| 1. |
- Bredin, Y. K., et al.
(författare)
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Above- and below-ground biodiversity responses to the prolonged flood pulse in central-western Amazonia, Brazil
- 2022
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Ingår i: Environmental DNA. - : Wiley. - 2637-4943. ; 4:3, s. 533-548
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Tidskriftsartikel (refereegranskat)abstract
- Amazonia encompasses extensive forests in areas that are periodically inundated by overflowing rivers. The inundation depth and duration vary according to the slope of the terrain and distance to major water bodies. This creates a flooding gradient from the lowest lying seasonally flooded forest up into the unflooded forest, which directly affects the biota. However, the effect of this gradient on soil organisms remains elusive. Here, we use DNA metabarcoding to estimate prokaryote and eukaryote diversity from soil and litter samples along the flooding gradient in central-western Amazonia using 16S and 18S gene sequences, respectively. We characterize the below-ground diversity and community composition based on amplicon sequence variants (ASVs). We examine relationships between the soil biota and the flooding gradient, soil properties, and above-ground woody plant diversity. The flooding gradient does not explain below-ground biodiversity, nor is below-ground diversity explained by the above-ground woody plant diversity. We uncover several taxonomic groups—such as Patescibacteria—not previously reported from Amazonian seasonally flooded forests. The flooding gradient and woody plant diversity partly explain the community composition of soil bacteria. Although the effects of the flooding gradient, soil properties, and above-ground woody plant diversity are difficult to quantify, our results indicate that flood stress may influence below-ground bacterial community composition. © 2021 The Authors. Environmental DNA published by John Wiley & Sons Ltd.
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| 2. |
- Broman, Elias, 1985-, et al.
(författare)
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No evidence of light inhibition on aerobic methanotrophs in coastal sediments using eDNA and eRNA
- 2023
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Ingår i: Environmental DNA. - 2637-4943. ; 5:4, s. 766-781
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Tidskriftsartikel (refereegranskat)abstract
- It is estimated that up to half of global methane (CH4) emissions are derived from microbial processes in aquatic ecosystems. However, it is not fully understood which factors explain the spatial and temporal variability of these emissions. For example, light has previously been shown to both inhibit and stimulate aerobic methane-oxidizing bacteria (i.e., methanotrophs) in the water column. These contrasting results indicate that the mechanisms that light has on CH4 oxidation are not yet clearly known, even less so for benthic aerobic methanotrophs. Here, we tested whether light reaching the seafloor can inhibit methanotrophic activity on the sediment surface. We sampled and distributed over 40 intact sediment cores from two coastal sites (illuminated 10 m, and a dark site at 33 m water depth) into 0, 50, and 100 PAR light treatments. After 10 days, we found no difference between treatments for each site in pore-water CH4 concentrations, relative abundance of aerobic methanotrophs, or the number of RNA transcripts related to methane oxidation. Our results suggest that light attenuation in coastal waters does not significantly affect aerobic methanotrophs in coastal sediments.
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| 3. |
- Capo, Eric, et al.
(författare)
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Droplet digital PCR applied to environmental DNA, a promising method to estimate fish population abundance from humic-rich aquatic ecosystems
- 2021
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Ingår i: Environmental DNA. - : John Wiley & Sons. - 2637-4943. ; 3:2, s. 343-352
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Tidskriftsartikel (refereegranskat)abstract
- Measures of environmental DNA (eDNA) concentrations in water samples have the potential to be both a cost-efficient and a nondestructive method to estimate fish population abundance. However, the inherent temporal and spatial variability in abiotic and biotic conditions in aquatic systems have been suggested to be a major obstacle to determine relationships between fish eDNA concentrations and fish population abundance. Moreover, once water samples are collected, methodological biases are common, which introduces additional sources of variation to potential relationships between eDNA concentrations and fish population abundance. Here, we evaluate the performance of applying the droplet digital PCR (ddPCR) method to estimate fish population abundance in experimental enclosures. Using large-scale enclosure ecosystems that contain populations of nine-spined stickleback (Pungitius pungitius), we compared the concentrations of fish eDNA (COI mitochondrial region, 134 bp) obtained with the ddPCR method with high precision estimates of fish population abundance (i.e., number of individuals) and biomass. To evaluate the effects of contrasted concentrations of humic substances (potential PCR inhibitors) on the performance of ddPCR assays, we manipulated natural dissolved organic carbon (DOC) concentrations (range 4–11 mg/L) in the enclosures. Additionally, water temperature (+2°C) was manipulated in half of the enclosures. Results showed positive relationships between eDNA concentration and fish abundance and biomass estimates although unexplained variation remained. Still and importantly, fish eDNA estimates from high DOC enclosures were not lowered by potential inhibitory effects with our procedure. Finally, water temperature (although only 2°C difference) was neither detected as a significant factor influencing fish eDNA estimates. Altogether, our work highlights that ddPCR-based eDNA is a promising method for future quantification of fish population abundance in natural systems.
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| 4. |
- Capo, Eric, et al.
