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Osathanunkul, Maslin, Nipitpong Sawongta, Wittaya Pheera, Nikolaos Pechlivanis, Fotis Psomopoulos, and Panagiotis Madesis. "Exploring plant diversity through soil DNA in Thai national parks for influencing land reform and agriculture planning." PeerJ 9 (August 2, 2021): e11753. http://dx.doi.org/10.7717/peerj.11753.
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Background The severe deforestation, as indicated in national forest data, is a recurring problem in many areas of Northern Thailand, including Doi Suthep-Pui National Park. Agricultural expansion in these areas, is one of the major drivers of deforestation, having adverse consequences on local plant biodiversity. Conserving biodiversity is mainly dependent on the biological monitoring of species distribution and population sizes. However, the existing conventional approaches for monitoring biodiversity are rather limited. Methods Here, we explored soil DNA at four forest types in Doi Suthep-Pui National Park in Northern Thailand. Three soil samples, composed of different soil cores mixed together, per sampling location were collected. Soil biodiversity was investigated through eDNA metabarcoding analysis using primers targeting the P6 loop of the plastid DNA trnL (UAA) intron. Results The distribution of taxa for each sample was found to be similar between replicates. A strong congruence between the conventional morphology- and eDNA-based data of plant diversity in the studied areas was observed. All species recorded by conventional survey with DNA data deposited in the GenBank were detected through the eDNA analysis. Moreover, traces of crops, such as lettuce, maize, wheat and soybean, which were not expected and were not visually detected in the forest area, were identified. It is noteworthy that neighboring land and areas in the studied National Park were once used for crop cultivation, and even to date there is still agricultural land within a 5–10 km radius from the forest sites where the soil samples were collected. The presence of cultivated area near the forest may suggest that we are now facing agricultural intensification leading to deforestation. Land reform for agriculture usage necessitates coordinated planning in order to preserve the forest area. In that context, the eDNA-based data would be useful for influencing policies and management towards this goal.
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Wakelin, SA, VM Cave, BE Dignam, C. D’Ath, M. Tourna, LM Condron, J. Zhou, JD Van Nostrand, and M. O’Callaghan. "Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture." New Zealand Journal of Agricultural Research 59, no. 4 (July 25, 2016): 333–50. http://dx.doi.org/10.1080/00288233.2016.1209529.
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Hayes, Endia Louise, and Norah MacKendrick. "“Leave No Stone Unturned”." Gastronomica 22, no. 2 (2022): 64–74. http://dx.doi.org/10.1525/gfc.2022.22.2.64.
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African American foodways have historically shared many of the same imperatives prized by writers, experts, and pundits concerned with making food systems more sustainable—namely, encouraging farm-to-table food distribution networks, using “natural” or low-impact agricultural methods, and inspiring scratch cooking with local, fresh ingredients. Contemporary writing about sustainable food and agriculture in the United States locates the origins of this movement in Europe and northern California. In this article, we challenge this conceptualization by presenting what we call the “food imaginaries” of three key historical figures: George Washington Carver, Fannie Lou Hamer, and Edna Lewis. These imaginaries not only reflect the knowledge constructions of a social group and map future possibilities through foodways but also challenge damaging narratives about African American food histories, particularly across the south. We find that these imaginaries envision food as a pathway to freedom, autonomy, pleasure, and joy, and tell greater stories of how “organic” and “natural” falters when imagined outside of Blackness. These imaginaries, we argue, are central to American agricultural and political histories, and have important implications for sustainability and food justice movements in the United States.
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Soares, Tales Miler, Ênio Farias de França e Silva, Sergio Nascimento Duarte, Ralini Ferreira Melo, Cristiano de Andrade Jorge, and Edna Maria Bonfim-Silva. "PRODUÇÃO DE ALFACE UTILIZANDO ÁGUAS SALINAS EM SISTEMA HIDROPÔNICO." IRRIGA 12, no. 2 (August 10, 2007): 235–48. http://dx.doi.org/10.15809/irriga.2007v12n2p235-248.
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PRODUÇÃO DE ALFACE UTILIZANDO ÁGUAS SALINAS EM SISTEMA HIDROPÔNICO Tales Miler Soares1; Ênio Farias de França e Silva1; Sergio Nascimento Duarte1; Ralini Ferreira Mélo1; Cristiano de Andrade Jorge1; Edna Maria Bonfim-Silva21Departamento de Engenharia Rural, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, talesmiler@bol.com.br 2Departamento de Solos e Nutrição de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP 1 RESUMO A tolerância das culturas à salinidade deve ser maior em sistemas hidropônicos do que em sistemas convencionais de cultivo. Essa possibilidade pode contribuir para uma nova perspectiva à agricultura do semi-árido brasileiro, colaborando, inclusive, para uma maior segurança ambiental. No período de 02/10/2006 a 03/11/2006, foi conduzido um experimento com o objetivo de avaliar os efeitos de águas salinas sobre a produção de alface crespa (Lactuca sativa L.) em condições hidropônicas. Os diferentes níveis de salinidade da água (0,43; 1,40; 2,23; 3,08 e 3,93 dS m-1) foram preparados com a adição de NaCl e CaCl2 (1:1, base peso). O aumento da salinidade da água não interferiu significativamente na acumulação de massa seca das raízes e na relação raiz/parte aérea, mas reduziu com significância estatística a produção de matéria seca da parte aérea e o consumo de água pelas plantas. Também foi constatada diminuição de 4,08% na produção de matéria seca da parte aérea para cada acréscimo unitário (dS m-1) na condutividade elétrica da água. UNITERMOS: salinidade, condutividade elétrica, Lactuca sativa L., cultivo sem solo. SOARES, T.M.; SILVA, E.F.F.S.; DUARTE, S.N.; MÉLO, R.F.; JORGE, C.A.; BONFIM-SILVA, E.M.B. HYDROPONIC LETTUCE PRODUCTION USING SALINE WATERS 2 ABSTRACT Plant tolerance to salt is supposed to be greater in hydroponic systems than in conventional systems. This possibility can contribute to a new perspective in Brazilian semi-arid agriculture, besides improving environmental safety. From October 2 to November 3, 2006, astudy aiming to evaluate the effects of saline water on crisp head lettuce production under hydroponic conditions was carried out. Different water salinity levels (0.43; 1.40; 2.23; 3.08 and 3.93 dS m‾¹) were prepared with NaCl and CaCl2 (1:1, weight basis). Water salinity increase did not affect root dry mass accumulation and root/shoot ratio whereas it significantly decreased shoot dry mass and water consumption. For each unit increase in water salinity (dS m‾¹), lettuce production decreased in 4.08% KEYWORDS: salinity, electrical conductivity, Latuca sativa L., soil less cultivation
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Moro, L. N., G. Vichera, and D. Salamone. "240 QUALITY AND VIABILITY OF IVF BOVINE EMBRYOS AFTER INTRACYTOPLASMIC INJECTION OF DNA–LIPOSOME COMPLEXES." Reproduction, Fertility and Development 24, no. 1 (2012): 232. http://dx.doi.org/10.1071/rdv24n1ab240.
