/or species-specific eDNA detection methods, novel uses are increasingly published. These include studies of animal behavior and population genetics. We record three types of sampling strategies, eight different substrate types, and seven different preservation methods, suggesting that there is no “one size fits all” eDNA-based sampling methodology when detecting terrestrial vertebrates. With a multitude of study aims, across different environments, and target organisms with different ecologies, the standardization of eDNA sampling approaches in terrestrial systems is extremely challenging. We summarize in a table known factors influencing eDNA detection within terrestrial environments. Furthermore, we identify five key considerations to be addressed when sampling for eDNA studies targeting terrestrial vertebrate species, with the aim of guiding decision making.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70056","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143117438","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":"Evaluating the Effectiveness of Sodium Hypochlorite for Genomic DNA Decontamination","authors":"Ashinsa de Silva Wijeyeratne,&nbsp;Hyun S. Gweon","doi":"10.1002/edn3.70057","DOIUrl":"https://doi.org/10.1002/edn3.70057","url":null,"abstract":"<p>Environmental DNA (eDNA) is an increasingly popular, sensitive, and cost-efficient method for studying biodiversity and detecting species. This noninvasive approach involves collecting environmental samples that contain genetic material shed by organisms into their surroundings. Due to the method's sensitivity, robust decontamination strategies are crucial, with sodium hypochlorite, commonly known as bleach, frequently employed. Despite its widespread use, there is no consensus on the most effective bleach concentration, leading to inconsistencies in how the chemical is used in research. This study aimed to determine the minimum concentration of bleach needed for effective decontamination. Genomic DNA of signal crayfish was treated with various concentrations of bleach, ranging from 0.01% to 5% (w/w). Results were observed using Qubit High Sensitivity reagents, quantitative PCR, agarose gel electrophoresis, and the Agilent TapeStation. Our results indicate that a minimum concentration of 0.5% (w/w) bleach is sufficient to prevent the detection of genomic DNA by the techniques tested. These results provide important insights into the use of bleach for decontamination in eDNA research. Establishing a standard bleach concentration for decontamination protocols will help to reduce inconsistencies and enhance the reliability of eDNA studies.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70057","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143116318","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":"Optimization of Wetland Environmental DNA Metabarcoding Protocols for Great Lakes Region Herpetofauna","authors":"Olivia M. Ruppert,&nbsp;Jared J. Homola,&nbsp;Jeannette Kanefsky,&nbsp;Alyssa Swinehart,&nbsp;Kim T. Scribner,&nbsp;John D. Robinson","doi":"10.1002/edn3.70047","DOIUrl":"https://doi.org/10.1002/edn3.70047","url":null,"abstract":"<p>Many species of reptiles and amphibians (herpetofauna) rely on wetlands that are being degraded and lost at a high rate. Characterization of herpetofauna diversity in different wetland types may help guide conservation strategies. However, traditional survey methods often involve sampling within small temporal windows, and the gear deployed may be taxonomically biased, thus, they may fail to accurately characterize species presence/absence and diversity. In contrast, environmental (e)DNA metabarcoding has been shown to effectively survey entire aquatic communities and can provide a useful complement to traditional surveys. The objective of this study was to design and optimize eDNA sampling and laboratory protocols for wetland herpetofauna. Protocols evaluated included different water sampling approaches (point versus transect sampling), seasonality of sampling, and choice of metabarcoding marker (mitochondrial 12S versus 16S rDNA). Samples collected from 10 sites across southern Michigan detected 17 amphibian and five reptile species, including four species of conservation concern (<i>Ambystoma texanum</i>, <i>Clemmys guttata</i>, <i>Rana palustris</i>, and <i>Sternotherus odoratus</i>). We observed no difference in the number of species detected between point and transect samples (<i>p</i> = 0.70), but point sampling required less time (<i>p</i> = 0.03) and allowed significantly larger volumes of water to be filtered (<i>p</i> = 1.13e-5). No difference in species richness was observed between the 12S and 16S mitochondrial DNA markers (<i>p</i> = 0.96). However, a greater number of taxa were identifiable at the species level when using the 16S locus. There was also a significant difference in the number of species detected between early and late summer sampling periods (more species detected in the earlier period; <i>p</i> = 6.31e-6), and some species were only found in the early or late sampling period. Sampling during multiple periods to fully characterize species composition, the use of point sampling, and the 16S mtDNA marker for herpetofauna eDNA metabarcoding studies may increase efficiency and reliability of results.