Environmental DNA最新文献

{"title":"Systematic evaluation of the influence of Taq enzyme choice and amplification conditions on targeted environmental DNA assay performance and detection in field samples","authors":"Neha Acharya-Patel,&nbsp;Emma T. Groenwold,&nbsp;Michael J. Allison,&nbsp;Caren C. Helbing","doi":"10.1002/edn3.578","DOIUrl":"https://doi.org/10.1002/edn3.578","url":null,"abstract":"<p>Targeted environmental DNA (eDNA) studies mainly rely on quantitative real-time polymerase chain reaction (qPCR) to amplify extremely low concentrations of DNA present in environmental samples. Understanding factors that influence targeted eDNA assay performance and detection in field samples, such as Taq DNA polymerase enzyme type and thermocycle protocol, is critical for the interpretation of qPCR results. We completed a systematic performance evaluation of five distinct targeted eDNA assays (eANFI6, eFISH1, eANBO5, eGLIN1, and eLICA3 targeting sablefish, general fish, Boreal toad, wood turtle, and the American bullfrog) by subjecting the same samples to analysis by five different Taq enzyme reagent mixes (Immolase, Environmental Master Mix (EMM), Amplitaq, QIAcuity, and QuantiNova) and the commonly used 2-step (95°C, 60°C) and 3-step (95°C, 64°C, 72°C) thermocycle protocols. We evaluated assay performance using a standardized dilution series of synthetic dsDNA target sequences and calculated limits of detection (LOD) and quantification (LOQ) and 95% confidence intervals for each combination of Taq enzyme and thermocycle protocol. All assays performed within acceptable performance criteria as defined by the Canadian national standard for targeted eDNA assays. Based on data generated by synthetic dsDNA fragments, the eDNA assays performed comparably regardless of the enzyme reagent mix and protocol used, except for eANFI6 and eGLIN1 using EMM and the 3-step protocol, where no amplification was observed. On freshwater field samples, EMM and Immolase performed best. On marine field samples, Immolase, EMM, Qiacuity, and QuantiNova performed equally well, although EMM failed to amplify some samples. The work reveals that an enzyme reaction mix or thermocycle protocol can affect the result of an eDNA assay, but the appropriate choice also depends on the nature of the field sample. It is therefore imperative that these are considered when selecting appropriate reaction conditions and that they are clearly reported.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.578","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141424919","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":"Developing an eDNA approach for wetland biomonitoring: Insights on technical and conventional approaches","authors":"Starsha Bird,&nbsp;Paul Dutton,&nbsp;Shaun Wilkinson,&nbsp;Josh Smith,&nbsp;Ian Duggan,&nbsp;Angela McGaughran","doi":"10.1002/edn3.574","DOIUrl":"https://doi.org/10.1002/edn3.574","url":null,"abstract":"<p>Wetlands are ecologically and culturally significant ecosystems that are experiencing biodiversity declines globally. Biomonitoring techniques that use environmental DNA (eDNA) to detect and monitor biodiversity are well established in lake, riverine, and marine ecosystems. However, their use in wetlands requires further development due to the presence of sediments that block eDNA filters to limit water filtration, alongside a lack of standardized methodology. In this study, we examined eDNA dynamics to understand spatiotemporal biodiversity patterns in an Aotearoa New Zealand wetland and to optimize their application to wetland-specific challenges. We sampled four sites across Opuatia Wetland at three time points during an austral spring. We conducted conventional taxonomic surveys, tested three different filter sizes (1.2 μm, 5 μm, and semi-quantitative dacron filters), and assessed our ability to detect foreign DNA (from kea; <i>Nestor notabilis</i>) at different time points and distances post-release. We found significant differences in DNA sequence composition across time and space, and when using different sized filters. eDNA data generally complemented (versus replaced) conventional survey and identification methods, with certain species only detected by one method or the other. Taxonomic resolution of conventional sampling and identification methods often exceeded that of eDNA. Foreign DNA was detectable 10 m from its release point for up to 1 week post-release. Our results provide new considerations for future eDNA research in wetland environments, where rapid biomonitoring techniques are needed to support conservation and preservation.