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1
Yamamoto, Yuki, Misa Kohka, Yoshihiko Kobayashi, Izabela Woclawek-Potocka, and Kiyoshi Okuda. "Endothelin as a local regulating factor in the bovine oviduct." Reproduction, Fertility and Development 28, no. 6 (2016): 673. http://dx.doi.org/10.1071/rd14076.
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Endothelin (EDN) is a possible regulating factor of oviductal motility, which is important for the transport of gametes and embryo. To clarify the factors that control the secretion of EDN in the bovine oviduct, the expression of EDNs, EDN-converting enzymes (ECEs) and EDN receptors (EDNRs) were investigated. All isoforms of EDN (EDN1–3), ECE (ECE1 and ECE2) and EDNR (EDNRA and EDNRB) were immunolocalised in the epithelial cells of the ampulla and the isthmus. EDNRs were also immunolocalised in smooth-muscle cells. The mRNA expression of EDN2 and ECE2 was higher in cultured ampullary oviductal epithelial cells than in isthmic cells. The expression of EDN1, EDN2 and ECE2 in the ampullary tissue was highest on the day of ovulation. Oestradiol-17β increased EDN2 and ECE1 expression, while progesterone increased only ECE1 expression in cultured ampullary epithelial cells. These results indicate that EDNs are produced by epithelial cells and their target site is smooth-muscle and epithelial cells, and suggest that ovarian steroids are regulators of endothelin synthesis in ampullary oviductal epithelial cells.
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Nakamichi, Tomoki, Masahiro Ono, Masatoshi Hayashi, Takahiko Okamura, Toshihiro Wada, and Kenji Saitoh. "Environmental DNA Analysis in a River Detected a Possible Distribution of Fish Species Difficult to Capture." Fishes 8, no. 10 (October 4, 2023): 496. http://dx.doi.org/10.3390/fishes8100496.
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Environmental DNA (eDNA) analysis is a biological survey method that has drawn much attention in recent years. However, the results of eDNA analysis and capture surveys often do not completely match, and the validity of the eDNA analysis needs to be verified. Verification of eDNA metabarcoding was conducted in a river in Fukushima Prefecture, Japan, in comparison with capture survey data. Most of the captured species were detected, and 13 uncaptured lineages (two genera and 11 species) were detected in the eDNAs. Some rare species detected in the eDNAs were also identified, including exotic eels and an endangered yet out-of-range bitterling fish. To confirm the validity of the exotic Anguilla spp. detected in eDNAs, mitochondrial Cytb sequencing was performed on captured eel specimens. All eel specimens were sequenced as the native Anguilla japonica, indicating a small biomass of the exotic species difficult to capture. Our results clearly indicated the eDNA analysis as a powerful tool for detecting possible habitats of rare fish species without disturbance to the natural environment.
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Kobayashi, Yoshihiko, Yuka Yoshimoto, Yuki Yamamoto, Koji Kimura, and Kiyoshi Okuda. "Roles of EDNs in regulating oviductal NO synthesis and smooth muscle motility in cows." Reproduction 151, no. 6 (June 2016): 615–22. http://dx.doi.org/10.1530/rep-15-0586.
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AbstractEndothelins (EDNs) participate in various physiological events including smooth muscle contraction, nitric oxide (NO) synthesis, and embryonic development. In this study, we investigated the regional roles of EDNs produced by bovine oviductal epithelial cells in NO synthesis and smooth muscle motility. Quantification of mRNA expressions indicated that expression of EDN receptor B (EDNRB) in the ampullary region was higher after ovulation than before ovulation, whereas expression ofEDNRAin the isthmic region was higher after ovulation than before ovulation. Immunohistochemistry revealed that the EDN receptors (EDNRA and EDNRB) were expressed in the epithelium, whereas smooth muscle showed positive staining only for EDNRA. The expressionsPlease suggest whether 'NOS2' can be treated as the updated symbol for 'iNOS' as per gene nomenclature. ofinducible NO synthase (iNOS) protein and its mRNA (NOS2)in cultured epithelial cells isolated from the ampulla were stimulated by EDN1, but not by EDN2 or EDN3, after 1h of incubation. In isthmic epithelial cells, none of the EDNs affected the expression ofNOS2. Isometric contraction tests indicated that spontaneous waves were strong in the isthmic region but weak in the ampullary region. EDN1 modulated smooth muscle motility in both the regions. The overall findings suggest that EDN1 plays region-specific roles in smooth muscle motility and epithelial NO synthesis, providing an optimal oviductal microenvironment for transport of gametes, fertilization, and development/transport of early embryo.
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Mori, Kensuke, Akio Imamura, Itsuki Hirayama, and Toshifumi Minamoto. "Detection of Echinococcus multilocularis in repurposed environmental DNA samples from river water." PeerJ 11 (June 14, 2023): e15431. http://dx.doi.org/10.7717/peerj.15431.
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Environmental DNA (eDNA) is an increasingly popular tool in biological and ecological studies. As a biproduct of its increasing use, large number of eDNA samples are being collected and stored, that potentially contain information of many non-target species. One potential use for these eDNA samples is a surveillance and early detection of pathogens and parasites that are otherwise difficult to detect. Echinococcus multilocularis is such a parasite with serious zoonotic concern, and whose range has been expanding. If eDNA samples from various studies can be repurposed in detecting the parasite, it can significantly reduce the costs and efforts in surveillance and early detection of the parasite. We designed and tested a new set of primer-probe for detecting E. multilocularis mitochondrial DNA in environmental medium. Using this primer-probe set, we conducted real-time PCR on repurposed eDNA samples collected from three streams flowing through an area of Japan endemic to the parasite. We detected the DNA of E. multilocularis in one of the 128 samples (0.78%). The discovery suggests that while detecting E. multilocularis using eDNA samples is possible, the rate of detection appear to be very low. However, given the naturally low prevalence of the parasite among wild hosts in endemic areas, the repurposed eDNAs may still be a valid option for surveillance in newly introduced areas with the reduced cost and efforts. Further work is needed to assess and improve the effectiveness of using eDNA for detection of E. multilocularis.
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Nigliazzo, Stacy. "Edna." Annals of Internal Medicine 152, no. 2 (January 19, 2010): 130. http://dx.doi.org/10.7326/0003-4819-152-2-201001190-00017.
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Zhang, Jing, Yu Zheng, and Jian Hua. "Effect of microplastics on the transport of extracellular DNA in an agricultural soil." E3S Web of Conferences 536 (2024): 03015. http://dx.doi.org/10.1051/e3sconf/202453603015.
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The transport of eDNA is one of the key environmental behaviors for its spreading and dispersal. Microplastics (MPs) are widely present in the soil environment and directly affect the environmental behavior of co-coexisting soil pollutants. However, the effect of MPs on eDNA transport and its mechanism remain unclear. In this study, we systematically investigated the effect of MPs types and functional groups on eDNA transport. The results showed that different kinds of MPs promoted eDNA transport, but there was no significant difference between these two MPs types. MPs with two different functional groups inhibited eDNA transport, and the transport rate of eDNA decreased by 8.9% and 7.0%, respectively. PSNH2 inhibited eDNA transport by reducing electrostatic repulsion, enhancing electrostatic adsorption, and reducing porosity of porous media, enhancing the interaction between eDNA and MPs. In the presence of kaolin, the inhibition effect of MPs on eDNA transport increased with the proportion of kaolin increased. The positive charge of kaolin enhanced the electrostatic adsorption between MPs and eDNA, and inhibited the transport of eDNA. This study revealed the transport rule of eDNA in the presence of MPs, and provided a theoretical basis for a comprehensive assessment of the environmental and ecological risks of coexistence of MPs and eDNA.
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Paulson, C. "Edna Ashy." Insight - the Journal of the American Society of Ophthalmic Registered Nurses 26, no. 2 (April 2001): 51–52. http://dx.doi.org/10.1067/min.2001.115708.
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Hawkes, Mary Q. "Edna Mahan." Women & Criminal Justice 9, no. 3 (March 9, 1998): 1–21. http://dx.doi.org/10.1300/j012v09n03_01.
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York, Ashley. "Electrified eDNA." Nature Reviews Microbiology 18, no. 10 (August 17, 2020): 543. http://dx.doi.org/10.1038/s41579-020-0436-6.
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Lewenza, Shawn, Lori Johnson, Laetitia Charron-Mazenod, Mia Hong, and Heidi Mulcahy-O'Grady. "Extracellular DNA controls expression of Pseudomonas aeruginosa genes involved in nutrient utilization, metal homeostasis, acid pH tolerance and virulence." Journal of Medical Microbiology 69, no. 6 (June 1, 2020): 895–905. http://dx.doi.org/10.1099/jmm.0.001184.