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70047","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143115421","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":"Estimating Rapid Diversity Changes During Acute Herbicide Contamination Using Environmental DNA","authors":"Alessandra Loria,&nbsp;Orianne Tournayre,&nbsp;Marie-Pier Hébert,&nbsp;Naíla Barbosa da Costa,&nbsp;Vincent Fugère,&nbsp;Rowan D. H. Barrett,&nbsp;Beatrix E. Beisner,&nbsp;Andrew Gonzalez,&nbsp;Melania E. Cristescu","doi":"10.1002/edn3.70029","DOIUrl":"https://doi.org/10.1002/edn3.70029","url":null,"abstract":"<p>The biodiversity of freshwater ecosystems globally is facing severe threats due to various anthropogenic stressors, such as habitat degradation, introduction of invasive species, and pollution. Assessing the effects of human-induced environmental stressors on population and community persistence requires accurate biodiversity estimates. While environmental DNA (eDNA) metabarcoding has emerged as a promising tool, its effectiveness in capturing rapid biodiversity responses to acute stressors across levels of biological organization (community, population, and intra-specific levels) remains to be investigated. In this study, we tested the efficacy of eDNA metabarcoding in assessing rapid changes in aquatic zooplankton and insect communities by conducting a two-month mesocosm experiment with pulses of glyphosate-based herbicide under contrasting nutrient levels (mesotrophic and eutrophic). We examined the effects of treatments on community assemblages, family richness, and intraspecific diversity, and compared our findings with those obtained through a microscopy approach. Metabarcoding revealed partially congruent ecological findings with microscopy, indicating its potential in assessing rapid community changes. The herbicide induced shifts in community composition and differentially impacted zooplankton and insect family richness (increase in insects, and decrease in crustaceans and rotifers), suggesting a gradient of tolerance to the herbicide among taxa and potential top-down regulation by insect larvae that may counteract the advantage gained by herbicide-tolerant zooplankton. Finally, we showed that nutrient enrichment exacerbated the negative effects of the herbicide on intraspecific diversity, highlighting concerns about genetic erosion. Our findings underscore the complexity of responses to herbicide and nutrient enrichment in freshwater ecosystems. We conclude that eDNA metabarcoding can not only be used to estimate rapid changes in invertebrate communities but also provides additional value by offering a broader perspective on diversity dynamics and potential cascading effects at different scales of biological organization.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143114571","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 DNA Haplotyping Reveals Dispersal Patterns of Invasive Bluegill Sunfish, Lepomis macrochirus, in Japan","authors":"Kei Wakimura,&nbsp;Ryuji Yonekura,&nbsp;Hiroki Yamanaka,&nbsp;Kimiko Uchii","doi":"10.1002/edn3.70055","DOIUrl":"https://doi.org/10.1002/edn3.70055","url":null,"abstract":"<p>Biological invasions represent a significant threat to global biodiversity. Population genetics plays a crucial role in addressing the invasion history of invasive species, as information on the genetic structure of local populations of invasive species is useful in estimating their source and dispersal. This study aimed to demonstrate the potential of an environmental DNA (eDNA)-based approach for estimating the dispersal patterns of invasive species, using bluegill sunfish (<i>Lepomis macrochirus</i>), a freshwater fish introduced to Japan in 1960. We developed an eDNA haplotyping assay based on high-throughput sequencing and validated its ability to reproduce the haplotype distribution of bluegill sunfish in Japan, which had previously been determined through DNA analysis of individual fish. We also detected a negative relationship between the number of detected haplotypes and the geographic distance from Lake Biwa, one of the initial introduction sites, to each study site. This genetic pattern can occur in introduced species as a result of serial founder events during their range expansion. Our results suggested that Lake Biwa is the source of bluegill sunfish distribution in Japan, which is consistent with the invasion records of this species. We demonstrated the potential of the eDNA haplotyping assay for estimating the dispersal patterns of invasive species, which would aid the preparation of countermeasures against emerging biological invasions by simultaneously enabling the early detection and tracking of invasive species.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70055","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143114343","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":"Persistence of Reptile DNA in a Terrestrial Substrate: A Case Study Using the Eastern Indigo Snake","authors":"Leah R. N. Samuels,&nbsp;Houston C. Chandler,&nbsp;Michelle Hoffman,&nbsp;John A. Kronenberger,&nbsp;Michele Elmore,&nbsp;Robert Aldredge,&nbsp;Benjamin S. Stegenga,&nbsp;James E. Bogan Jr.,&nbsp;Mark A. Davis,&nbsp;Stephanie Hertz,&nbsp;Michael K. Schwartz,&nbsp;Taylor Wilcox","doi":"10.1002/edn3.70053","DOIUrl":"https://doi.org/10.1002/edn3.70053","url":null,"abstract":"<p>Environmental DNA (eDNA) analysis of terrestrial substrates, such as soil and sand, is a rapid and potentially cost-effective way to monitor rare wildlife species. A promising use-case in the southeastern United States is provided by the eastern indigo snake (<i>Drymarchon couperi</i>), for which accurate monitoring has been challenging due to large home ranges