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.574","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141424994","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 can inform the trade-off between proactive and reactive strategies for crayfish conservation","authors":"Jack A. Greenhalgh,&nbsp;Rebecca Banks,&nbsp;Rupert A. Collins,&nbsp;Ursula Juta,&nbsp;Sharon Reeves,&nbsp;Ben Siggery,&nbsp;Michael J. Sweet,&nbsp;James Tibbitts,&nbsp;Andrew D. Saxon,&nbsp;Kate E. Warwick,&nbsp;Glenn Wiseman,&nbsp;Gareth Jones,&nbsp;Martin J. Genner","doi":"10.1002/edn3.571","DOIUrl":"https://doi.org/10.1002/edn3.571","url":null,"abstract":"<p>The introduction of the signal crayfish <i>Pacifastacus leniusculus</i> to British rivers has led to ecological degradation and the decline of the native white-clawed crayfish <i>Austropotamobius pallipes</i>. To manage and mitigate the impact of the signal crayfish, conservation agencies and government bodies employ multiple conservation strategies. These take the form of proactive native crayfish breeding and stocking programs and reactive invasive crayfish control programs. Here, we used eDNA to assess the populations of native and invasive crayfish species across 50 sites in 10 river catchments in Norfolk, United Kingdom (UK). The sites were chosen to enable assessment of the potential of eDNA to inform proactive and reactive crayfish conservation strategies. Three of the catchments sampled were selected to assess the success of recent <i>A</i>. <i>pallipes</i> reintroduction, whereas the remaining seven were selected to better understand the distribution of each species at the landscape scale. Combining results of eDNA-based methods with net searches within an occupancy model enabled us to confidently determine the presence of <i>P</i>. <i>leniusculus</i> at eight sites, and <i>A</i>. <i>pallipes</i> at three sites, which was more than visual searches alone (five and two study sites, respectively). Neither eDNA nor net searches detected <i>A</i>. <i>pallipes</i> at sites where <i>A</i>. <i>pallipes</i> had been reintroduced. We recommend that practitioners using eDNA-based surveys for management and conservation of crayfish should consider: (1) designing eDNA surveys with an emphasis on large spatial scales to comprehensively describe the distributions of native and invasive crayfish in a region of interest; (2) work with local conservation organizations and/or government bodies to inform the selection of study sites to generate results that are meaningful to real-world conservation actions; and (3) use results from eDNA-based crayfish surveys to target limited conservation resources to appropriate proactive and/or reactive conservation actions.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.571","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425030","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 recovery for dissolved eDNA state: A comparative analysis of isopropanol precipitation, magnetic bead extraction, and centrifugal dialysis","authors":"Anish Kirtane,&nbsp;Kristy Deiner","doi":"10.1002/edn3.572","DOIUrl":"https://doi.org/10.1002/edn3.572","url":null,"abstract":"<p>Environmental DNA consists of multiple states including but not limited to membrane-bound, adsorbed, and dissolved states. Because of their chemical and physical properties, each of these states may have different degradation and transport potential. Essential to the study of eDNA states is being able to isolate them from an environmental sample. Here, we focus on improving the DNA recovery of the dissolved state of eDNA from water. We compared three recovery methods, namely isopropanol precipitation, magnetic bead extraction, and centrifugal dialysis. We evaluated the effectiveness of these methods based on the measured DNA recovery of two different species' DNA of different sizes. DNA recovery was assessed with qPCR. We also checked for the effect of inhibitor removal, and lastly, we estimated the cost of reagents and consumables (not labor). The DNA recovery varied among extraction methods, with isopropanol precipitation yielding the highest recovery (52.47 ± 19.69%), followed by centrifugal dialysis (12.58 ± 7.15%) and magnetic bead extraction (9.92 ± 3.89%). However, isopropanol precipitation's efficacy was influenced by humic acid concentration in the water matrix. The presence of humic acids significantly affected isopropanol precipitation, with higher humic acid concentrations leading to increased DNA recovery. This suggests that humic acids act as co-precipitators during isopropanol precipitation. We observed that longer DNA fragments (chicken) had lower recovery compared to shorter fragments (salmon) across all extraction methods. Magnetic bead extraction effectively removed inhibitors, while centrifugal dialysis and isopropanol extraction required an additional inhibitor removal step. Isopropanol, magnetic bead extraction, and centrifugal dialysis methods have estimated costs of 7.74, 8.53, and 23.62 USD in 2023 respectively. Overall, isopropanol precipitation was the least expensive and most effective with the highest measured recoveries, but it was dependent on humic acid concentration in the environmental sample.