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Introduction. Pseudomonas aeruginosa grows in extracellular DNA (eDNA)-enriched biofilms and infection sites. eDNA is generally considered to be a structural biofilm polymer required for aggregation and biofilm maturation. In addition, eDNA can sequester divalent metal cations, acidify growth media and serve as a nutrient source. Aim. We wanted to determine the genome-wide influence on the transcriptome of planktonic P. aeruginosa PAO1 grown in the presence of eDNA. Methodology. RNA-seq analysis was performed to determine the genome-wide effects on gene expression of PAO1 grown with eDNA. Transcriptional lux fusions were used to confirm eDNA regulation and to validate phenotypes associated with growth in eDNA. Results. The transcriptome of eDNA-regulated genes included 89 induced and 76 repressed genes (FDR<0.05). A large number of eDNA-induced genes appear to be involved in utilizing DNA as a nutrient. Several eDNA-induced genes are also induced by acidic pH 5.5, and eDNA/acidic pH promoted an acid tolerance response in P. aeruginosa . The cyoABCDE terminal oxidase is induced by both eDNA and pH 5.5, and contributed to the acid tolerance phenotype. Quantitative metal analysis confirmed that DNA binds to diverse metals, which helps explain why many genes involved in a general uptake of metals were controlled by eDNA. Growth in the presence of eDNA also promoted intracellular bacterial survival and influenced virulence in the acute infection model of fruit flies. Conclusion. The diverse functions of the eDNA-regulated genes underscore the important role of this extracellular polymer in promoting antibiotic resistance, virulence, acid tolerance and nutrient utilization; phenotypes that contribute to long-term survival.
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Ely, Taylor, Paul H. Barber, Lauren Man, and Zachary Gold. "Short-lived detection of an introduced vertebrate eDNA signal in a nearshore rocky reef environment." PLOS ONE 16, no. 6 (June 4, 2021): e0245314. http://dx.doi.org/10.1371/journal.pone.0245314.
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Environmental DNA (eDNA) is increasingly used to measure biodiversity of marine ecosystems, yet key aspects of the temporal dynamics of eDNA remain unknown. Of particular interest is in situ persistence of eDNA signals in dynamic marine environments, as eDNA degradation rates have predominantly been quantified through mesocosm studies. To determine in situ eDNA residence times, we introduced an eDNA signal from a non-native fish into a protected bay of a Southern California rocky reef ecosystem, and then measured changes in both introduced and background eDNA signals across a fixed transect over 96 hours. Foreign eDNA signal was no longer detected only 7.5 hours after introduction, a time substantially shorter than the multi-day persistence times in laboratory studies. Moreover, the foreign eDNA signal spread along the entire 38 m transect within 1.5 hours after introduction, indicating that transport and diffusion play a role in eDNA detectability even in protected low energy marine environments. Similarly, native vertebrate eDNA signals varied greatly over the 96 hours of observation as well as within two additional nearby fixed transects sampled over 120 hours. While community structure did significantly change across time of day and tidal direction, neither accounted for the majority of observed variation. Combined, results show that both foreign and native eDNA signatures can exhibit substantial temporal heterogeneity, even on hourly time scales. Further work exploring eDNA decay from lagrangian perspective and quantifying effects of sample and technical replication are needed to better understand temporal variation of eDNA signatures in nearshore marine environments.
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Adams, Clare, Luke Hoekstra, Morgan Muell, and Fredric Janzen. "A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA Under Field Conditions." Diversity 11, no. 4 (March 29, 2019): 50. http://dx.doi.org/10.3390/d11040050.
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Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, and present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have shown mixed results in detecting the presence of these animals under field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored non-avian reptile eDNA quantification by sampling four lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months to detect differences in eDNA using a qPCR assay amplifying the COI gene of the mtDNA genome. Only one sample of the highest-density pond amplified eDNA for a positive detection. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present the “shedding hypothesis”—the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms—as a potential challenge for eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.
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Sansom, Brandon J., Dannise V. Ruiz-Ramos, Nathan L. Thompson, Maura O. Roberts, Zachary A. Taylor, Katie Ortiz, Jess W. Jones, Catherine A. Richter, and Katy E. Klymus. "Detection and transport of environmental DNA from two federally endangered mussels." PLOS ONE 19, no. 10 (October 17, 2024): e0304323. http://dx.doi.org/10.1371/journal.pone.0304323.
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Environmental DNA (eDNA) offers a novel approach to supplement traditional surveys and provide increased spatial and temporal information on species detection, and it can be especially beneficial for detecting at risk or threatened species with minimal impact on the target species. The transport of eDNA in lotic environments is an important component in providing more informed descriptions of where and when a species is present, but eDNA transport phenomena are not well understood. In this study, we used species-specific assays to detect eDNA from two federally endangered mussels in two geographically distinct rivers. Using the eDNA concentrations measured from field samples, we developed a one-dimensional (1D) hydrodynamic transport model to predict the downstream fate and transport of eDNA. We detected eDNA from both federally endangered mussels across several seasons and flow rates and up to 3.5 km downstream from the source populations, but the detection rates and eDNA concentrations were highly variable across and within rivers and study reaches. Our 1D transport models successfully integrated the variability of the eDNA field samples into the model predictions and overall model results were generally within ±1 standard error of the eDNA field concentration values. Overall, the results of this study demonstrate the importance of optimizing the spatial locations from where eDNA is collected downstream from a source population, and it highlights the need to improve understanding on the shedding mechanisms and magnitude of eDNA from source populations and biogeomorphic processes that influence eDNA transport.
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Pilliod, David S., Caren S. Goldberg, Robert S. Arkle, and Lisette P. Waits. "Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples." Canadian Journal of Fisheries and Aquatic Sciences 70, no. 8 (August 2013): 1123–30. http://dx.doi.org/10.1139/cjfas-2013-0047.
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Environmental DNA (eDNA) methods for detecting aquatic species are advancing rapidly, but with little evaluation of field protocols or precision of resulting estimates. We compared sampling results from traditional field methods with eDNA methods for two amphibians in 13 streams in central Idaho, USA. We also evaluated three water collection protocols and the influence of sampling location, time of day, and distance from animals on eDNA concentration in the water. We found no difference in detection or amount of eDNA among water collection protocols. eDNA methods had slightly higher detection rates than traditional field methods, particularly when species occurred at low densities. eDNA concentration was positively related to field-measured density, biomass, and proportion of transects occupied. Precision of eDNA-based abundance estimates increased with the amount of eDNA in the water and the number of replicate subsamples collected. eDNA concentration did not vary significantly with sample location in the stream, time of day, or distance downstream from animals. Our results further advance the implementation of eDNA methods for monitoring aquatic vertebrates in stream habitats.
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Xin, Yi, Yu Guo, Meijing Sun, Gang Yu, Zhenhua Ma, Kun Pei, and Chuanxin Qin. "Optimal Conditions to Quantify the Relationship between eDNA Concentration and Biomass in Acanthopagrus latus." Water 14, no. 21 (November 3, 2022): 3521. http://dx.doi.org/10.3390/w14213521.
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Environmental DNA (eDNA) analysis is a useful tool for monitoring the distributions of aquatic species. eDNA can produce quantitative estimates of fish abundance, but its accuracy depends on the species and system. Therefore, its performance must be evaluated and an investigation of how fish biomass affects eDNA dynamics must be conducted on a case-by-case basis. This study evaluates how the biomass of an ecologically and socioeconomically important fish, Acanthopagrus latus, relates to the eDNA concentration in aquariums. We conducted experiments using juvenile individuals and evaluated eDNA and biomass relationships at seven different time points using a previously developed TaqMan assay targeting the cytochrome oxidase I gene to understand the effect of environmental factors on eDNA concentrations. The results from A. latus showed a strong positive linear correlation between eDNA concentration and A. latus biomass (R2 = 0.72–0.93). The eDNA concentration was negatively correlated with time 20 d after removing A. latus. Salinity significantly affected the eDNA concentration of A. latus at 3 h, and temperature significantly affected the eDNA concentration from 3 to 14 d. The combinations of factors with the greatest effect on the yellowfin seabream eDNA concentration were 35‰/30 °C/8.5, 35‰/30 °C/8.0, and 35‰/25 °C/8.5 (salinity/temperature/pH). This study identified the conditions for detecting A. latus eDNA and provided environmental data to monitor and survey yellowfin seabream biomass resources.
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Park, Seongsik, Seokjin Yoon, and Kyunghoi Kim. "Numerical Study on Evaluation of Environmental DNA Approach for Estimating Fish Abundance and Distribution in Semi-Enclosed Bay." Journal of Marine Science and Engineering 12, no. 10 (October 21, 2024): 1891. http://dx.doi.org/10.3390/jmse12101891.
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Despite efforts to use environmental DNA (eDNA), accurately quantifying fish populations remains a challenge. A recent eDNA approach provided reliable estimates of coastal fish population abundance, but it was not as effective for assessing spatial distribution due to a lack of eDNA samples relative to the study area. Therefore, we conducted a numerical case study to evaluate the ability of the eDNA approach to estimate fish (Jack mackerel) abundance and distribution based on the number of eDNA samples in a semi-enclosed bay (Jinhae Bay). Our study revealed that the eDNA approach can provide reliable estimates of fish abundance, even with knowledge of the eDNA concentration in just 1% of the study area. However, for estimating spatial distribution and fish school, significant estimates were obtained only when the eDNA concentration was identified in more than 70% of the study area. Our results confirm that the eDNA approach can reflect fish abundance but has limitations in estimating fish distribution.