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Transgenic animals have important applications in agriculture and human medicine; nevertheless the available techniques still remain inefficient and technically difficult. We have recently developed a novel method to transfect bovine embryos that consists of intracytoplasmic injection of exogenous DNA–liposome complexes (eDNA-LC) in IVF zygotes. This study was designed to evaluate the quality and viability of IVF bovine embryos, after intracytoplasmic injection of pCX-EGFP–liposome complexes (EGFP-LC) or pBCKIP2.8-liposome complexes (plasmid that codifies the human insulin gene, HI-LC). First, we evaluated embryo development and enhanced green fluorescent protein (EGFP) expression of IVF embryos injected with both plasmids separately. This treatment was analysed by Fisher's Exact test (P ≤ 0.05). Cleavage rates for EGFP-LC, HI-LC and IVF embryos injected with liposomes alone (IVF-L) and IVF control (IVF-C) were 62% (63/102), 67% (67/100), 66% (67/101) and 79% (98/124); blastocysts rates were 17% (17/102), 21% (21/100), 21% (21/101) and 23% (28/124), respectively. No statistical differences were seen among groups. The percentage of EGFP-positive embryos (EGFP+) after EGFP-LC injection was 42.9% after 3 days of culture and 41.8% at the blastocyst stage. In the second experiment, the blastocysts obtained, EGFP+ or EGFP-negative (EGFP–), were analysed by TUNEL assay at Day 6 (Bd6), 7 (Bd7) and 8 (Bd8) of in vitro culture, in order to evaluate the effect of the transgene and culture length, on DNA fragmentation. This treatment was analysed by the difference of proportions test (P ≤ 0.05) using statistical INFOSTAT software. All EGFP+ blastocysts showed TUNEL positive cells (T+). The percentage of T+ in Bd6, Bd7 and Bd8 were 91, 73.7 and 99.5%, respectively (P ≤ 0.05). EGFP– blastocysts showed lower fragmented nuclei (0, 44.6 and 85%, respectively; P ≤ 0.05). Groups IVF-L and IVF-C were also evaluated. In both groups, there was no evidence of DNA fragmentation in Bd6 and Bd7, but T+ were detected in Bd8 (66.4 and 85.8%, respectively; P ≤ 0.05). In the third experiment, bovine blastocysts obtained from the HI-LC group were individually transferred to recipient cows after 6 (n = 11), 7 (n = 5) and 8 (n = 5) days of culture post-IVF and HI-LC injection. The pregnancies obtained were from Bd6 [18.2% (2/11)] and Bd7 [40% (2/5)], although none of the recipients receiving Bd8 were diagnosed pregnant. Two pregnancies developed to term, one derived from Bd6 and the other from Bd7. Analysis by PCR determined that none of the born cows were transgenic. In summary, IVF bovine embryos could be easily transfected after the injection of eDNA-LC and the technique did not affect offspring viability. The results indicate that extended time in in vitro culture increases the percentage of fragmented nuclei in blastocysts. Moreover, this parameter increases in blastocysts with transgene expression compared with those without expression. Finally, more transfers are required in order to obtain the real efficiency of this new technique and to overcome the drawbacks generated by in vitro culture length and transgene expression.
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Adame, Maria Fernanda, and Ruth Reef. "Potential Pollution Sources from Agricultural Activities on Tropical Forested Floodplain Wetlands Revealed by Soil eDNA." Forests 11, no. 8 (August 17, 2020): 892. http://dx.doi.org/10.3390/f11080892.
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Tropical floodplain wetlands are found in low-lying areas that are periodically inundated. During wet periods, these wetlands can receive large amounts of suspended and dissolved material from the catchment, including many potential pollutants. In this study, we use traditional isotope tracers (δ15N and δ13C) along with soil eDNA to investigate the sources of transported materials and potential contaminants in seven forested floodplain wetlands in tropical Australia. We hypothesised that eDNA and isotope tracers in the soil would reflect the land use of the catchment. Our goal was to test whether eDNA could be used as a potential tool to identify and monitor pollutants in floodplain wetlands. The sampling sites were located within catchments that have a mosaic of land types, from well-conserved rainforests to intensive agricultural land uses, such as grazing, sugar cane, wood production, and horticulture. The soil eDNA was comprised of a mix of plant species consistent with the land use of the catchments. Most of the eDNA pool was derived from native trees, accounting for 46.2 ± 6.5% of the total; while cultivated species associated with agricultural activities contributed to 1–24% of the total. From the cultivated species, highest contributions (>5%) were from Sorghum sp. used for grazing, banana (Musa ornata), melons (Cucumis melo), and Pinus radiata and Juniperus sp. grown for wood production. Interestingly, tropical wetlands on sites 15 km offshore had soil eDNA from agricultural activities of the mainland, highlighting the connectivity of these wetlands, probably during extensive floods. Overall, soil eDNA, more than isotopic tracers, showed promising results for tracing and monitoring potential pollutants in tropical floodplain wetlands that are highly connected and susceptible to environmental degradation.
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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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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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Ogden, Lesley Evans. "The Emergence of eDNA." BioScience 72, no. 1 (December 7, 2021): 5–12. http://dx.doi.org/10.1093/biosci/biab120.
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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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Ponce, Jake J., Ivan Arismendi, and Austen Thomas. "Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters." PeerJ 9 (August 9, 2021): e11835. http://dx.doi.org/10.7717/peerj.11835.
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Environmental DNA (eDNA) detection of aquatic invasive species is currently at the forefront of aquatic conservation efforts because the methodology provides a cost effective and sensitive means to detect animals at low densities. Developments in eDNA technologies have improved detection probabilities for rare, indicator, and invasive species over the past decade. However, standard lab analysis can take days or weeks before results are available and is prohibitive when rapid management decisions are required for mitigation. Here, we investigated the performance of a real-time quantitative PCR system for on-site eDNA detection of New Zealand mud snails (Potamopyrgus antipodarum). Six sites in western Washington, USA were sampled using the rapid eDNA technique and traditional methods, with five samples per site. On-site eDNA detection of mud snails resulted in a 10% increase in positive sites (16/30 = 53% positive) relative to visual surveys (13/30 = 43% positive). In addition, positive associations were observed between mud snail eDNA concentration (eDNA copies per reaction) and the number of mud snail individuals at each site (R2 = 0.78). We show that the rapid on-site eDNA technology can be effective for detection and quantification of New Zealand mud snails in freshwaters. This on-site eDNA detection approach could possibly be used to initiate management protocols that allow for more rapid responses during the onset of biological invasions.