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.572","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141304209","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":"Investigating pelagic biodiversity and gelatinous zooplankton communities in the rapidly changing European Arctic: An eDNA metabarcoding survey","authors":"Ayla Murray,&nbsp;Taylor Priest,&nbsp;Adria Antich,&nbsp;Wilken-Jon von Appen,&nbsp;Stefan Neuhaus,&nbsp;Charlotte Havermans","doi":"10.1002/edn3.569","DOIUrl":"https://doi.org/10.1002/edn3.569","url":null,"abstract":"<p>Fram Strait, the gateway between the Arctic and Atlantic Oceans, is undergoing major climate change-induced physical and biological transformations. In particular, rapid warming and ongoing “Atlantification” are driving species range shifts and altering food web structures in the Arctic. Understanding and predicting the consequences of these processes on future ecosystems requires detailed assessments of local and pelagic biodiversity. Gelatinous zooplankton (GZP) is an important component of pelagic communities, and recent evidence indicates that such communities are undergoing major changes in the Fram Strait. However, as sampling GZP is challenging, they are regularly underestimated in biodiversity, distribution, and abundance. To overcome this and address existing ecological knowledge gaps, we investigated patterns of pelagic metazoan diversity in Fram Strait using environmental DNA (eDNA) metabarcoding of the cytochrome <i>c</i> oxidase I (COI) gene. We successfully detected a broad range of taxa from the marine metazoan and GZP communities across sampling locations and ocean depth zones. We demonstrate the vertical structuring of diversity and elucidate relationships between taxa and water mass indicators, such as salinity and temperature. Furthermore, when comparing eDNA data with net and video transect data for GZP at the same period and location, we found that eDNA uncovered a higher number of taxa, including several that were not detected by the other methods. This study is a contribution to the formation of baseline Arctic GZP biodiversity datasets, as well as future research on changing marine metazoan biodiversity and community composition.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.569","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141245425","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 comparison of eDNA sampling methods in an estuarine environment on presence of longfin smelt (Spirinchus thaleichthys) and fish community composition","authors":"Lizabeth Bowen,&nbsp;Shannon Waters,&nbsp;Lyndsay Rankin,&nbsp;Karen Thorne,&nbsp;Daphne Gille,&nbsp;Susan De La Cruz,&nbsp;Isa Woo,&nbsp;Levi Lewis,&nbsp;Katie Karpenko,&nbsp;Cheryl Dean,&nbsp;Gregg Schumer","doi":"10.1002/edn3.560","DOIUrl":"https://doi.org/10.1002/edn3.560","url":null,"abstract":"<p>The loss of tidal wetlands in the San Francisco Bay estuary have led to declines in native fish presence. Restoration of tidal wetlands in this area has intensified, with a primary goal of increasing the number of native fishes. We compared the presence of longfin smelt in naturally accreted and beneficial dredge reuse wetlands as a measure of successful restoration. We used environmental DNA (eDNA) analyses as our metric for fish presence and fish community composition, employing two different water sampling methods for comparison (standard and high-volume). Longfin smelt were present in multiple sites, but at numbers too low for accurate comparisons across sites. Community composition varied based on the water sampling method, but the presence/absence of longfin smelt was consistent across sampling methods. As this represents a pilot study, further refinement of methodology is necessary, but the use of high-volume water sampling methods is promising.