(författare)
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Effects of filtration methods and water volume on the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) eDNA concentrations via droplet digital PCR
- 2020
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Ingår i: Environmental DNA. - : John Wiley & Sons. - 2637-4943. ; 2:2, s. 152-160
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Tidskriftsartikel (refereegranskat)abstract
- The quantification of the abundance of aquatic organisms via the use of environmental DNA (eDNA) molecules present in water is potentially a useful tool for efficient and noninvasive population monitoring. However, questions remain about the reliability of molecular methods. Among the factors that can hamper the reliability of the eDNA quantification, we investigated the influence of five filtration methods (filter pore size, filter type) and filtered water volume (1 and 2 L) on the total eDNA and the fish eDNA concentrations of two species, brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from tanks with known number of individuals and biomass. We applied a droplet digital PCR (ddPCR) approach to DNA extracted from water samples collected from two cultivation tanks (each of them containing one of the targeted species). Results showed that the quantification of fish eDNA concentrations of both species varies with filtration methods. More specifically, the 0.45-µm Sterivex enclosed filters were identified to recover the highest eDNA concentrations. Difficulties to filter 2 L water samples were present for small pore size filters (≤0.45 µm) and likely caused by filter clogging. To overcome issues related to filter clogging, common in studies aiming to quantify fish eDNA molecules from water samples, we recommend a procedure involving filtration of multiple 1 L water samples with 0.45-µm enclosed filters, to recover both high quality and high concentrations of eDNA from targeted species, and subsequent processing of independent DNA extracts with the ddPCR method.
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| 5. |
- Di Bernardi, Cecilia, et al.
(författare)
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Experimental feeding validates nanofluidic array technology for DNA detection of ungulate prey in wolf scats
- 2023
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Ingår i: Environmental DNA. - 2637-4943. ; 5, s. 723-732
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Tidskriftsartikel (refereegranskat)abstract
- The study of carnivores' diet is a key component to enhance knowledge on the ecology of predators and their effect on prey populations. Although molecular approaches to detect prey DNA in carnivore scats are improving, the validation of their accuracy, a prerequisite for reliable applications within ecological frameworks, is still lagging behind the methodological advances. Indeed, variation in detection probability among prey species can occur, representing a potentially insidious source of bias in food-habit studies of carnivores. Calibration of DNA-based methods involves the optimization of specificity and sensitivity and, whereas priority is usually given to the former to avoid false positives, sensitivity is rarely investigated so that false negatives may be largely overlooked. We conducted feeding trials with captive wolves (Canis lupus) to validate a nanofluidic array technology recently developed for the detection of multiple prey species in scats. Using 371 scat samples from 12 wolves fed with a single-prey diet, the sensitivity of our nanofluidic array method varied between 0.45 and 0.95 for the six main ungulate prey species. The method sensitivity was enhanced by using multiple markers per species and by a relatively low threshold of number of amplifying markers required to confirm a detection. Yet, at least two markers should be used to avoid false positives. By acknowledging sources of bias in sensitivity to reliably interpret the results of DNA-based dietary methods, our study highlights the relevance of feeding experiments to optimally calibrate the relative thresholds to define a positive detection and investigate the occurrence and extent of biases in sensitivity.
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| 6. |
- Hestetun, Jon, et al.
(författare)
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Environmental DNA reveals spatial patterns of fish and plankton diversity at a floating offshore wind farm
- 2023
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Ingår i: Environmental DNA. - 2637-4943. ; 00, s. 1-18
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we collected water eDNA from sampling stations at the first full scale floating offshore wind farm (OWF), the Hywind Pilot Park, east of Peterhead, UK, and a nearby reference area. We combined targeted droplet digital PCR (ddPCR) quanti-fication of two commercially important species, Atlantic mackerel (Scombrus scom-brus) and Atlantic herring (Clupea harengus), with metabarcoding of fish and plankton communities. The goal of this study was to assess the performance of eDNA data to characterize pelagic communities and its use for environmental monitoring. The me-tabarcoding recovered 26 fish species including both pelagic and demersal taxa. The plankton data were dominated by dinoflagellates (Karenia) and calanoid copepods. We found that both specific quantification of eDNA from mackerel and herring and eDNA metabarcoding of fish communities were able to reveal spatial patterns: Mackerel was most abundant in the surface across both OWF and reference sites; herring was pre-sent at a wider depth range. While ddPCR and metabarcoding data for these two species were broadly congruent, we observed detection/non-detection mismatches for both methods, highlighting the need for robust sampling design. There was no consistent OWF versus reference area pattern in the demersal fraction of fish as-semblages. We interpret our findings as representing a snapshot of fish school loca-tion around the time of sampling, and do not consider the single timepoint data from this pilot study to be sufficient to attribute any effects to the OWF itself. As a non- invasive tool, we conclude that eDNA has a high potential in future environmental monitoring of OWFs. We recommend further ground-truthing and biomass correla-tion of eDNA data with catch data and establishing eDNA time series as next steps towards implementation of eDNA in OWF environmental monitoring.