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Takahashi, Sayaka, Shingo Takada, Hiroki Yamanaka, Reiji Masuda, and Akihide Kasai. "Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel." PLOS ONE 16, no. 9 (September 16, 2021): e0255576. http://dx.doi.org/10.1371/journal.pone.0255576.
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Environmental DNA (eDNA) analysis with species-specific primer/probe sets is promising as a tool to quantify fish abundance and distribution. Nevertheless, several factors could reduce the accuracy of this method. Here, we aimed to analyze whether intraspecific variability and diel activity rhythm affect eDNA detection in Japanese eels (Anguilla japonica). For this purpose, we performed tank experiments focusing on two points. First, we assessed the effects of base pair sequences with probe region polymorphism on eDNA detection. Next, we evaluated the influences of diel rhythm, activity, and individual differences in eDNA release rate on eDNA concentration. We examined the base pair sequences of the probe regions of 20 individuals and found genetic mismatches in two of them. The eDNA concentration was estimated to be much lower in these variants than it was in the other individuals. We conducted a rearing experiment on four non-variant individuals to explore the influences of diel activity and inter-individual differences in eDNA detection. Nocturnal eel activity was reflected in the eDNA detection but the inter-individual differences remained large. The observed weak positive correlations between eDNA concentration and activity suggest that eDNA emission is highly dependent on basal metabolism. The present study suggests that consideration of polymorphic sites at the probe region and diel activity rhythms should improve the accuracy and precision of abundance estimation through eDNA. Such fine-tuning is applicable not only for eels but also for other fishes to be targeted by eDNA technology.
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Kakuda, Aozora, Hideyuki Doi, Rio Souma, Mariko Nagano, Toshifumi Minamoto, and Izumi Katano. "Environmental DNA detection and quantification of invasive red-eared sliders, Trachemy scripta elegans, in ponds and the influence of water quality." PeerJ 7 (December 6, 2019): e8155. http://dx.doi.org/10.7717/peerj.8155.
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Environmental DNA (eDNA) is a powerful tool for monitoring the distribution of aquatic macro-organisms. However, environmental factors, including the water temperature and water quality, can affect the inhibition and/or degradation of eDNA, which complicates accurate estimations of eDNA concentrations and the detection of the presence/absence of species in natural habitats. Further very few eDNA studies have been conducted for reptiles, especially with respect to estimating their biomass and/or abundances. Here we examined the relationship between the visually-observed number of red-eared sliders (Trachemys scripta elegans) and eDNA concentrations across 100 ponds. Additionally, we evaluated the effect of water quality on red-eared slider eDNA concentration in these ponds. We found that there was a significant positive correlation between the observed number of red-eared sliders and the eDNA concentration in the ponds. On comparing various water quality indicators, including dissolved nitrogen, dissolved phosphorous, organic matter, and chlorophyll a (Chl. a), we found that only Chl. a had a negative correlation with the red-eared slider eDNA concentration, while we did not find any inhibition in the quantitative PCR. We conclude that concentrations of eDNA can potentially be used for estimating the abundance of the red-eared slider. Additionally, Chl. a might indirectly influence the degradation of eDNA through the microorganisms bonded to the phytoplankton in the ponds, as microbial activity is thought to decrease eDNA persistence.
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Klobucar, Stephen L., Torrey W. Rodgers, and Phaedra Budy. "At the forefront: evidence of the applicability of using environmental DNA to quantify the abundance of fish populations in natural lentic waters with additional sampling considerations." Canadian Journal of Fisheries and Aquatic Sciences 74, no. 12 (December 2017): 2030–34. http://dx.doi.org/10.1139/cjfas-2017-0114.
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Environmental DNA (eDNA) sampling has proven to be a valuable tool for detecting species in aquatic ecosystems. Within this rapidly evolving field, a promising application is the ability to obtain quantitative estimates of relative species abundance based on eDNA concentration rather than traditionally labor-intensive methods. We investigated the relationship between eDNA concentration and Arctic char (Salvelinus alpinus) abundance in five well-studied natural lakes; additionally, we examined the effects of different temporal (e.g., season) and spatial (e.g., depth) scales on eDNA concentration. Concentrations of eDNA were linearly correlated with char population estimates ([Formula: see text] = 0.78) and exponentially correlated with char densities ([Formula: see text] = 0.96 by area; 0.82 by volume). Across lakes, eDNA concentrations were greater and more homogeneous in the water column during mixis; however, when stratified, eDNA concentrations were greater in the hypolimnion. Overall, our findings demonstrate that eDNA techniques can produce effective estimates of relative fish abundance in natural lakes. These findings can guide future studies to improve and expand eDNA methods while informing research and management using rapid and minimally invasive sampling.
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Wang, Zhaoyue, Jiahui Xiao, Fengjie Hu, Qiao Yu, Taiping Zhang, and Shaoqi Zhou. "Adsorption of extracellular DNA to biochar derived from Chinese herbal medicine residues and impact on DNA degradation by DNase I." AIP Advances 12, no. 7 (July 1, 2022): 075304. http://dx.doi.org/10.1063/5.0095208.
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The relationship between biochar physicochemical characteristics and the adsorption and the degradation of extracellular DNA (eDNA) was studied to assess controls on the fate and transport of eDNA in the environment. Biochar samples were generated by pyrolysis of Chinese herbal medicine residues of sweet wormwood ( Artemisia annua L.) at 500, 600, and 700 °C. Selected physicochemical properties of the biochar were characterized. Adsorption dynamics (adsorption capacity and kinetics) of eDNA to biochar were quantified using several adsorption kinetic and isotherm models. Furthermore, gel electrophoresis was used to detect the impact of biochar on the degradation of eDNA by DNase I. Characterization results indicated that biochar generated from Chinese herbal medicine residues was dominantly aromatic, stable, and polar. Adsorption data showed that the biochar–eDNA interactions were dominated by an electrostatic interaction mechanism. Based on eDNA adsorption capacity and gel electrophoresis of eDNA fragments, we demonstrated that larger eDNA fragments were adsorbed to the biochar and protected from degradation by DNase I. The Chinese herbal medicine residues generated a superior biochar product to adsorb eDNA and protect it from degradation by DNase I. The results of this study provide a mechanistic understanding of factors controlling the fate and transport of eDNA in the environment.
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Havermans, Charlotte, Annkathrin Dischereit, Dmitrii Pantiukhin, Madlen Friedrich, and Ayla Murray. "ENVIRONMENTAL DNA IN AN OCEAN OF CHANGE: STATUS, CHALLENGES AND PROSPECTS." Arquivos de Ciências do Mar 55, Especial (March 18, 2022): 298–337. http://dx.doi.org/10.32360/acmar.v55iespecial.78188.
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Environmental DNA (eDNA) studies have burgeoned over the last two decades and the application of eDNA has increased exponentially since 2010, albeit at a slower pace in the marine system. We provide a literature overview on marine metazoan eDNA studies and assess recent achievements in answering questions related to species distributions, biodiversity and biomass. We investigate which are the better studied taxonomic groups, geographic regions and the genetic markers used. We evaluate the use of eDNA for addressing ecological and environmental issues through food web, ecotoxicological, surveillance and management studies. Based on this state of the art, we highlight exciting prospects of eDNA for marine time series, population genetic studies, the use of natural sampler DNA, and eDNA data for building trophic networks and ecosystem models. We discuss the current limitations, in terms of marker choice and incompleteness of reference databases. We also present recent advances using experiments and modeling to better understand persistence, decay and dispersal of eDNA in coastal and oceanic systems. Finally, we explore promising avenues for marine eDNA research, including autonomous or passive eDNA sampling, as well as the combined applications of eDNA with different surveillance methods and further molecular advances.
Keywords: environmental DNA, DNA metabarcoding, marine metazoa, biodiversity, population genetics, natural sampler DNA, diet analysis.
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Shogren, Arial J., Jennifer L. Tank, Elizabeth A. Andruszkiewicz, Brett Olds, Christopher Jerde, and Diogo Bolster. "Modelling the transport of environmental DNA through a porous substrate using continuous flow-through column experiments." Journal of The Royal Society Interface 13, no. 119 (June 2016): 20160290. http://dx.doi.org/10.1098/rsif.2016.0290.
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Detecting environmental DNA (eDNA) in water samples is a powerful tool in determining the presence of rare aquatic species. However, many open questions remain as to how biological and physical conditions in flowing waters influence eDNA. Motivated by what one might find in a stream/river benthos we conducted experiments in continuous flow columns packed with porous substrates to explore eDNA transport and ask whether substrate type and the presence of colonized biofilms plays an important role for eDNA retention. To interpret our data, and for modelling purposes, we began with the assumption that eDNA could be treated as a classical tracer. Comparing our experimental data with traditional transport models, we found that eDNA behaves anomalously, displaying characteristics of a heterogeneous, polydisperse substance with particle-like behaviour that can be filtered by the substrate. Columns were quickly flushed of suspended eDNA particles while a significant amount of particles never made it through and were retained in the column, as calculated from a mass balance. Suspended eDNA was exported through the column, regardless of biofilm colonization. Our results indicate that the variable particle size of eDNA results in stochastic retention, release and transport, which may influence the interpretation eDNA detection in biological systems.