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.560","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141156517","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":"Detecting the invisible through DNA metabarcoding: The role of gelatinous taxa in the diet of two demersal Antarctic key stone fish species (Notothenioidei)","authors":"Micaela B. Ruiz,&nbsp;Eugenia Moreira,&nbsp;Manuel Novillo,&nbsp;Stefan Neuhaus,&nbsp;Florian Leese,&nbsp;Charlotte Havermans","doi":"10.1002/edn3.561","DOIUrl":"https://doi.org/10.1002/edn3.561","url":null,"abstract":"<p>Gelatinous zooplankton (GZP), i.e., ctenophores, cnidarian medusae, chaetognaths, appendicularians and salps, are considered climate change winners. This becomes particularly obvious in the Southern Ocean, which has undergone a significant shift from a krill-based to a salp-based ecosystem over the last decades. A better knowledge on the role of gelatinous invertebrates as prey is needed to predict the impact of such a gelatinous shift. Until recently, GZP was considered as a “trophic dead end”. However, their true importance in diets has remained unresolved due to the rapid digestion of their watery and soft tissues in predators' stomachs. In this study, we want to validate the paradigm shift from GZP being considered as “survival food” to be considered a “regular” prey item for two demersal fish species (<i>Notothenia rossii</i> and <i>N. coriiceps</i>) of Potter Cove, South Shetland Islands, using a multimarker (COI and 18S) metabarcoding approach. We found that GZP taxa commonly occurred in the diets of both species, represented by pelagic tunicates (appendicularians, salps), cnidarians, chaetognaths and ctenophores. Salps were the most abundant prey group, preyed upon by each individual of both species, reaching 98.7% relative read abundance for 18S. We recovered a wide range of different taxa in their diets, from primary producers to highly abundant invertebrates, thus the two nototheniid species can be regarded as “natural samplers” of the ecosystem in study. Finally, we want to point out the importance of multimarker metabarcoding approaches for broad ecological assessments, given the differential amplification and sequencing success of different markers for specific groups and the unequal taxonomic coverage of the reference databases. The output of each marker was highly complementary, since an important prey item such as salps, was only detected with 18S, while other taxa (e.g., Arthropoda) were represented with a higher taxonomic resolution with COI.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.561","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141091516","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":"Assessing the gut microbiome and the influence of host genetics on a critically endangered primate, the northern muriqui (Brachyteles hypoxanthus)","authors":"Naiara Guimaraes Sales,&nbsp;Mariane da Cruz Kaizer,&nbsp;Samuel S. Browett,&nbsp;Sofia I. Gabriel,&nbsp;Allan D. McDevitt","doi":"10.1002/edn3.559","DOIUrl":"https://doi.org/10.1002/edn3.559","url":null,"abstract":"<p>The Northern muriqui (<i>Brachyteles hypoxanthus</i>) is one of the world's most critically endangered primates, with only ~1000 mature individuals remaining in the wild. Habitat loss and hunting have led to its sharp decline, making conservation efforts crucial. Analyses of gut microbiomes in wild populations can provide valuable information on host health and vulnerability, and ultimately, contribute to baseline knowledge toward improving conservation programs and reintroduction efforts. In this study, we analyzed the microbiome (16S rRNA metabarcoding) of fecal samples belonging to 53 uniquely genotyped individuals from three social groups from the Caparaó National Park, aiming to provide the first assessment of the microbiome diversity and composition for this species. Our results showed the muriqui gut microbiome was predominantly composed of the phyla Bacteroidetes and Firmicutes, with the dominant classes represented by Bacteroidia and Clostridia. High similarity in bacterial diversity and composition was found for individuals from distinct groups, suggesting a negligible geographical effect at the fine spatial scale analyzed. No significant effect of host genotype heterozygosity levels on microbiota diversity was recovered, but a significant influence of genetic distance on microbiota community structure and composition was demonstrated. Our findings stress the importance of considering associations between host genetics and the microbiome and suggest that the analyzed populations host a similar microbiome composition. This detailed microbiome assessment can aid conservation actions, including future anthropogenic impact assessments and animal reintroductions.