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Chen, Ying, Orianne Tournayre, Haolun Tian, and Stephen C. Lougheed. "Assessing the breeding phenology of a threatened frog species using eDNA and automatic acoustic monitoring." PeerJ 11 (January 23, 2023): e14679. http://dx.doi.org/10.7717/peerj.14679.
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Background Climate change has driven shifts in breeding phenology of many amphibians, causing phenological mismatches (e.g., predator-prey interactions), and potentially population declines. Collecting data with high spatiotemporal sensitivity on hibernation emergence and breeding times can inform conservation best practices. However, monitoring the phenology of amphibians can be challenging because of their cryptic nature over much of their life cycle. Moreover, most salamanders and caecilians do not produce conspicuous breeding calls like frogs and toads do, presenting additional monitoring challenges. Methods In this study, we designed and evaluated the performance of an environmental DNA (eDNA) droplet digital PCR (ddPCR) assay as a non-invasive tool to assess the breeding phenology of a Western Chorus Frog population (Pseudacris maculata mitotype) in Eastern Ontario and compared eDNA detection patterns to hourly automatic acoustic monitoring. For two eDNA samples with strong PCR inhibition, we tested three methods to diminish the effect of inhibitors: diluting eDNA samples, adding bovine serum albumin to PCR reactions, and purifying eDNA using a commercial clean-up kit. Results We recorded the first male calling when the focal marsh was still largely frozen. Chorus frog eDNA was detected on April 6th, 6 days after acoustic monitoring revealed this first calling male, but only 2 days after males attained higher chorus activity. eDNA signals were detected at more sampling locales within the marsh and eDNA concentrations increased as more males participated in the chorus, suggesting that eDNA may be a reasonable proxy for calling assemblage size. Internal positive control revealed strong inhibition in some samples, limiting detection probability and quantification accuracy in ddPCR. We found diluting samples was the most effective in reducing inhibition and improving eDNA quantification. Conclusions Altogether, our results showed that eDNA ddPCR signals lagged behind male chorusing by a few days; thus, acoustic monitoring is preferable if the desire is to document the onset of male chorusing. However, eDNA may be an effective, non-invasive monitoring tool for amphibians that do not call and may provide a useful complement to automated acoustic recording. We found inhibition patterns were heterogeneous across time and space and we demonstrate that an internal positive control should always be included to assess inhibition for eDNA ddPCR signal interpretations.
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Carbajal-Valenzuela, Ireri Alejandra, Gabriela Medina-Ramos, Laura Helena Caicedo-Lopez, Alejandra Jiménez-Hernández, Adrian Esteban Ortega-Torres, Luis Miguel Contreras-Medina, Irineo Torres-Pacheco, and Ramón Gerardo Guevara-González. "Extracellular DNA: Insight of a Signal Molecule in Crop Protection." Biology 10, no. 10 (October 11, 2021): 1022. http://dx.doi.org/10.3390/biology10101022.
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Agricultural systems face several challenges in terms of meeting everyday-growing quantities and qualities of food requirements. However, the ecological and social trade-offs for increasing agricultural production are high, therefore, more sustainable agricultural practices are desired. Researchers are currently working on diverse sustainable techniques based mostly on natural mechanisms that plants have developed along with their evolution. Here, we discuss the potential agricultural application of extracellular DNA (eDNA), its multiple functioning mechanisms in plant metabolism, the importance of hormetic curves establishment, and as a challenge: the technical limitations of the industrial scale for this technology. We highlight the more viable natural mechanisms in which eDNA affects plant metabolism, acting as a damage/microbe-associated molecular pattern (DAMP, MAMP) or as a general plant biostimulant. Finally, we suggest a whole sustainable system, where DNA is extracted from organic sources by a simple methodology to fulfill the molecular characteristics needed to be applied in crop production systems, allowing the reduction in, or perhaps the total removal of, chemical pesticides, fertilizers, and insecticides application.
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Nevers, Meredith B., Kasia Przybyla-Kelly, Dawn Shively, Charles C. Morris, Joshua Dickey, and Murulee N. Byappanahalli. "Influence of sediment and stream transport on detecting a source of environmental DNA." PLOS ONE 15, no. 12 (December 28, 2020): e0244086. http://dx.doi.org/10.1371/journal.pone.0244086.
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Environmental DNA (eDNA) can be used for early detection, population estimations, and assessment of potential spread of invasive species, but questions remain about factors that influence eDNA detection results. Efforts are being made to understand how physical, chemical, and biological factors—settling, resuspension, dispersion, eDNA stability/decay—influence eDNA estimations and potentially population abundance. In a series of field and controlled mesocosm experiments, we examined the detection and accumulation of eDNA in sediment and water and the transport of eDNA in a small stream in the Lake Michigan watershed, using the invasive round goby fish (Neogobius melanostomus) as a DNA source. Experiment 1: caged fish (average n = 44) were placed in a stream devoid of round goby; water was collected over 24 hours along 120-m of stream, including a simultaneous sampling event at 7 distances from DNA source; stream monitoring continued for 24 hours after fish were removed. Experiment 2: round goby were placed in laboratory tanks; water and sediment were collected over 14 days and for another 150 days post-fish removal to calculate eDNA shedding and decay rates for water and sediment. For samples from both experiments, DNA was extracted, and qPCR targeted a cytochrome oxidase I gene (COI) fragment specific to round goby. Results indicated that eDNA accumulated and decayed more slowly in sediment than water. In the stream, DNA shedding was markedly lower than calculated in the laboratory, but models indicate eDNA could potentially travel long distances (up to 50 km) under certain circumstances. Collectively, these findings show that the interactive effects of ambient conditions (e.g., eDNA stability and decay, hydrology, settling-resuspension) are important to consider when developing comprehensive models. Results of this study can help resource managers target representative sites downstream of potential invasion sites, thereby maximizing resource use.
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Banerjee, Pritam, Gobinda Dey, Caterina M. Antognazza, Raju Kumar Sharma, Jyoti Prakash Maity, Michael W. Y. Chan, Yi-Hsun Huang, et al. "Reinforcement of Environmental DNA Based Methods (Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review." Biology 10, no. 12 (November 23, 2021): 1223. http://dx.doi.org/10.3390/biology10121223.