and low-density populations. However, knowledge gaps regarding eDNA deposition and persistence in this system currently limit our ability to apply eDNA sampling effectively at the landscape scale. To overcome some of these gaps, we used an optimized soil and sand eDNA extraction protocol and species-specific qPCR assay to conduct a full factorial experiment of eastern indigo snake DNA detection in sand as a function of the duration of snake presence and time since snake removal. We then used these data and a generalized linear mixed model to predict detection probability. Of the 224 total experimental samples, 68 (30.4%) tested positive for eastern indigo snake eDNA. Our model predicted that, with long periods in the enclosure and sampling soon after snake removal, eastern indigo snake eDNA is detectable 68.7% of the time. Eastern indigo snake DNA was detectable in as little as 100 s of snake presence in the enclosure (Pr = 21.1%) and for as long as 10 days after snake presence (Pr = 27.7%). These results suggest that DNA sampling in terrestrial systems may be an effective tool for increasing the temporal window of rare snake detection and a useful complement to existing sampling methods for eastern indigo snakes.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143113606","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":"Taxonomic Blind Spots: A Limitation of Environmental DNA Metabarcoding-Based Detection for Canadian Freshwater Fishes","authors":"Kevin C. Morey,&nbsp;Erika Myler,&nbsp;Robert Hanner,&nbsp;Gerald Tetreault","doi":"10.1002/edn3.70054","DOIUrl":"https://doi.org/10.1002/edn3.70054","url":null,"abstract":"<p>With increasing utilization of eDNA metabarcoding for fish community assessment, it is critical to identify, address, and communicate its capabilities and limitations. One limitation of great concern is the reliability of taxonomic coverage. Taxonomic blind spots, defined as consistent false negatives for specific taxa despite known presence, reduce corroboration with conventional surveys and can limit the uptake of eDNA metabarcoding for biomonitoring. These blind spots result from gaps in reference sequence libraries, issues with taxonomic resolution, inefficient binding of universal primers to the DNA of certain species, and ineffective collection during the sampling of eDNA. To explore this, a multiproject empirical dataset was compiled and analyzed to evaluate the taxonomic coverage of eDNA metabarcoding for a subset of Canadian freshwater fishes using a standardized workflow for two genetic markers: 12S MiFish-U and Vertebrate COI. The compiled dataset consists of species lists generated by eDNA surveys, paired conventional surveys, and historical records. In total, 59 fish species across 15 families were evaluated of which approximately 40% were unable to be consistently detected by either marker because of a blind spot. The 12S and COI markers also differed in which kinds of blind spots were most frequently observed, with 12S markers exhibiting more reference and resolution blind spots and the COI marker exhibiting more unclassified blind spots. Additionally, in silico primer testing exhibited inconsistent predictions for amplification when using multiple software packages, suggesting the need for further in vitro analysis to troubleshoot primer-related blind spots. This study highlights the impact of these blind spots in taxonomic coverage on eDNA metabarcoding studies of Canadian freshwater fishes. The limitations imposed by taxonomic blind spots should be addressed in future optimization efforts as eDNA metabarcoding sees broader acceptance as an applied method for fish biomonitoring.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70054","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143119654","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":"Assessment of Allometry in Environmental DNA and RNA Production From Ayu (Plecoglossus altivelis) in an Experimental Condition Using Mitochondrial and Nuclear Gene Markers","authors":"Toshiaki S. Jo,&nbsp;Yusuke Ozaki,&nbsp;Nao Matsuda,&nbsp;Hiroki Yamanaka","doi":"10.1002/edn3.70052","DOIUrl":"https://doi.org/10.1002/edn3.70052","url":null,"abstract":"<p>Recent studies demonstrated that integrating allometric scaling could strengthen the relationship between environmental DNA (eDNA) concentration and organism abundance. The finding has been supported mainly by field surveys but has not been verified sufficiently at the individual level in a controlled experimental condition. In addition, it remains unknown whether not only eDNA but also environmental RNA (eRNA) production scales allometrically with body mass. To address the knowledge gaps, we conducted a long-term rearing experiment using ayu (<i>Plecoglossus altivelis</i>) to monitor the production of their eDNA and messenger and ribosomal eRNA in their growth from larvae to adults. Water samples were collected from the experimental tanks and <i>P. altivelis</i> eDNA and eRNA (eNAs) concentrations in water samples were estimated using a quantitative real-time PCR with the mitochondrial and nuclear gene markers. In parallel with each water sampling, the number of fish individuals and total biomass in the tank were recorded. Regardless of gene and RNA types, individual-level <i>P. altivelis</i> eNA concentrations were related to their allometric scaled mass (ASM), with the scaling coefficient (<i>b</i>) = 0.75, more strongly than their mean body mass. The result indicated that a larger individual produces lesser mass-specific eNA particles, supporting the relevance of the allometric scaling in eDNA production at the population level observed in field surveys. Moreover, the ratios of some eNA concentrations significantly decreased with larger mean fish body mass in the tank. The finding may relate to the changes in intracellular physiology with individual growth and/or aging, having the potential to indicate the population's average body size. Our study offered insights into the production of various eNA particles depending on body size and metabolic rate and implications for a better understanding of the population's ecology and more effective stock management.