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Pinakhina, Daria V., and Elena M. Chekunova. "Environmental DNA: history of studies, current and perspective applications in fundamental and applied research." Ecological genetics 18, no. 4 (December 12, 2020): 493–509. http://dx.doi.org/10.17816/ecogen25900.
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This review article is dedicated to a relatively young, actively developing approach to biodiversity assessment analysis of environmental DNA (or eDNA). Current views on the nature of eDNA, a brief overview of the history of this approach and methods of eDNA analysis are presented. Major research directions, utilizing eDNA techniques, and perspectives of their application to the study of biodiversity are described. Key issues in development of eDNA approach, its advantages and drawbacks are outlined.
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Shu, Lu, Arne Ludwig, and Zuogang Peng. "Standards for Methods Utilizing Environmental DNA for Detection of Fish Species." Genes 11, no. 3 (March 11, 2020): 296. http://dx.doi.org/10.3390/genes11030296.
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Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection. Herein, we reviewed 168 papers to supplement and highlight the key criteria for each step of eDNA technology in fish detection and provide general suggestions for eliminating detection errors. Although there is no unified recommendation for the application of diverse eDNA in detecting fish species, in most cases, 1 or 2 L surface water collection and eDNA capture on 0.7-μm glass fiber filters followed by extraction with a DNeasy Blood and Tissue Kit or PowerWater DNA Isolation Kit are useful for obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based on mitochondrial cytochrome b gene markers or eDNA metabarcoding based on both 12S and 16S rRNA markers via high-throughput sequencing can effectively detect target DNA or estimate species richness. Furthermore, detection errors can be minimized by mitigating contamination, negative control, PCR replication, and using multiple genetic markers. Our aim is to provide a useful strategy for fish eDNA technology that can be applied by researchers, advisors, and managers.
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Gu, Siyu, Peng Zhang, Shuai Luo, Kai Chen, Chuanqi Jiang, Jie Xiong, and Wei Miao. "Microbial Community Colonization Process Unveiled through eDNA-PFU Technology in Mesocosm Ecosystems." Microorganisms 11, no. 10 (October 5, 2023): 2498. http://dx.doi.org/10.3390/microorganisms11102498.
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Microbial communities are essential components of aquatic ecosystems and are widely employed for the detection, protection, and restoration of water ecosystems. The polyurethane foam unit (PFU) method, an effective and widely used environmental monitoring technique, has been improved with the eDNA-PFU method, offering efficiency, rapidity, and standardization advantages. This research aimed to explore the colonization process of microbial communities within PFUs using eDNA-PFU technology. To achieve this, we conducted ten-day monitoring and sequencing of microbial communities within PFUs in a stable and controlled artificial aquatic ecosystem, comparing them with water environmental samples (eDNA samples). Results showed 1065 genera in eDNA-PFU and 1059 in eDNA, with eDNA-PFU detecting 99.95% of eDNA-identified species. Additionally, the diversity indices of bacteria and eukaryotes in both methods showed similar trends over time in the colonization process; however, relative abundance differed. We further analyzed the colonization dynamics of microbes in eDNA-PFU and identified four clusters with varying colonization speeds. Notably, we found differences in colonization rates between bacteria and eukaryotes. Furthermore, the Molecular Ecological Networks (MEN) showed that the network in eDNA-PFU was more modular, forming a unique microbial community differentiated from the aquatic environment. In conclusion, this study, using eDNA-PFU, comprehensively explored microbial colonization and interrelationships in a controlled mesocosm system, providing foundational data and reference standards for its application in aquatic ecosystem monitoring and beyond.
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Millard-Martin, Ben, Kate Sheridan, Evan Morien, Matthew A. Lemay, Margot Hessing-Lewis, Rute B. G. Clemente-Carvalho, and Jennifer M. Sunday. "Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveys." PeerJ 12 (October 14, 2024): e17967. http://dx.doi.org/10.7717/peerj.17967.
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Sampling and sequencing marine environmental DNA (eDNA) provides a tool that can increase our ability to monitor biodiversity, but movement and mixing of eDNA after release from organisms before collection could affect our inference of species distributions. To assess how conditions at differing spatial scales influence the inferred species richness and compositional turnover, we conducted a paired eDNA metabarcoding and capture (beach seining) survey of fishes on the coast of British Columbia. We found more taxa were typically detected using eDNA compared to beach seining. eDNA identified more taxa with alternative habitat preferences, and this richness difference was greater in areas of high seawater movement, suggesting eDNA has a larger spatial grain influenced by water motion. By contrast, we found that eDNA consistently missed low biomass species present in seining surveys. Spatial turnover of communities surveyed using beach seining differed from that of the eDNA and was better explained by factors that vary at small (10–1000s meters) spatial scales. Specifically, vegetation cover and shoreline exposure explained most species turnover from seining, while eDNA turnover was not explained by those factors and showed a distance decay pattern (a change from 10% to 25% similarity from 2 km to 10 km of distance), suggesting unmeasured environmental variation at larger scales drives its turnover. Our findings indicate that the eDNA sample grain is larger than that of capture surveys. Whereas seining can detect differences in fish distributions at scales of 10s–100s of meters, eDNA can best summarize fish biodiversity at larger scales possibly more relevant to regional biodiversity assessments.
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Sakata, Masayuki K., Megumi Sato, Marcello Otake Sato, Tomoe Watanabe, Honami Mitsuishi, Tomoyuki Hikitsuchi, Jun Kobayashi, and Toshifumi Minamoto. "Detection and persistence of environmental DNA (eDNA) of the different developmental stages of a vector mosquito, Culex pipiens pallens." PLOS ONE 17, no. 8 (August 10, 2022): e0272653. http://dx.doi.org/10.1371/journal.pone.0272653.
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Preventing mosquito-borne infectious diseases requires that vector mosquitoes are monitored and controlled. Targeting immature mosquitoes (eggs, larvae, and pupae), which have less mobility than adults, is an effective management approach. However, conducting these surveys is often difficult due to the limitations of morphological classification and survey costs. The application of environmental DNA (eDNA) analysis can solve these issues because it allows easy estimation of species distribution and morphology-independent species identification. Although a few previous studies have reported mosquito eDNA detection, there is a gap in knowledge regarding the dynamics related to the persistence of immature mosquito eDNA. We used Culex pipiens pallens, a vector of West Nile fever, as a model species. First, we developed a species-specific detection assay and confirmed its specificity using in silico and in vitro tests. Next, we conducted laboratory experiments using breeding tanks. Water samples were collected at each developmental stage. In addition, water samples were collected daily until the seventh day after emergence from the pupae. We quantified eDNA using real-time PCR with the developed assay to investigate the dynamics of mosquito eDNA. The specificity of the developed assay was confirmed by in silico and in vitro tests. Mosquito eDNA was detected at all developmental stages and detected up to seven days after emergence of pupae. In particular, high concentrations of eDNA were detected immediately after hatching from eggs and after emergence from pupae. Highly frequent positive eDNA signals were continuously detected between egg hatching and pupa hatching. Mosquito eDNA was detected immediately after the eggs were introduced, and eDNA-positive detections continued until pupae emergence, suggesting that eDNA analysis is useful for monitoring mosquito larvae. In the future, monitoring immature mosquitoes using eDNA analysis will contribute to prevent mosquito-borne infectious diseases.
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Hervé, Alix, Isabelle Domaizon, Jean-Marc Baudoin, Tony Dejean, Pierre Gibert, Pauline Jean, Tiphaine Peroux, et al. "Spatio-temporal variability of eDNA signal and its implication for fish monitoring in lakes." PLOS ONE 17, no. 8 (August 12, 2022): e0272660. http://dx.doi.org/10.1371/journal.pone.0272660.
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Environmental DNA (eDNA) metabarcoding is revolutionizing the monitoring of aquatic biodiversity. The use of eDNA has the potential to enable non-invasive, cost-effective, time-efficient and high-sensitivity monitoring of fish assemblages. Although the capacity of eDNA metabarcoding to describe fish assemblages is recognised, research efforts are still needed to better assess the spatial and temporal variability of the eDNA signal and to ultimately design an optimal sampling strategy for eDNA monitoring. In this context, we sampled three different lakes (a dam reservoir, a shallow eutrophic lake and a deep oligotrophic lake) every 6 weeks for 1 year. We performed four types of sampling for each lake (integrative sampling of sub-surface water along transects on the left shore, the right shore and above the deepest zone, and point sampling in deeper layers near the lake bottom) to explore the spatial variability of the eDNA signal at the lake scale over a period of 1 year. A metabarcoding approach was applied to analyse the 92 eDNA samples in order to obtain fish species inventories which were compared with traditional fish monitoring methods (standardized gillnet samplings). Several species known to be present in these lakes were only detected by eDNA, confirming the higher sensitivity of this technique in comparison with gillnetting. The eDNA signal varied spatially, with shoreline samples being richer in species than the other samples. Furthermore, deep-water samplings appeared to be non-relevant for regularly mixed lakes, where the eDNA signal was homogeneously distributed. These results also demonstrate a clear temporal variability of the eDNA signal that seems to be related to species phenology, with most of the species detected in spring during the spawning period on shores, but also a peak of detection in winter for salmonid and coregonid species during their reproduction period. These results contribute to our understanding of the spatio-temporal distribution of eDNA in lakes and allow us to provide methodological recommendations regarding where and when to sample eDNA for fish monitoring in lakes.