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Recently developed non-invasive environmental DNA-based (eDNA) techniques have enlightened modern conservation biology, propelling the monitoring/management of natural populations to a more effective and efficient approach, compared to traditional surveys. However, due to rapid-expansion of eDNA, confusion in terminology and collection/analytical pipelines can potentially jeopardize research progression, methodological standardization, and practitioner adoption in several ways. Present investigation reflects the developmental progress of eDNA (sensu stricto) including highlighting the successful case studies in conservation management. The eDNA technique is successfully relevant in several areas of conservation research (invasive/conserve species detection) with a high accuracy and authentication, which gradually upgrading modern conservation approaches. The eDNA technique related bioinformatics (e.g., taxon-specific-primers MiFish, MiBird, etc.), sample-dependent methodology, and advancement of sequencing technology (e.g., oxford-nanopore-sequencing) are helping in research progress. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique with a high accuracy and authentication can be applicable alone or coupled with traditional surveys in conservation biology. However, a comprehensive eDNA-based monitoring program (ecosystem modeling and function) is essential on a global scale for future management decisions.
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Gold, Zachary, Adam R. Wall, Teia M. Schweizer, N. Dean Pentcheff, Emily E. Curd, Paul H. Barber, Rachel S. Meyer, et al. "A manager’s guide to using eDNA metabarcoding in marine ecosystems." PeerJ 10 (November 15, 2022): e14071. http://dx.doi.org/10.7717/peerj.14071.
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Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.
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Persaud, Sadhna Fiona, Karl Cottenie, and Jennifer Erin Gleason. "Ethanol eDNA Reveals Unique Community Composition of Aquatic Macroinvertebrates Compared to Bulk Tissue Metabarcoding in a Biomonitoring Sampling Scheme." Diversity 13, no. 1 (January 17, 2021): 34. http://dx.doi.org/10.3390/d13010034.
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Freshwater ecosystems provide essential ecosystem services and support biodiversity; however, their water quality and biological communities are influenced by adjacent agricultural land use. Aquatic macroinvertebrates are commonly used as bioindicators of stream conditions in freshwater biomonitoring programs. Sorting benthic samples for molecular identification is a time-consuming process, and this study investigates the potential of ethanol-collected environmental DNA (eDNA) for metabarcoding macroinvertebrates, especially for common bioindicator groups. The objective of this study was to compare macroinvertebrate composition between paired bulk tissue and ethanol eDNA samples, as eDNA could provide a less time-consuming and non-destructive method of sampling macroinvertebrates. We collected benthic samples from streams in Ontario, Canada, and found that community composition varied greatly between sampling methods and that few taxa were shared between paired tissue and ethanol samples, suggesting that ethanol eDNA is not an acceptable substitute. It is unclear why we did not detect all the organisms that were preserved in the ethanol, or the origin of the DNA we did detect. Furthermore, we also detected no difference in community composition for bioindicator taxa due to surrounding land use or water chemistry, suggesting sites were similar in ecological condition.
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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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Ji, Chang Woo, Hye-Ji Oh, Kwang-Hyeon Chang, Young-Seuk Park, and Ihn-Sil Kwak. "A Comparative Analyzing of Zooplankton Community Diversity in Surface Layer Water of Reservoir Via eDNA Metabarcoding and Microscopy." Diversity 14, no. 10 (September 25, 2022): 797. http://dx.doi.org/10.3390/d14100797.
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We compared two sampling methods, eDNA metabarcoding and microscope identification (MSI), for the analysis of zooplankton diversity in reservoirs with its inflow and outflow streams. The dynamic patterns of Cladocera and Rotifera at different time points were similar between the two sampling methods, but there was a slight difference in the Copepoda. Specifically, the members of the Copepoda subclass could not be easily classified using the MSI method, whereas eDNA metabarcoding could detect minor taxa of Cladocera and Rotifera. Upon comparing the list of zooplankton communities in Korea with the gene database of NCBI, only ~56% of the zooplankton genera reported in Korea could be detected based on the 18S rRNA gene. However, eDNA metabarcoding detected a more diverse range of zooplankton despite the lack of genetic information. As water temperature increased after May, the zooplankton diversity decreased according to the MSI method but increased according to the eDNA metabarcoding method. Although eDNA metabarcoding has some limitations, it was able to detect a wider diversity of zooplankton compared to the MSI. eDNA metabarcoding provides a more reliable means to identify zooplankton.
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Farrell, Jessica A., Liam Whitmore, and David J. Duffy. "The Promise and Pitfalls of Environmental DNA and RNA Approaches for the Monitoring of Human and Animal Pathogens from Aquatic Sources." BioScience 71, no. 6 (April 21, 2021): 609–25. http://dx.doi.org/10.1093/biosci/biab027.
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Abstract Novel forensics-inspired molecular approaches have revolutionized species detection in the wild and are particularly useful for tracing endangered or invasive species. These new environmental DNA or RNA (eDNA or eRNA)–based techniques are now being applied to human and animal pathogen surveillance, particularly in aquatic environments. They allow better disease monitoring (presence or absence and geographical spread) and understanding of pathogen occurrence and transmission, benefitting species conservation and, more recently, our understanding of the COVID-19 global human pandemic. In the present article, we summarize the benefits of eDNA-based monitoring, highlighted by two case studies: The first is a fibropapillomatosis tumor-associated herpesvirus (chelonid herpesvirus 5) driving a sea turtle panzootic, and the second relates to eRNA-based detection of the SARS-CoV-2 coronavirus driving the COVID-19 human pandemic. The limitations of eDNA- or eRNA-based approaches are also summarized, and future directions and recommendations of the field are discussed. Continuous eDNA- or eRNA-based monitoring programs can potentially improve human and animal health by predicting disease outbreaks in advance, facilitating proactive rather than reactive responses.
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Curtis, Amanda N., and Eric R. Larson. "No evidence that crayfish carcasses produce detectable environmental DNA (eDNA) in a stream enclosure experiment." PeerJ 8 (June 11, 2020): e9333. http://dx.doi.org/10.7717/peerj.9333.