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.559","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141091512","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":"Assessing the impacts of aquaculture on local fish communities using environmental DNA metabarcoding analysis","authors":"Shota Suzuki,&nbsp;Yuri Otomo,&nbsp;Akihiro Dazai,&nbsp;Takuzo Abe,&nbsp;Michio Kondoh","doi":"10.1002/edn3.551","DOIUrl":"https://doi.org/10.1002/edn3.551","url":null,"abstract":"<p>Fish aquaculture potentially affects the local ecosystem through feed (leftovers) and feces. However, evaluation of its impacts on biodiversity, especially those of mobile organisms such as fish, is not straightforward. Here, we report a case study in which environmental DNA (eDNA) metabarcoding with MiFish universal primers for the 12S rRNA region of fish is used to detect and assess the impact of aquaculture on local fish communities. In Shizugawa Bay, Minamisanriku Town, Miyagi Prefecture, Japan, <i>Oncorhynchus kisutch</i> (coho salmon) is aquacultured in sea cages from November to July, but is absent from August to October. We conducted eDNA surveys in June, August, October, and December 2021 of water at depths of 5 m and 1 m above the bottom obtained from two sites, one approximately 100 m and the other approximately 2500 m from the nearest aquaculture site. The total number of operational taxonomic units (OTUs) detected was 122, with a maximum of 50 and a minimum of 10. With distance-based redundancy analysis (dbRDA) and PERMANOVA applied to the eDNA-based community compositional data, we detected a significant effect of the presence of <i>O. kisutch</i> aquaculture on fish biodiversity. The generalized linear model (GLM) applied to each detected OTUs indicated that the aquaculture was associated positively with <i>Leucopsarion petersii</i> (ice goby), and <i>Oncorhynchus</i> spp. and negatively with <i>Chaenogobius annularis</i> (forktongue goby). Environmental DNA metabarcoding surveys, combined with multivariate statics, are a promising tool to identify the dimension of biodiversity that human activity affects and would serve as a basic survey for sustainable use of the sea.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.551","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141073699","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":"Field collections and environmental DNA surveys reveal topographic complexity of coral reefs as a predictor of cryptobenthic biodiversity across small spatial scales","authors":"O. B. Brodnicke,&nbsp;M. R. Jensen,&nbsp;P. F. Thomsen,&nbsp;T. Brorly,&nbsp;B. L. Andersen,&nbsp;S. W. Knudsen,&nbsp;K. Præbel,&nbsp;S. J. Brandl,&nbsp;M. J. Sweet,&nbsp;P. R. Møller,&nbsp;K. Worsaae","doi":"10.1002/edn3.545","DOIUrl":"10.1002/edn3.545","url":null,"abstract":"<p>Coral reefs represent some of the most biodiverse ecosystems in the world but are currently undergoing large-scale degradation due to anthropogenic stressors. Such degradation usually begins with coral bleaching, and if the stress condition is inflicted for too long may eventually result in loss of structural complexity (or “flattening”) of the reef, dramatically changing habitat availability for reef-associated fauna. Despite having been linked to important ecosystem functions, cryptobenthic organisms are often overlooked in ecological monitoring programs, and their microhabitat dependencies are poorly understood. Here, we combined collection-based biodiversity monitoring techniques with five different environmental DNA (eDNA) sampling techniques (Reef water, sediment, crevice water, slurp gun, and bulk sediment) to survey cryptobenthic fishes and annelids on a Maldivian fringing coral reef. Collectively, 176 fish and 140 annelid taxa were detected with eDNA across 14 surveyed sites, more than doubling the reported annelid taxa in the region with 88 new occurrences. Water filtered near the reef structure revealed the highest species richness out of the five eDNA sampling techniques tested. Furthermore, we found correlations between fish species richness and topographic complexity for both collection- and eDNA-based techniques. This suggests that detection by eDNA may be linked to site-specific predictors and reveal community differences across small spatial scales (tens of meters). We also report that reef flattening (going from structural complex to less complex sites) can cause a 50% reduction in fish diversity and that cryptobenthic fish species richness was highly associated with branching corals. In contrast, annelid communities showed no clear correlations with environmental predictors, but co-amplification of non-target, non-annelid taxa may have distorted such correlations if present. This suggest that the predictive powers of eDNA for environmental gradients may be dependent on the targeted taxa.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.545","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141055451","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}