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Kim, Keonhee, Hyeonjin Cho, Jeong-Hui Kim, Yun-Mo Yang, Hyunji Ju, Min-Ho Jang, and Hyun-Gi Jeong. "Environmental DNA in a Biofilm Can Be Used to Assess Diatom Ecological Health in Stream Water Ecology." Diversity 16, no. 1 (December 22, 2023): 8. http://dx.doi.org/10.3390/d16010008.
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In urban and agricultural streams, assessing aquatic ecosystem health is critical due to widespread pollution. Traditional methods for evaluating attached diatoms crucial for ecosystem monitoring face limitations such as species misidentification and sample damage. This study was conducted in the Miho River within the Geum River system and highlights the effectiveness of environmental DNA (eDNA) techniques for more accurate and efficient genetic-based analysis than conventional microscopic analysis methods. When eDNA-based assessments were compared with traditional microscopic methods, this study found that eDNA analysis often revealed poorer ecosystem health. Notably, eDNA assessments showed a stronger correlation with phosphorus concentrations, underlining their precision and importance in ecological studies. These findings suggest that eDNA has potential as a valuable tool for comprehensive biomonitoring. However, the use of international genetic barcode databases in eDNA analysis could lead to the identification of unrecorded species in Korea. Therefore, this study recommends developing a localized genetic barcode database and constructing eDNA information through meta-barcoding, focusing on native species. This approach is crucial for enhancing the accuracy and applicability of eDNA-based health assessments in national biomonitoring efforts.
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Li, Wen-Pan, Zi-Fang Liu, Tong Guo, He Chen, and Xin Xie. "Using Optimal Environmental DNA Method to Improve the Fish Diversity Survey—From Laboratory to Aquatic Life Reserve." Water 13, no. 11 (May 24, 2021): 1468. http://dx.doi.org/10.3390/w13111468.
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Conserving aquatic ecosystems requires efficient tools to accurately assess the biodiversity of aquatic species. However, existing knowledge is insufficient in terms of the reliability and the comparability of methods measuring fish diversity. Environmental DNA (eDNA), as a promising method, was used to detect fish taxa in this study. We optimized the eDNA method in the laboratory, and applied the optimal eDNA method to survey fish diversity in a natural aquatic life reserve. We simulated necessary steps of the eDNA method in the lab to increase the confidence of the field survey. Specifically, we compared different eDNA sampling, extraction, and sequencing strategies for accurately capturing fish species of the target area. We found that 1L water samples were sufficient for sampling eDNA information of the majority taxa. The filtration was more effective than the centrifugal precipitation for the eDNA extraction. The cloning sequencing was better than the high-throughput sequencing. The field survey showed that the Shannon–Wiener diversity index of fish taxa was the highest in Huairou Reservoir. The diversity index also showed seasonal changes. The accuracy rate of detecting fish taxa was positively correlated with the eDNA concentration. This study provides a scientific reference for an application of the eDNA method in terms of surveying and estimating the biodiversity of aquatic species.
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Jones, Rhys Aled, Chelsea N. Davis, Dewi Llyr Jones, Fiona Tyson, Emma Davies, David Cutress, Peter M. Brophy, Michael T. Rose, Manod Williams, and Hefin Wyn Williams. "Temporal dynamics of trematode intermediate snail host environmental DNA in small water body habitats." Parasitology 148, no. 12 (June 30, 2021): 1490–96. http://dx.doi.org/10.1017/s0031182021001104.
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AbstractEnvironmental DNA (eDNA) surveying has potential to become a powerful tool for sustainable parasite control. As trematode parasites require an intermediate snail host that is often aquatic or amphibious to fulfil their lifecycle, water-based eDNA analyses can be used to screen habitats for the presence of snail hosts and identify trematode infection risk areas. The aim of this study was to identify climatic and environmental factors associated with the detection of Galba truncatula eDNA. Fourteen potential G. truncatula habitats on two farms were surveyed over a 9-month period, with eDNA detected using a filter capture, extraction and PCR protocol with data analysed using a generalized estimation equation. The probability of detecting G. truncatula eDNA increased in habitats where snails were visually detected, as temperature increased, and as water pH decreased (P < 0.05). Rainfall was positively associated with eDNA detection in watercourse habitats on farm A, but negatively associated with eDNA detection in watercourse habitats on farm B (P < 0.001), which may be explained by differences in watercourse gradient. This study is the first to identify factors associated with trematode intermediate snail host eDNA detection. These factors should be considered in standardized protocols to evaluate the results of future eDNA surveys.
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Iwai, Noriko, Kiyomi Yasumiba, and Teruhiko Takahara. "Efficacy of environmental DNA to detect and quantify stream tadpoles of Odorrana splendida." Royal Society Open Science 6, no. 1 (January 2019): 181798. http://dx.doi.org/10.1098/rsos.181798.
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Environmental DNA (eDNA) can be used to detect and estimate the density of rare or secretive species, especially in aquatic systems. However, the efficacy of eDNA method has not been validated in lotic systems. We examined the efficacy of the eDNA method to detect and estimate abundance and biomass of a stream-dwelling frog species, Odorrana splendida . We conducted eight field surveys over 2 years and obtained 53 water samples from 10 streams with known distribution of O. splendida tadpoles. The eDNA method accurately detected the presence of O. splendida in 79.2% of survey samples. The amount of O. splendida eDNA (copies s −1 ) in the water samples fluctuated seasonally and each site showed different peaks during different seasons. The relationship between the abundance or biomass of tadpoles and the amount of eDNA was significantly positive, but was not strong, probably because of a large difference in the relationship patterns among streams. In lotic systems, water flow might prevent even distribution of eDNA and thus make it difficult to obtain eDNA reflecting its total amount in the water. Sampling a larger amount of water or higher number of subsamples might more accurately reflect the presence and absolute amount of eDNA in water.
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Das, Theerthankar, Prashant K. Sharma, Henk J. Busscher, Henny C. van der Mei, and Bastiaan P. Krom. "Role of Extracellular DNA in Initial Bacterial Adhesion and Surface Aggregation." Applied and Environmental Microbiology 76, no. 10 (April 2, 2010): 3405–8. http://dx.doi.org/10.1128/aem.03119-09.
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ABSTRACT Extracellular DNA (eDNA) is an important component of the biofilm matrix. We show that removal of eDNA from Gram-positive bacteria reduces initial adhesion to and aggregation of bacteria on surfaces. Thermodynamic analyses indicated that eDNA introduces favorable acid-base interactions, explaining the effect of eDNA on aggregation and adhesion to the surface.
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Uchida, Noriko, Kengo Kubota, Shunsuke Aita, and So Kazama. "Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment." PeerJ 8 (June 11, 2020): e9176. http://dx.doi.org/10.7717/peerj.9176.
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Environmental DNA (eDNA) analysis provides an efficient and objective approach for monitoring and assessing ecological status; however, studies on the eDNA of aquatic insects, such as Ephemeroptera, Plecoptera, and Trichoptera (EPT), are limited despite its potential as a useful indicator of river health. Here, we investigated the community structures of aquatic insects using eDNA and evaluated the applicability of eDNA data for calculating assessment indices. Field surveys were conducted to sample river water for eDNA at six locations from upstream to downstream of two rivers in Japan in July and November 2016. Simultaneously, aquatic insects were collected using the traditional Surber net survey method. The communities of aquatic insects were revealed using eDNA by targeting the cytochrome oxidase subunit I gene in mitochondrial DNA via metabarcoding analyses. As a result, the eDNA revealed 63 families and 75 genera of aquatic insects, which was double than that detected by the Surber net survey (especially for families in Diptera and Hemiptera). The seasonal differences of communities were distinguished by both the eDNA and Surber net survey data. Furthermore, the total nitrogen concentration, a surrogate of organic pollution, showed positive correlations with biotic environmental assessment indices (i.e., EPT index and Chironomidae index) calculated using eDNA at the genus-level resolution but the indices calculated using the Surber net survey data. Our results demonstrated that eDNA analysis with higher taxonomic resolution can provide as a more sensitive environmental assessment index than the traditional method that requires biotic samples.
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DeHart, Hayley M., Mark T. Gasser, Jarret Dixon, and Peter Thielen. "An aquatic environmental DNA filtration system to maximize recovery potential and promote filtration approach standardization." PeerJ 11 (July 12, 2023): e15360. http://dx.doi.org/10.7717/peerj.15360.