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Environmental DNA (eDNA) is an emerging tool for monitoring invasive and imperiled species, particularly at low densities. However, the factors that control eDNA production, transport, and persistence in aquatic systems remain poorly understood. For example, the extent to which carcasses produce detectable eDNA is unknown. If positive detections are associated with dead organisms, this could confound monitoring for imperiled or invasive species. Here, we present results from one of the first studies to examine carcass eDNA in situ by deploying carcasses of the invasive red swamp crayfish (Procambarus clarkii) in a stream enclosure experiment for 28 days. We predicted that carcasses would initially produce eDNA that would decline over time as carcasses decayed. Unsurprisingly, crayfish carcasses lost biomass over time, but at the conclusion of our experiment much of the carapace and chelae remained. However, no eDNA of P. clarkii was detected in any of our samples at the crayfish density (15 P. clarkii carcasses at ∼615 g of biomass initially), stream flow (520–20,319 L/s), or temperature (∼14–25 °C) at our site. Subsequent analyses demonstrated that these results were not the consequence of PCR inhibition in our field samples, poor performance of the eDNA assay for intraspecific genetic diversity within P. clarkii, or due to the preservation and extraction procedure used. Therefore, our results suggest that when crayfish are relatively rare, such as in cases of new invasive populations or endangered species, carcasses may not produce detectable eDNA. In such scenarios, positive detections from field studies may be more confidently attributed to the presence of live organisms. We recommend that future studies should explore how biomass, flow, and differences in system (lentic vs. lotic) influence the ability to detect eDNA from carcasses.
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Takeshita, Daiki, Shigeharu Terui, Kousuke Ikeda, Takashi Mitsuzuka, Maslin Osathanunkul, and Toshifumi Minamoto. "Projection range of eDNA analysis in marshes: a suggestion from the Siberian salamander (Salamandrella keyserlingii) inhabiting the Kushiro marsh, Japan." PeerJ 8 (August 20, 2020): e9764. http://dx.doi.org/10.7717/peerj.9764.
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Background Freshwater ecosystems are rapidly declining. The Siberian salamander (Salamandrella keyserlingii) which inhabits the Kushiro marsh in Hokkaido, Japan has lost some habitat due to human activity. There are many challenges associated with conventional monitoring methods, including cost, the need for specialist personnel, environmental impact, and ability to detect the presence of this species; thus, we investigated the feasibility of using environmental DNA (eDNA) analysis to detect its presence and identify its breeding grounds. Methods We performed tank experiments to confirm eDNA emission from egg sacs, larvae, and adult Siberian salamanders in the water. We also performed water sampling and visual observation of egg sacs in the Kushiro marsh during the end of the breeding season and the larval season. Results The tank experiments found eDNA emission from all growth stages. It also implied concentrated emissions just after spawning and after hatching, and limited emissions during the incubation phase in egg sacs. We also detected eDNA in the field, likely reflecting the distribution of egg sacs or larvae. Combining this data with visual observations, it was determined that the eDNA results from the field were best explained by the number of egg sacs within 7–10 m of the sampling point. Conclusions The results of this investigation show that the breeding sites and habitats of marshland species can successfully be monitored using eDNA analysis. They also suggest that the eDNA results from the marshes may reflect the biomass that is in close range to the sampling point. These results support the increased use of eDNA analysis in marshes and provide knowledge that could improve the interpretation of future results.
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Hassan, Shahnawaz, Sabreena, Peter Poczai, Bashir Ah Ganai, Waleed Hassan Almalki, Abdul Gafur, and R. Z. Sayyed. "Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity." Biology 11, no. 9 (August 31, 2022): 1297. http://dx.doi.org/10.3390/biology11091297.
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The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.
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Cornman, Robert S., James E. McKenna, Jr., and Jennifer A. Fike. "Composition and distribution of fish environmental DNA in an Adirondack watershed." PeerJ 9 (February 26, 2021): e10539. http://dx.doi.org/10.7717/peerj.10539.
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Background Environmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration. Methods We characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our goals were to determine: (1) spatiotemporal variation in eDNA abundance, (2) the filtrate needed to achieve strong sequencing libraries, (3) the taxonomic resolution of 12S ribosomal sequences in the study environment, (4) the portion of the expected fish community detectable by 12S sequencing, (5) biases in species recovery, (6) correlations between eDNA compositions and catch per unit effort (CPUE) and (7) the extent that eDNA profiles reflect major watershed features. Our bioinformatic approach included (1) estimation of sequencing error from unambiguous mappings and simulation of taxonomic assignment error under various mapping criteria; (2) binning of species based on inferred assignment error rather than by taxonomic rank; and (3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented within the St. Regis River, NY, USA, which supports tribal and recreational fisheries and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. Results We found that 300 mL drawn through 25-mm cellulose nitrate filters yielded greater than 5 ng/µL DNA at most sites in summer, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state checklist into 85 single-species bins and seven multispecies bins. Of 48 bins observed by capture survey in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence. Summed log-ratio compositions of eDNA-detected taxa correlated with log(CPUE) (Pearson’s R = 0.655, P < 0.001). Shifts in eDNA composition of several taxa and a genotypic shift in channel catfish (Ictalurus punctatus) coincided with the Hogansburg Dam, NY, USA. In summary, a simple filtering apparatus operated by field crews without prior expertise gave useful summaries of eDNA composition with minimal evidence of field contamination. 12S sequencing achieved useful taxonomic resolution despite the short marker length, and data exploration with standard bioinformatic tools clarified taxonomic uncertainty and sources of error.
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Li, Wenhao, Tianjian Song, Xianglei Hou, Mingshuo Qin, Chunxia Xu, and Yiming Li. "Application of eDNA Metabarcoding for Detecting Anura on a Tropical Island." Diversity 13, no. 9 (September 12, 2021): 440. http://dx.doi.org/10.3390/d13090440.
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As anuran biodiversity quickly declines, it is important to understand local patterns of anuran occurrence. However, the limitations of traditional sampling methods make anuran biodiversity surveys inadequate. Tropical environments are rich in anuran species, which makes biodiversity measurements more difficult. Therefore, it is important to develop a rapid, inexpensive and nondestructive method to measure anuran biodiversity in tropical environments. We used eDNA metabarcoding to measure anuran diversity at 288 sites in 18 regions of Hainan Island. We also used traditional methods and compared the results with those obtained through the eDNA metabarcoding methods. We detected 9 anuran species by traditional sampling methods. We produced 626 million reads by eDNA metabarcoding and assigned them to 15 anuran species. Therefore, eDNA metabarcoding can be used for rapid and large-scale anuran biodiversity surveys.
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Wang, Xiaoyan, Guoqing Lu, Linlin Zhao, Qiao Yang, and Tianxiang Gao. "Assessment of fishery resources using environmental DNA: Small yellow croaker (Larimichthys polyactis) in East China Sea." PLOS ONE 15, no. 12 (December 29, 2020): e0244495. http://dx.doi.org/10.1371/journal.pone.0244495.