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70052","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143119655","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":"Experimental Evidence of Rapidly Decaying Environmental DNA Highlights Infection Risk from Two Major Amphibian Pathogens","authors":"Joseph D. Trafford,&nbsp;Trenton W. J. Garner,&nbsp;David J. Murrell,&nbsp;Julia J. Day","doi":"10.1002/edn3.70051","DOIUrl":"https://doi.org/10.1002/edn3.70051","url":null,"abstract":"<p>Infectious diseases spread through international wildlife trade networks, presenting major conservation and welfare challenges. The diseases amphibian chytridiomycosis (caused predominantly by chytrid fungus <i>Batrachochytrium dendrobatidis, Bd</i>) and ranavirosis (caused by iridoviruses in the genus <i>Ranavirus, Rv</i>) are the result of infection by globally distributed pathogens. These pathogens spread internationally through live-animal trade networks and have driven population declines, mass mortalities, and community collapse for a broad range of amphibian species. Environmental (e)DNA methods may provide highly sensitive and non-invasive pathogen surveillance for traded or wild amphibians. To investigate the relationship between eDNA detection and environmental pathogen persistence, eDNA degradation rates were quantified across a range of temperatures (15°C–25°C) for both <i>Bd</i> and <i>Ranavirus.</i> Estimated decay rates suggest that overall pathogen eDNA concentration degrades by 99% between 18.9–52.4 h. Low levels of pathogen eDNA remained detectable for the duration of the experiment (&gt; 28 days). Time was found to have a significant negative effect on eDNA concentration for both pathogens (<i>p</i> &lt; 0.001). The negative effect of temperature on eDNA concentration was significant for both pathogens (20°C for <i>Rv</i>, <i>p</i> &lt; 0.05; 25°C for <i>Bd/Rv p</i> &lt; 0.001). We argue that high concentrations of eDNA represent viable pathogen in the environment, demonstrating the usefulness of eDNA for the monitoring of disease status of consignments of traded amphibians.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143118639","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":"Rare Taxa Are Key Links in Regional Antimicrobial Resistance Profiles in Dusts Across Diverse North American Regions","authors":"Paul B. L. George,&nbsp;Florent Rossi,&nbsp;Marc Veillette,&nbsp;Amélia Bélanger Cayouette,&nbsp;Samantha Leclerc,&nbsp;Cindy Dumais,&nbsp;Nathalie Turgeon,&nbsp;Caroline Duchaine","doi":"10.1002/edn3.70049","DOIUrl":"https://doi.org/10.1002/edn3.70049","url":null,"abstract":"<p>The role of bioaerosols in the dispersal of antimicrobial resistance genes (ARGs) and resistant microorganisms is poorly understood. In addition, bioaerosols are powerful composite samples representative of the surrounding environment and can be used as sentinels of many local habitats. Evidence suggests that using environmental DNA from dust collected on vehicle cabin air filters can define regional resistance profiles. Here, this method was used to investigate differences in resistance gene profiles, their underlying bacterial communities, and their links to anthropogenic and environmental variables across Canada. In total, 477 car filter samples were collected, with every province and territory being represented. DNA was extracted from filter dust. High-throughput qPCR was used to detect and quantify a panel of 36 ARGs and 3 mobile genetic elements. Bacterial biomass was assessed using standard qPCR methods of the 16S rRNA gene, which was also used to assess bacterial biodiversity via metabarcoding. Results indicated that <i>qepA</i> dominates antimicrobial resistance profiles across Canada. However, after they were removed from the dataset, regional profiles were evident based on gene type and richness. Factors positively linked to total numbers of ARGs included human and livestock populations; whereas mean annual precipitation was negatively linked to resistance gene quantities. Measures of α-diversity were generally greater in the western regions of Canada than in the east and the north. Community composition analyses showed similarities between the prairies and territories, which were separated from other regions. Finally, network analyses revealed a relatively stable group of core ARGs across regions, which were largely correlated with low-abundance genera. Such findings suggest that rare taxa are key links in the diffusion of antimicrobial resistance in environmental contexts. Furthermore, this study highlights the potential application of vehicle air filters in building long-term monitoring capacity of outdoor bioaerosols.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70049","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143118279","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}