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Background Aquatic environmental DNA (eDNA) has emerged as a promising approach to identify organisms in freshwater and marine environments. While the recovery of eDNA from water most commonly involves capture of biological debris on a filter matrix, practitioners are yet to converge on standardized approaches for filtration, particularly in the field. This lack of standardization has resulted in inconsistent handling of samples following collection, limiting interpretation of results across studies and burdening groups with inconvenient storage and transport logistics that may compromise eDNA integrity. Methods A simple to assemble and low-cost ($350 USD) water filtration system is demonstrated that can be used in field and laboratory settings to reduce time between sample acquisition and eDNA filtration, maximizing eDNA sample recovery. Quantitative PCR is used to show the utility of the platform for laboratory and marine eDNA analysis. Results The resulting eDNA collection system is easily transported in a rugged water-resistant case, operates for more than eight hours on a 12-volt lead-acid battery, and has an unobstructed filtration rate of 150.05 ± 7.01 mL/min and 151.70 ± 6.72 mL/min with 0.22 µm and 0.45 µm Sterivex filters, respectively. We show that immediate sample filtration increases eDNA recovery in the laboratory, and demonstrate collections in aquaria and marine environments. We anticipate that providing easy to obtain, open hardware designs for eDNA sample collection will increase standardization of aquatic eDNA collection methods and improve cross-study comparisons.
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Shao, Yun, Shuping Wang, Pengyuan Wang, Shuhui Men, Miaomiao Qian, Aopu Li, Meiping Feng, and Zhenguang Yan. "Environmental DNA in different media reveals distribution characteristics and assembly mechanisms of fish assemblages in a complex river–lake system." Web Ecology 24, no. 2 (August 2, 2024): 59–70. http://dx.doi.org/10.5194/we-24-59-2024.
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Abstract. Capture-based methods are commonly used for biomonitoring fish assemblages in freshwater. The recent advancement in environmental DNA (eDNA) metabarcoding provides a sensitive, cost-effective, and non-intrusive alternative to traditional methods. Nevertheless, the effectiveness of this approach in river–lake systems has yet to be assessed, and there is ongoing debate regarding the selection of sampling media. In this study, we investigated fish assemblages based on traditional approaches and the eDNA metabarcoding method by analyzing water and sediment from 30 locations along the Baiyang Lake and its inflow rivers (China). The results showed that 21 species were identified based on traditional methods, and a total of 29 species were detected using eDNA, with 22 species found in river water eDNA, 25 species in lake water eDNA, and 27 species in surface sediment samples. Nine benthic fish species were detected exclusively in sediment. The community composition of rivers and lakes revealed by water eDNA is similar, reflecting the biotic homogenization in this river–lake system. A neutral community model (NCM) analysis based on lake water and river water eDNA showed that fish assemblages were not dominated by random processes (5.3 % and 2.7 % concordance with the neutral model, respectively), while analysis of surface sediment eDNA showed more support for random processes (50.2 %). Temperature was the main environmental factor correlated with water eDNA, while NH3–N and TP were the main factors correlating with sediment eDNA.
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Harrison, Jori B., Jennifer M. Sunday, and Sean M. Rogers. "Predicting the fate of eDNA in the environment and implications for studying biodiversity." Proceedings of the Royal Society B: Biological Sciences 286, no. 1915 (November 20, 2019): 20191409. http://dx.doi.org/10.1098/rspb.2019.1409.
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Environmental DNA (eDNA) applications are transforming the standard of characterizing aquatic biodiversity via the presence, location and abundance of DNA collected from environmental samples. As eDNA studies use DNA fragments as a proxy for the presence of organisms, the ecological properties of the complex and dynamic environments from which eDNA is sampled need to be considered for accurate biological interpretation. In this review, we discuss the role that differing environments play on the major processes that eDNA undergoes between organism and collection, including shedding, decay and transport. We focus on a mechanistic understanding of these processes and highlight how decay and transport models are being developed towards more accurate and robust predictions of the fate of eDNA. We conclude with five recommendations for eDNA researchers and practitioners, to advance current best practices, as well as to support a future model of eDNA spatio-temporal persistence.
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Sahu, Praveen K., Pavithra S. Iyer, Amrita M. Oak, Karishma R. Pardesi, and Balu A. Chopade. "Characterization of eDNA from the Clinical StrainAcinetobacter baumanniiAIIMS 7 and Its Role in Biofilm Formation." Scientific World Journal 2012 (2012): 1–10. http://dx.doi.org/10.1100/2012/973436.
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Release of extracellular DNA (eDNA) was observed duringin vitrogrowth of a clinical strain ofAcinetobacter baumannii. Membrane vesicles (MV) of varying diameter (20–200 nm) containing DNA were found to be released by transmission electron microscopy (TEM) and atomic force microscopy (AFM). An assessment of the characteristics of the eDNA with respect to size, digestion pattern by DNase I/restriction enzymes, and PCR-sequencing, indicates a high similarity with genomic DNA. Role of eDNA in static biofilm formed on polystyrene surface was evaluated by biofilm augmentation assay using eDNA available in different preparations, for example, whole cell lysate, cell-free supernatant, MV suspension, and purified eDNA. Biofilm augmentation was seen up to 224.64%, whereas biofilm inhibition was 59.41% after DNase I treatment: confirming that eDNA facilitates biofilm formation inA. baumannii. This is the first paper elucidating the characteristics and role of eDNA inA. baumanniibiofilm, which may provide new insights into its pathogenesis.
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Pachucki, Ryan J., Chelsea Corradetti, Sarah Tursi, Lynne Kohler, Lauren Nicastro, Stefania Gallucci, Laurie Kilpatrick, Çagla Tükel, and Roberto Caricchio. "Bacterial biofilm product Curli/eDNA induces NETs and serum anti-Curli/eDNA levels correlate with bacteriuria and lupus activity." Journal of Immunology 200, no. 1_Supplement (May 1, 2018): 162.7. http://dx.doi.org/10.4049/jimmunol.200.supp.162.7.
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Abstract Infections are a major contributor to lupus disease. We have previously demonstrated that bacterial amyloid curli, produced by E.coli, can accelerate disease in mouse models of lupus. Interestingly curli incorporates extracellular DNA, which in turn can be both adjuvant and a self-antigen in lupus. Finally, uropathogenic E. coli (UPEC) is responsible for the majority of urinary tract infections in SLE. Based on our previous results, we hypothesize that exposure to UPEC triggers anti-curli/eDNA antibodies and curli/eDNA complexes can stimulate the innate immune system. We investigated 98 lupus patients who met at least 4 SLICC criteria. Results were compared to 54 age, sex and race matched healthy controls. We tested the production of anti-curli/DNA complex of both IgG and IgA subclasses. We than correlated the levels of anti-curli/DNA antibodies with clinical parameters. Finally, we stimulated human neutrophils with curli/eDNA complexes. We found that anti-curli/eDNA IgG levels were detected in both lupus and controls plasma. In lupus patients, anti-curli/eDNA levels correlated with persistent bacteriuria and disease flares (p<0.05). In addition, anti-curli/eDNA antibodies recognized dsDNA suggesting a potential molecular mimicry mechanism for curli/eDNA with self-antigens such as dsDNA. We also found that IgA anti-curli/eDNA levels were higher (p<0.01) in lupus donors compared to controls. Finally we found that curli/eDNA induced neutrophil extracellular traps (NETs) and the induction was ROS-dependent. We conclude that curli/eDNA complexes from UTIs can activate the innate immune system and IgG and IgA anti-curli/eDNA are strong biomarkers for disease activity and severity.
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Cristescu, Melania E., and Paul D. N. Hebert. "Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation." Annual Review of Ecology, Evolution, and Systematics 49, no. 1 (November 2, 2018): 209–30. http://dx.doi.org/10.1146/annurev-ecolsys-110617-062306.
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The study of environmental DNA (eDNA) has the potential to revolutionize biodiversity science and conservation action by enabling the census of species on a global scale in near real time. To achieve this promise, technical challenges must be resolved. In this review, we explore the main uses of eDNA as well as the complexities introduced by its misuse. Current eDNA methods require refinement and improved calibration and validation along the entire workflow to lessen false positives/negatives. Moreover, there is great need for a better understanding of the “natural history” of eDNA—its origins, state, lifetime, and transportation—and for more detailed insights concerning the physical and ecological limitations of eDNA use. Although eDNA analysis can provide powerful information, particularly in freshwater and marine environments, its impact is likely to be less significant in terrestrial settings. The broad adoption of eDNA tools in conservation will largely depend on addressing current uncertainties in data interpretation.
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Hua, Zhengshuang, Matthew Ouellette, Andrea M. Makkay, R. Thane Papke, and Olga Zhaxybayeva. "Nutrient supplementation experiments with saltern microbial communities implicate utilization of DNA as a source of phosphorus." ISME Journal 15, no. 10 (April 12, 2021): 2853–64. http://dx.doi.org/10.1038/s41396-021-00960-8.