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Species distribution monitoring and biomass assessment are crucial for fishery management and resource conservation. However, traditional methods such as motor trawling are costly and less effective than the novel environmental DNA (eDNA) approach. This study employs eDNA approach to investigate horizontal and vertical distributions of small yellow croaker (Larimichthys polyactis), an economically important species, in the East China Sea. The analysis of 171 eDNA samples collected from 44 stations using the species-specific primers and Taqman probe suggests a presence of small yellow croaker at 28 sampling layers in 44 stations. Significant differences in croaker eDNA concentrations were revealed among sampling stations and layers, consistent with previous findings through motor-trawl capture offshore and nearshore ichthyoplakton surveys, indicating small yellow croaker exhibits strong regional distribution and layer preference. In addition, we found a high eDNA concentration of small yellow croaker in the surface waters beyond the motor-trawl prohibition line, which confirms spawning grounds have been expanded from nearshore to offshore areas. Such expansion of spawning grounds could be a response by small yellow croaker to stressors such as overfishing, climate change, and nearshore environment contamination. To identify environmental variables potentially associated with small yellow croaker presence and absence, we conducted a correlation analysis between eDNA concentration and environmental variables, and the results provide a guideline for further investigation of fishery resources in the future. In conclusion, this study demonstrates the power of the eDNA approach in monitoring small yellow croaker at extensive geographic scales. The developed protocols and the findings are expected to assist in long-term monitoring and protection programs and benefit sustainable fishery in small yellow croaker.
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Helmer, Nikolaus, Christoph Hörweg, Helmut Sattmann, Susanne Reier, Nikolaus U. Szucsich, Jana Bulantová, and Elisabeth Haring. "DNA Barcoding of Trichobilharzia (Trematoda: Schistosomatidae) Species and Their Detection in eDNA Water Samples." Diversity 15, no. 1 (January 12, 2023): 104. http://dx.doi.org/10.3390/d15010104.
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We designed and tested species-specific PCR primers to detect Trichobilharzia species via environmental DNA (eDNA) barcoding in selected Austrian water bodies. Tests were performed with eDNA samples from the field as well as with artificial samples from the lab, where snails releasing cercariae were kept in aquariums. From two localities, Trichobilharzia was documented based on the release of cercariae from snails, enabling morphological species identification. In both cases, the corresponding species were detected via eDNA: Trichobilharzia szidati and Trichobilharzia physellae. Nonetheless, the stochasticity was high in the replicates. PCR tests with aquarium water into which the cercariae had been released allowed eDNA detection even after 44 days. As in the PCRs with eDNA samples from the field, positive results of these experiments were not obtained for all samples and replicates. PCR sensitivity tests with dilution series of T. szidati genomic DNA as well as of PCR amplification products yielded successful amplification down to concentrations of 0.83 pg/µL and 0.008 pg/µL, respectively. Our results indicate that the presumed species specificity of PCR primers may not be guaranteed, even if primers were designed for specific species. This entails misidentification risks, particularly in areas with incomplete species inventories.
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Laroche, Olivier, Susanna A. Wood, Louis A. Tremblay, Gavin Lear, Joanne I. Ellis, and Xavier Pochon. "Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities." PeerJ 5 (May 17, 2017): e3347. http://dx.doi.org/10.7717/peerj.3347.
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Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.
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Juhel, Jean-Baptiste, Rizkie S. Utama, Virginie Marques, Indra B. Vimono, Hagi Yulia Sugeha, Kadarusman, Laurent Pouyaud, Tony Dejean, David Mouillot, and Régis Hocdé. "Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle." Proceedings of the Royal Society B: Biological Sciences 287, no. 1930 (July 8, 2020): 20200248. http://dx.doi.org/10.1098/rspb.2020.0248.
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Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict ( R ² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.
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Clarke, Laurence J., Leonie Suter, Bruce E. Deagle, Andrea M. Polanowski, Aleks Terauds, Glenn J. Johnstone, and Jonathan S. Stark. "Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems." PeerJ 9 (November 15, 2021): e12458. http://dx.doi.org/10.7717/peerj.12458.
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Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.
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Kelly, Ryan P., Ramón Gallego, and Emily Jacobs-Palmer. "The effect of tides on nearshore environmental DNA." PeerJ 6 (March 19, 2018): e4521. http://dx.doi.org/10.7717/peerj.4521.
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We can recover genetic information from organisms of all kinds using environmental sampling. In recent years, sequencing this environmental DNA (eDNA) has become a tractable means of surveying many species using water, air, or soil samples. The technique is beginning to become a core tool for ecologists, environmental scientists, and biologists of many kinds, but the temporal resolution of eDNA sampling is often unclear, limiting the ecological interpretations of the resulting datasets. Here, in a temporally and spatially replicated field study using ca. 313 bp of eukaryotic COI mtDNA as a marker, we find that nearshore organismal communities are largely consistent across tides. Our findings suggest that nearshore eDNA from both benthic and planktonic taxa tends to be endogenous to the site and water mass sampled, rather than changing with each tidal cycle. However, where physiochemical water mass characteristics change, we find that the relative contributions of a broad range of organisms to eDNA communities shift in concert.
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Igawa, Takeshi, Teruhiko Takahara, Quintin Lau, and Shohei Komaki. "An application of PCR-RFLP species identification assay for environmental DNA detection." PeerJ 7 (October 3, 2019): e7597. http://dx.doi.org/10.7717/peerj.7597.
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Recent advancement of environmental DNA (eDNA) methods for surveying species in aquatic ecosystems has been used for various organisms and contributed to monitoring and conservation of species and environments. Amphibians are one of the promising taxa which could be monitored efficiently by applying quantitative PCR (qPCR) or next generation sequencing to eDNA. However, the cost of eDNA detection using these approaches can be quite high and requires instruments that are not usually installed in ecology laboratories. For aiding researchers in starting eDNA studies of amphibians, especially those not specialized in molecular biology, we developed a cost efficient protocol using PCR-RFLP method. We attempted to detect eDNA of three Japanese Rana species (Rana japonica, Rana ornativentris, and Rana tagoi tagoi) in various spatial scales including an area close to the Fukushima nuclear power plant where the environment is recovering after the disaster in 2011. Our PCR-RFLP protocol was successful in detecting Rana species in static water in both laboratory and field; however, it could not detect Rana species in non-static water samples from the field. Even a more sensitive detection method (standard qPCR) was unable to detect frogs in all non-static water samples. We speculate that our new protocol is effective for frogs living in lentic habitats, but not for lotic habitats which may still require the gold standard of field observation for detection approach.
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Leempoel, Kevin, Trevor Hebert, and Elizabeth A. Hadly. "A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity." Proceedings of the Royal Society B: Biological Sciences 287, no. 1918 (January 15, 2020): 20192353. http://dx.doi.org/10.1098/rspb.2019.2353.