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| 7. |
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| 8. |
- Hupało, Kamil, et al.
(författare)
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An urban Blitz with a twist : rapid biodiversity assessment using aquatic environmental DNA
- 2021
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Ingår i: Environmental DNA. - : John Wiley & Sons. - 2637-4943 .- 2637-4943. ; 3:1, s. 200-213
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Tidskriftsartikel (refereegranskat)abstract
- As global biodiversity declines, there is an increasing need to create an educated and engaged society. Having people of all ages participate in measuring biodiversity where they live helps to create awareness. Recently, the use of environmental DNA (eDNA) for biodiversity surveys has gained momentum. Here, we explore whether sampling eDNA and sequencing it can be used as a means of rapidly surveying urban biodiversity for educational purposes. We sampled 2 × 1 L of water from each of 15 locations in the city of Trondheim, Norway, including a variety of freshwater, marine, and brackish habitats. DNA was extracted, amplified in triplicate targeting the barcoding fragment of COI gene, and sequenced. The obtained data were analyzed on the novel mBRAVE platform, an online open‐access software and computing resource. The water samples were collected in 2 days by two people, and the laboratory analysis was completed in 5 days by one person. Overall, we detected the presence of 506 BINs identified as belonging to 435 taxa, representing at least 265 putative species. On average, only 5.4% of the taxa were shared among six replicates per site. Based on the observed diversity, three distinct clusters were detected and related to the geographic distribution of sites. There were some taxa shared between the habitats, with a substantial presence of terrestrial biota. Here we propose a new form of BioBlitz, where with noninvasive sampling effort combined with swift processing and straightforward online analyses, hundreds of species can be detected. Thus, using eDNA analysis of water is useful for rapid biodiversity surveys and valuable for educational purposes. We show that rapid eDNA surveys, combined with openly available services and software, can be used as an educational tool to raise awareness about the importance of biodiversity.
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| 9. |
- Huston, Grayson P., et al.
(författare)
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Detection of fish sedimentary DNA in aquatic systems : A review of methodological challenges and future opportunities
- 2023
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Ingår i: Environmental DNA. - : John Wiley & Sons. - 2637-4943. ; 5:6, s. 1449-1472
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Tidskriftsartikel (refereegranskat)abstract
- Environmental DNA studies have proliferated over the last decade, with promising data describing the diversity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short- and long-term data on a wide range of biological groups (e.g., photosynthetic organisms, zooplankton species) and has advanced our understanding of how environmental changes have affected aquatic communities. However, substantial challenges remain for recovering the genetic material of macro-organisms (e.g., fish) from sediments, preventing complete reconstructions of past aquatic ecosystems, and limiting our understanding of historic, higher trophic level interactions. In this review, we outline the biotic and abiotic factors affecting the production, persistence, and transport of fish DNA from the water column to the sediments, and address questions regarding the preservation of fish DNA in sediment. We identify sources of uncertainties around the recovery of fish sedDNA arising during the sedDNA workflow. This includes methodological issues related to experimental design, DNA extraction procedures, and the selected molecular method (quantitative PCR, digital PCR, metabarcoding, metagenomics). By evaluating previous efforts (published and unpublished works) to recover fish sedDNA signals, we provide suggestions for future research and propose troubleshooting workflows for the effective detection and quantification of fish sedDNA. With further research, the use of sedDNA has the potential to be a powerful tool for inferring fish presence over time and reconstructing their population and community dynamics.
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| 10. |
- Kahlert, Maria, et al.
(författare)
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Revisiting global diversity and biogeography of freshwater diatoms: New insights from molecular data
- 2023
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Ingår i: Environmental DNA. - 2637-4943. ; 5, s. 1505-1515
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Tidskriftsartikel (refereegranskat)abstract
- The distribution of microorganisms has long been assumed to be cosmopolitan and primarily controlled by the environment, but recent studies suggest that microbes may also exhibit strong biogeographical patterns driven by dispersal limitation. Past attempts to study the global biogeography of freshwater diatoms have always encountered the great difficulty of collecting taxonomically harmonized large-scale data. However, developments in molecular techniques and DNA metabarcoding provide a unique opportunity to overcome these limitations and to disclose diatom biodiversity at an unprecedented scale and resolution. Here, we assembled DNA metabarcoding data of freshwater benthic diatom communities sampled in seven geographic regions across the world to investigate how diatom diversity varies along latitude and to assess the proportion of genetic variants of these microorganisms which are exclusive or shared across regions. We observed significant differences in assemblages among climate zones and found that genetic richness is not affected by latitude, but by an island effect. The genetic resolution directly impacts the proportion of variants shared across regions; however, the majority of taxa remained specific to a single geographic region. Freshwater diatoms disperse over long distances and across oceans but at rates that allow the appearance of local genetic variants and the regionalization of assemblages. Future work should focus on putting these diversity dynamics into a temporal context, an approach that should be possible by bringing together new sequencing techniques and phylogeography.
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