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AbstractAll environments including hypersaline ones harbor measurable concentrations of dissolved extracellular DNA (eDNA) that can be utilized by microbes as a nutrient. However, it remains poorly understood which eDNA components are used, and who in a community utilizes it. For this study, we incubated a saltern microbial community with combinations of carbon, nitrogen, phosphorus, and DNA, and tracked the community response in each microcosm treatment via 16S rRNA and rpoB gene sequencing. We show that microbial communities used DNA only as a phosphorus source, and provision of other sources of carbon and nitrogen was needed to exhibit a substantial growth. The taxonomic composition of eDNA in the water column changed with the availability of inorganic phosphorus or supplied DNA, hinting at preferential uptake of eDNA from specific organismal sources. Especially favored for growth was eDNA from the most abundant taxa, suggesting some haloarchaea prefer eDNA from closely related taxa. The preferential eDNA consumption and differential growth under various nutrient availability regimes were associated with substantial shifts in the taxonomic composition and diversity of microcosm communities. Therefore, we conjecture that in salterns the microbial community assembly is driven by the available resources, including eDNA.
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Wilton, Mike, Tyler W. R. Halverson, Laetitia Charron-Mazenod, Michael D. Parkins, and Shawn Lewenza. "Secreted Phosphatase and Deoxyribonuclease Are Required by Pseudomonas aeruginosa To Defend against Neutrophil Extracellular Traps." Infection and Immunity 86, no. 9 (July 2, 2018). http://dx.doi.org/10.1128/iai.00403-18.
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ABSTRACT Neutrophil extracellular traps (NETs) are produced by neutrophils as an innate immune defense mechanism to trap and kill microbial pathogens. NETs are comprised of ejected chromatin that forms a lattice structure enmeshed with numerous antimicrobial proteins. In addition to forming the structural backbone of NETs, extracellular DNA (eDNA) has membrane-disrupting antimicrobial activity that contributes to NET killing. Many pathogens produce secreted extracellular DNases to evade the antimicrobial activity of NETs. Pseudomonas aeruginosa encodes an operon of two secreted enzymes, a predicted alkaline phosphatase and a DNase. The DNase (eddB) degrades eDNA to use as a nutrient source. Here we report that both eDNA and NETs are potent inducers of this DNase-phosphatase operon. Furthermore, the secreted DNase contributes to degrading NET DNA and defends P. aeruginosa against NET-mediated killing. We demonstrate that EddA has both alkaline phosphatase and phosphodiesterase (PDase) activities and also protects against the antimicrobial activity of NETs. Although the phosphatase does not cause DNA degradation similar to that of the DNase, its protective function is likely a result of removing the cation-chelating phosphates from the eDNA phosphodiester backbone. Therefore, both the DNase and PDase contribute to defense against NET killing of P. aeruginosa, highlighting the role of DNA-manipulating enzymes in targeting the eDNA in neutrophil extracellular traps.
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Sato, Masaaki, Nariaki Inoue, Ryogen Nambu, Naoki Furuichi, Tomohito Imaizumi, and Masayuki Ushio. "Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey." Scientific Reports 11, no. 1 (September 30, 2021). http://dx.doi.org/10.1038/s41598-021-98926-5.
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AbstractSince the early 1970s, many artificial reefs (ARs) have been deployed in Japanese coastal waters to create fisheries grounds. Recently, researchers began to use environmental DNA (eDNA) methods for biodiversity monitoring of aquatic species. A metabarcoding approach using internal standard DNAs [i.e., quantitative MiSeq sequencing (qMiSeq)] makes it possible to monitor eDNA concentrations of multiple species simultaneously. This method can improve the efficiency of monitoring AR effects on fishes. Our study investigated distributions of marine fishes at ARs and surrounding stations in the open oceanographic environment of Tateyama Bay, central Japan, using qMiSeq and echo sounder survey. Using the qMiSeq with 12S primers, we found higher quantities of fish eDNAs at the ARs than at surrounding stations and different fish species compositions between them. Comparisons with echo sounder survey also showed positive correlations between fish eDNA concentration and echo intensity, which indicated a highly localized signal of eDNA at each sampling station. These results suggest that qMiSeq is a promising technique to complement conventional methods to monitor distributions of multiple fish species.
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Cherny, Kathryn E., and Karin Sauer. "Pseudomonas aeruginosa Requires the DNA-Specific Endonuclease EndA To Degrade Extracellular Genomic DNA To Disperse from the Biofilm." Journal of Bacteriology 201, no. 18 (April 15, 2019). http://dx.doi.org/10.1128/jb.00059-19.
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ABSTRACT The dispersion of biofilms is an active process resulting in the release of planktonic cells from the biofilm structure. While much is known about the process of dispersion cue perception and the subsequent modulation of the c-di-GMP pool, little is known about subsequent events resulting in the release of cells from the biofilm. Given that dispersion coincides with void formation and an overall erosion of the biofilm structure, we asked whether dispersion involves degradation of the biofilm matrix. Here, we focused on extracellular genomic DNA (eDNA) due to its almost universal presence in the matrix of biofilm-forming species. We identified two probable nucleases, endA and eddB, and eddA encoding a phosphatase that were significantly increased in transcript abundance in dispersed cells. However, only inactivation of endA but not eddA or eddB impaired dispersion by Pseudomonas aeruginosa biofilms in response to glutamate and nitric oxide (NO). Heterologously produced EndA was found to be secreted and active in degrading genomic DNA. While endA inactivation had little effect on biofilm formation and the presence of eDNA in biofilms, eDNA degradation upon induction of dispersion was impaired. In contrast, induction of endA expression coincided with eDNA degradation and resulted in biofilm dispersion. Thus, released cells demonstrated a hyperattaching phenotype but remained as resistant to tobramycin as biofilm cells from which they egress, indicating EndA-dispersed cells adopted some but not all of the phenotypes associated with dispersed cells. Our findings indicate for the first time a role of DNase EndA in dispersion and suggest weakening of the biofilm matrix is a requisite for biofilm dispersion. IMPORTANCE The finding that exposure to DNase I impairs biofilm formation or leads to the dispersal of early stage biofilms has led to the realization of extracellular genomic DNA (eDNA) as a structural component of the biofilm matrix. However, little is known about the contribution of intrinsic DNases to the weakening of the biofilm matrix and dispersion of established biofilms. Here, we demonstrate for the first time that nucleases are induced in dispersed Pseudomonas aeruginosa cells and are essential to the dispersion response and that degradation of matrix eDNA by endogenously produced/secreted EndA is required for P. aeruginosa biofilm dispersion. Our findings suggest that dispersing cells mediate their active release from the biofilm matrix via the induction of nucleases.
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Rose, Sasha J., and Luiz E. Bermudez. "Identification of Bicarbonate as a Trigger and Genes Involved with Extracellular DNA Export in Mycobacterial Biofilms." mBio 7, no. 6 (December 6, 2016). http://dx.doi.org/10.1128/mbio.01597-16.
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ABSTRACTExtracellular DNA (eDNA) is an integral biofilm matrix component of numerous pathogens, including nontuberculous mycobacteria (NTM). Cell lysis is the source of eDNA in certain bacteria, but the source of eDNA remains unidentified for NTM, as well as for other eDNA-containing bacterial species. In this study, conditions affecting eDNA export were examined, and genes involved with the eDNA export mechanism were identified. After a method for monitoring eDNA in real time in undisturbed biofilms was established, different conditions affecting eDNA were investigated. Bicarbonate positively influenced eDNA export in a pH-independent manner inMycobacterium avium,M. abscessus, andM. chelonae. The surface-exposed proteome ofM. aviumin eDNA-containing biofilms revealed abundant carbonic anhydrases. Chemical inhibition of carbonic anhydrases with ethoxzolamide significantly reduced eDNA export. An unbiased transposon mutant library screen for eDNA export inM. aviumidentified many severely eDNA-attenuated mutants, including one not expressing a unique FtsK/SpoIIIE-like DNA-transporting pore, two with inactivation of carbonic anhydrases, and nine with inactivation of genes belonging to a unique genomic region, as well as numerous mutants involved in metabolism and energy production. Complementation of nine mutants that included the FtsK/SpoIIIE and carbonic anhydrase significantly restored eDNA export. Interestingly, several attenuated eDNA mutants have mutations in genes encoding proteins that were found with the surface proteomics, and many more mutations are localized in operons potentially encoding surface proteins. Collectively, our data strengthen the evidence of eDNA export being an active mechanism that is activated by the bacterium responding to bicarbonate.IMPORTANCEMany bacteria contain extracellular DNA (eDNA) in their biofilm matrix, as it has various biological and physical functions. We recently reported that nontuberculous mycobacteria (NTM) can contain significant quantities of eDNA in their biofilms. In some bacteria, eDNA is derived from dead cells, but that does not appear to be the case for all eDNA-containing organisms, including NTM. In this study, we found that eDNA export in NTM is conditionally dependent on the molecules to which the bacteria are exposed and that bicarbonate positively influences eDNA export. We also identified genes and proteins important for eDNA export, which begins to piece together a description of a mechanism for eDNA. Better understanding of eDNA export can give new targets for the development of antivirulence drugs, which are attractive because resistance to classical antibiotics is currently a significant problem.
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Liu, Yan, Mengyi Zhang, Liangming Wang, Changping Yang, Yukai Yang, Qijian Xie, Manting Liu, Cheng Chen, Chunbin Jia, and Binbin Shan. "Experimental assessment of Acanthopagrus schlegelii biomass based on environmental DNA technology." Scientific Reports 14, no. 1 (December 30, 2024). https://doi.org/10.1038/s41598-024-83590-2.