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Before environmental DNA (eDNA) can establish itself as a robust tool for biodiversity monitoring, comparison with existing approaches is necessary, yet is lacking for terrestrial mammals. Moreover, much is unknown regarding the nature, spread and persistence of DNA shed by animals into terrestrial environments, or the optimal experimental design for understanding these potential biases. To address some of these challenges, we compared the detection of terrestrial mammals using eDNA analysis of soil samples against confirmed species observations from a long-term (approx. 9-year) camera-trapping study. At the same time, we considered multiple experimental parameters, including two sampling designs, two DNA extraction kits and two metabarcodes of different sizes. All mammals regularly recorded with cameras were detected in eDNA. In addition, eDNA reported many unrecorded small mammals whose presence in the study area is otherwise documented. A long metabarcode (≈220 bp) offering a high taxonomic resolution, achieved a similar efficiency as a shorter one (≈70 bp) and a phosphate buffer-based extraction gave similar results as a total DNA extraction method, for a fraction of the price. Our results support that eDNA-based monitoring should become a valuable part of ecosystem surveys, yet mitochondrial reference databases need to be enriched first.
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Charvoz, Léo, Laure Apothéloz-Perret-Gentil, Emanuela Reo, Jacques Thiébaud, and Jan Pawlowski. "Monitoring newt communities in urban area using eDNA metabarcoding." PeerJ 9 (November 26, 2021): e12357. http://dx.doi.org/10.7717/peerj.12357.
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Newts are amphibians commonly present in small ponds or garden pools in urban areas. They are protected in many countries and their presence is monitored through visual observation and/or trapping. However, newts are not easy to spot as they are small, elusive and often hidden at the bottom of water bodies. In recent years, environmental DNA (eDNA) has become a popular tool for detecting newts, with a focus on individual species using qPCR assays. Here, we assess the effectiveness of eDNA metabarcoding compared to conventional visual surveys of newt diversity in 45 ponds within urban areas of Geneva canton, Switzerland. We designed newt-specific mitochondrial 16S rRNA primers, which assign the majority of amplicons to newts, and were able to detect four species known to be present in the region, including the invasive subspecies Lissotriton vulgaris meridionalis, native to the Italian peninsula, that has been introduced in the Geneva area recently. The obtained eDNA results were congruent overall with conventional surveys, confirming the morphological observations in the majority of cases (67%). In 25% of cases, a species was only detected genetically, while in 8% of cases, the observations were not supported by eDNA metabarcoding. Our study confirms the usefulness of eDNA metabarcoding as a tool for the effective and non-invasive monitoring of newt community and suggests its broader use for the survey of newt diversity in urban area at larger scales.
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Sansupa, Chakriya, Sara Fareed Mohamed Wahdan, Terd Disayathanoowat, and Witoon Purahong. "Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures." Biology 10, no. 7 (June 22, 2021): 569. http://dx.doi.org/10.3390/biology10070569.
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This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.
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Maguire, J. M. "DR EDNA P. PLUMSTEAD FRSSAf." Transactions of the Royal Society of South Africa 47, no. 3 (January 1990): 355–57. http://dx.doi.org/10.1080/00359199009520247.
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Pascher, Kathrin, Vid Švara, and Michael Jungmeier. "Environmental DNA-Based Methods in Biodiversity Monitoring of Protected Areas: Application Range, Limitations, and Needs." Diversity 14, no. 6 (June 9, 2022): 463. http://dx.doi.org/10.3390/d14060463.
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Novel methods for species detection based on collection of environmental DNA (eDNA) are not only important in biodiversity assessment in a scientific context, but are also increasingly being applied in conservation practice. The eDNA-based biodiversity detection methods have significant potential for regular use in biodiversity status assessments and conservation actions in protected areas (PAs) and other effective area-based conservation measures (OECMs) worldwide. Species detection based on DNA from environmental samples, such as water, sediment, soil, air, or organic material, has a broad application scope with precise, comprehensive, and rapid species identification. Here, we provide an overview of the application range of eDNA-based methods for biodiversity monitoring in PAs, evaluate environmental assessments in which this technology has already been implemented for nature conservation, and examine the challenges that can hamper further application in real world practice. Based on the outcomes of two projects, practical experience, and current scientific literature focusing on their application, we conclude that eDNA-based species detection methods provide promising novel approaches that have strong potential as supplement methods, or in some cases even as substitutes for the conventional monitoring methods used for PAs. This advancement is expected to affect decision-making in biodiversity conservation efforts in PAs and OECMs.
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Tsang, Hin Hung, Jose A. Domingos, Jacob A. F. Westaway, Maximilian H. Y. Kam, Roger Huerlimann, and Giana Bastos Gomes. "Digital Droplet PCR-Based Environmental DNA Tool for Monitoring Cryptocaryon irritans in a Marine Fish Farm from Hong Kong." Diversity 13, no. 8 (July 29, 2021): 350. http://dx.doi.org/10.3390/d13080350.
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The adoption of new investigative strategies based on environmental DNA (eDNA) can be used to monitor parasites, associated bacterial microbiomes, and physical-chemical parameters in fish farms. In this study, we used the economically important and globally distributed fish ciliate parasite Cryptocaryon irritans as a model to understand the parasite abundance and potential drivers of its presence in marine fish farms. Environmental (rainfall) and physical-chemical (temperature, oxygen, salinity, pH) data collected from a marine fish farm in Hong Kong were analyzed together with the eDNA approach targeting C. irritans abundance based on digital droplet PCR and 16S metagenomics to determine associations and triggers between parasites and specific bacterial groups. Rainfall and temperature demonstrated positive associations with high abundance of C. irritans (eDNA) at the studied marine fish cage farm. However, rainfall was the only parameter tested that demonstrated a significant association with parasite eDNA, indicating that the raining season is a risky period for fish farmers in Hong Kong. Coraliomargarita was the bacterial genus with the most significant relationship with low abundance of C. irritans in water. Understanding the environmental triggers of ciliate parasites propagation and associated bacterial microbiome could elucidate new insights into environmental control, microbial management, and promote the reduction of chemical use in marine fish farms.
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Bohara, Kailash, Amit K. Yadav, and Pabitra Joshi. "Detection of Fish Pathogens in Freshwater Aquaculture Using eDNA Methods." Diversity 14, no. 12 (November 22, 2022): 1015. http://dx.doi.org/10.3390/d14121015.