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AbstractThe Environmental DNA (eDNA) technology has attracted significant attention due to its convenience and high sensitivity. However, the variations of eDNA across diverse environments and biological species remain complex. Therefore, a detailed exploration of the release patterns of eDNA for specific species under different environments is crucial for the scientific utilization of eDNA detection techniques. This study conducted an experiment involving the aquaculture of Acanthopagrus schlegelii to explore the release and degradation mechanisms of eDNA. It also analyzed the influence of salinity and biomass on the concentration of eDNA in water. Through model simulations, the variation patterns of A. schlegelii eDNA were revealed. The study achieved three key findings: (1) The research on the release and degradation mechanisms of A. schlegelii eDNA indicated that the Generalized Additive Model (GAM) effectively fits the variation patterns of eDNA concentration. The peak concentration of eDNA released by A. schlegelii was observed at 42 h, and the degradation process exhibited two stages: rapid and slow degradation, with a negative correlation between eDNA concentration and time. (2) By investigating the relationship between the concentration of A. schlegelii eDNA and biomass, it was demonstrated that Linear Models (LM) effectively captured this relationship, indicating a correlation between eDNA concentration and biomass. (3) The detection of A. schlegelii eDNA concentration under different salinity conditions revealed that the GAM model better reflected the relationship between eDNA and salinity, exhibiting a negative correlation. As salinity increased, the concentration of eDNA decreased. This study lays a foundation for future assessments of the A. schlegelii biomass in natural waters using eDNA quantitative detection techniques, and provides relevant references for quantitative eDNA detection techniques in other marine fish species.
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Hirohara, Takaya, Kenji Tsuri, Koichi Miyagawa, Robert T. R. Paine, and Hiroki Yamanaka. "The Application of PMA (Propidium Monoazide) to Different Target Sequence Lengths of Zebrafish eDNA: A New Approach Aimed Toward Improving Environmental DNA Ecology and Biological Surveillance." Frontiers in Ecology and Evolution 9 (June 4, 2021). http://dx.doi.org/10.3389/fevo.2021.632973.
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Environmental DNA (eDNA) analysis has enabled more sensitive and efficient biological monitoring than traditional methods. However, since the target species is not directly observed, interpretation of results cannot preclude process Type I errors. Specifically, there may be a spatial or temporal gap between the target eDNA and the eDNA source in the sampled area. Moreover, eDNA surveillance lacks the ability to distinguish whether eDNA originated from a living or non-living source. This kind of Type I error is difficult to control for, in part, because the relationship between the state of eDNA (i.e., intracellular or extracellular) and the degradation rate is still unclear. Here, we applied PMA (Propidium monoazide) to eDNA analysis which enabled us to differentiate “intact cells” from “disrupted cells.” PMA is a dye that has a high affinity for double-stranded DNA and forms a covalent bond with double-stranded DNA and inhibits amplification of the bonded DNA molecules by PCR. Since PMA is impermeable to the cell membrane, DNA protected by an intact cell membrane can be selectively detected. In this study, we investigated the workability of PMA on vertebrate eDNA using zebrafish, Danio rerio. Aquarium water was incubated for 1 week to monitor the eDNA degradation process of both intracellular and extracellular eDNA. We developed ten species-specific quantitative PCR assays for D. rerio with different amplification lengths that enabled independent quantification of total eDNA (sum of intracellular and extracellular eDNA, commonly measured in other studies) and intracellular eDNA (DNA in intact cells) and allow for analyses of sequence length-dependent eDNA degradation in combination with PMA. We confirmed that PMA is effective at differentiating “intact” and “disrupted” fish cells. We found that total eDNA and intracellular eDNA have different degradation processes that are dependent on the length of target sequence. For future conservation efforts using eDNA analyses, it is necessary to increase the reliability of the analysis results. The research presented here provides new analysis tools that expand our understanding of the ecology of eDNA, so that more accurate and reliable conclusions can be determined.
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Bonk, Eric A., Robert H. Hanner, Adrienne J. Bartlett, and Gerald R. Tetreault. "Environmental DNA Metabarcoding Detects Predators at Higher Rates Than Electrofishing." Environmental DNA 6, no. 5 (September 2024). http://dx.doi.org/10.1002/edn3.70019.
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ABSTRACTThere are numerous downsides and risks associated with electrofishing; hence, environmental DNA (eDNA) metabarcoding is becoming increasingly common in aquatic ecological studies. Generally, researchers agree that eDNA metabarcoding is more sensitive than electrofishing, and that eDNA metabarcoding is better at detecting rare species. As predatory species tend to be rarer than prey species, eDNA metabarcoding should hypothetically detect more predator species than electrofishing. Instead of supporting the notion that eDNA must replace electrofishing, or that eDNA and electrofishing must display the same results, the current study aims to establish the strengths and weaknesses of eDNA metabarcoding when compared to electrofishing. eDNA metabarcoding and electrofishing data were collected on three sampling dates at four experimental sites. A RV coefficient analysis confirmed that the eDNA metabarcoding data (RV = 0.395, p = 0.057) are statistically different from the electrofishing data. A paired Wilcoxon signed rank test revealed that eDNA data collection techniques detect more predatory species than electrofishing (p = 0.041). When the analysis was conducted for prey species a statistically significant difference did not occur (p = 0.661). Overall, the results of the study suggest that eDNA metabarcoding does not display the same results as electrofishing due to eDNA metabarcoding detecting predatory species at higher rates. The combined use of eDNA alongside electrofishing can help mitigate electrofishing's bias against predatory species, while electrofishing can address reliability concerns associated with eDNA. This collaborative approach ultimately enhances the accuracy of fish community assessments.
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Allan, Elizabeth Andruszkiewicz, Michelle H. DiBenedetto, Andone C. Lavery, Annette F. Govindarajan, and Weifeng G. Zhang. "Modeling characterization of the vertical and temporal variability of environmental DNA in the mesopelagic ocean." Scientific Reports 11, no. 1 (October 28, 2021). http://dx.doi.org/10.1038/s41598-021-00288-5.
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AbstractIncreasingly, researchers are using innovative methods to census marine life, including identification of environmental DNA (eDNA) left behind by organisms in the water column. However, little is understood about how eDNA is distributed in the ocean, given that organisms are mobile and that physical and biological processes can transport eDNA after release from a host. Particularly in the vast mesopelagic ocean where many species vertically migrate hundreds of meters diurnally, it is important to link the location at which eDNA was shed by a host organism to the location at which eDNA was collected in a water sample. Here, we present a one-dimensional mechanistic model to simulate the eDNA vertical distribution after its release and to compare the impact of key biological and physical parameters on the eDNA vertical and temporal distribution. The modeled vertical eDNA profiles allow us to quantify spatial and temporal variability in eDNA concentration and to identify the most important parameters to consider when interpreting eDNA signals. We find that the vertical displacement by advection, dispersion, and settling has limited influence on the eDNA distribution, and the depth at which eDNA is found is generally within tens of meters of the depth at which the eDNA was originally shed from the organism. Thus, using information about representative vertical migration patterns, eDNA concentration variability can be used to answer ecological questions about migrating organisms such as what depths species can be found in the daytime and nighttime and what percentage of individuals within a species diurnally migrate. These findings are critical both to advance the understanding of the vertical distribution of eDNA in the water column and to link eDNA detection to organism presence in the mesopelagic ocean as well as other aquatic environments.
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West, Katrina M., Tyson R. Jones, Lara Denis‐Roy, Olivia J. Johnson, Ella Clausius, Graham Edgar, and Bruce Deagle. "Continual Day–Night eDNA Detectability Amidst Diel Reef Species Fluctuations on Diver Transects." Environmental DNA 6, no. 5 (September 2024). http://dx.doi.org/10.1002/edn3.70018.
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ABSTRACTRecent research into the spatiotemporal dynamics of eDNA in marine environments indicates that eDNA signals are highly localized and may dissipate beyond detection levels within a few hours of production. This affects whether single‐timepoint eDNA sampling, which generally occurs during daylight hours, or cyclic (day/night) interval eDNA sampling is necessary to detect both diurnal and nocturnal marine species. Our study investigated short‐term variability in eDNA derived from fishes and macroinvertebrates across three temperate reef sites in eastern Tasmania, Australia. Simultaneous eDNA and underwater visual census (UVC) diver transect surveys were conducted every 6 h over a 24‐h period to investigate whether eDNA was able to detect marine species outside of their UVC‐observed diel activity. We report that single‐timepoint eDNA sampling can detect both diurnal and nocturnal species on temperate reefscapes. A lack of eDNA compositional turnover between day and night suggests that eDNA persists beyond 12 h and/or is continuously produced by both diurnal and nocturnal reef taxa, irrespective of diel behavioral changes observed by UVC. Given high eDNA sample variability, however, we recommend a high replication level (> 10 × 1 L samples) to produce robust site community composition profiles. This study builds on emerging literature on short‐term variability in eDNA, assisting in the design of future eDNA studies at sites with pronounced variation in faunal activity between day and night.