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Organisms release their nucleic acid in the environment, including the DNA and RNA, which can be used to detect their presence. eDNA/eRNA techniques are being used in different sectors to identify organisms from soil, water, air, and ice. The advancement in technology led to easier detection of different organisms without impacting the environment or the organism itself. These methods are being employed in different areas, including surveillance, history, and conservation. eDNA and eRNA methods are being extensively used in aquaculture and fisheries settings to understand the presence of different fish species and pathogens in water. However, there are some challenges associated with the reliability of results because of the degradation of nucleic acid by several factors. In aquaculture, there are several diseases and parasites detected with these methods. In this review, we discuss different aquaculture diseases and parasites detected with eDNA/eRNA approach and the fate of these nucleic acids when subjected to different water quality and environmental parameters. This review intends to help the researcher with the potential of eDNA/eRNA-based detection of pathogens in aquaculture; this will be useful to predict a potential outbreak before it occurs. Along with that, this paper intends to help people understand several factors that degrade and can hamper the detection of these nucleic acids.
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Matsuoka, Shunsuke, Yoriko Sugiyama, Mariko Nagano, and Hideyuki Doi. "Influence of DNA extraction kits on freshwater fungal DNA metabarcoding." PeerJ 10 (May 27, 2022): e13477. http://dx.doi.org/10.7717/peerj.13477.
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Background Environmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes. Methods DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extractmicrobial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; i.e., operational taxonomic unit (OTU) number and composition of the extracted samples. Results No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.
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Boyd, Spencer H., K. Denise Kendall Niemiller, Katherine E. Dooley, Jennifer Nix, and Matthew L. Niemiller. "Using environmental DNA methods to survey for rare groundwater fauna: Detection of an endangered endemic cave crayfish in northern Alabama." PLOS ONE 15, no. 12 (December 10, 2020): e0242741. http://dx.doi.org/10.1371/journal.pone.0242741.
Full textAbstract:
The conservation and management of subterranean biodiversity is hindered by a lack of knowledge on the true distributions for many species, e.g., the Wallacean shortfall. In recent years, several studies have demonstrated the potential of environmental DNA (eDNA) as an effective approach to detect and monitor biodiversity, including rare, threatened, and endangered taxa. However, there are few eDNA studies of groundwater fauna. Here we report the results of the development and implementation of an eDNA assay targeting a short fragment of the mitochondrial CO1 locus of a critically imperiled cave crayfish, the Sweet Home Alabama Cave Crayfish (Cambarus speleocoopi), known from just four cave systems in the Interior Plateau karst region of northern Alabama. We detected C. speleocoopi DNA from water samples collected at 5 of 16 sites sampled (caves and springs), including two historical sites as well as three additional and potentially new sites in Marshall County, Alabama. All three of these sites were within 2 km of historical sites. Our study is the first to detect a groundwater crustacean in the Interior Plateau karst region. Additionally, our study contributes to the growing literature that eDNA is a viable complementary tool for detection and monitoring of a fauna that is difficult to survey and study using traditional approaches.
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Villacorta-Rath, Cecilia, Conrad J. Hoskin, Jan M. Strugnell, and Damien Burrows. "Long distance (>20 km) downstream detection of endangered stream frogs suggests an important role for eDNA in surveying for remnant amphibian populations." PeerJ 9 (September 27, 2021): e12013. http://dx.doi.org/10.7717/peerj.12013.
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Background Globally, amphibian species have suffered drastic population declines over the past 40 years. Hundreds of species are now listed as Critically Endangered, with many of these considered “possibly extinct”. Most of these species are stream-dwelling frogs inhabiting remote, montane areas, where remnant populations are hard to find using traditional surveys. Environmental DNA (eDNA) could revolutionize surveys for ‘missing’ and endangered amphibian populations by screening water samples from downstream sections to assess presence in the upstream catchments. However, the utility of this survey technique is dependent on quantifying downstream detection probability and distances. Methods Here we tested downstream detection distances in two endangered stream frogs (Litoria lorica and L. nannotis) that co-occur in a remote stream catchment in north-east Australia, and for which we know precise downstream distributional limits from traditional surveys. Importantly, the two last populations of L. lorica persist in this catchment: one small (~1,000 frogs) and one very small (~100 frogs). We conducted eDNA screening at a series of sites kilometers downstream from the populations using precipitation from two fixed water volumes (15 and 100 mL) and via water filtering (mean 1,480 L). Results We detected L. nannotis and the small L. lorica population (~1,000 frogs) at most sampling sites, including 22.8 km downstream. The filtration method was highly effective for far-downstream detection, as was precipitation from 100 mL water samples, which also resulted in consistent detections at the far-downstream sites (including to 22.8 km). In contrast, we had limited downstream detection success for the very small L. lorica population (~100 frogs). Discussion The ecological aspects of our study system, coupled with thorough traditional surveys, enabled us to measure downstream eDNA detection distances with accuracy. We demonstrate that eDNA from a small population of approximately 1,000 frogs can be detected as far as 22.8 km downstream from the population. Water filtration is considered best for eDNA detection of rare aquatic species—indeed it was effective in this study—but we also achieved far-downstream detections when precipitating eDNA from 100 mL water samples. Collecting small water volumes for subsequent precipitation in the lab is more practical than filtration when surveying remote areas. Our downstream detection distances (>20 km) suggest eDNA is a valuable tool for detecting rare stream amphibians. We provide recommendations on optimal survey methods.
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Pedersen, Mikkel Winther, Søren Overballe-Petersen, Luca Ermini, Clio Der Sarkissian, James Haile, Micaela Hellstrom, Johan Spens, et al. "Ancient and modern environmental DNA." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1660 (January 19, 2015): 20130383. http://dx.doi.org/10.1098/rstb.2013.0383.
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DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.
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Clare, Elizabeth L., Chloe K. Economou, Chris G. Faulkes, James D. Gilbert, Frances Bennett, Rosie Drinkwater, and Joanne E. Littlefair. "eDNAir: proof of concept that animal DNA can be collected from air sampling." PeerJ 9 (March 31, 2021): e11030. http://dx.doi.org/10.7717/peerj.11030.
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Environmental DNA (eDNA) is one of the fastest developing tools for species biomonitoring and ecological research. However, despite substantial interest from research, commercial and regulatory sectors, it has remained primarily a tool for aquatic systems with a small amount of work in substances such as soil, snow and rain. Here we demonstrate that eDNA can be collected from air and used to identify mammals. Our proof of concept successfully demonstrated that eDNA sampled from air contained mixed templates which reflect the species known to be present within a confined space and that this material can be accessed using existing sampling methods. We anticipate this demonstration will initiate a much larger research programme in terrestrial airDNA sampling and that this may rapidly advance biomonitoring approaches. Lastly, we outline these and potential related applications we expect to benefit from this development.
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Baeza, J. Antonio. "Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica." PeerJ 10 (December 6, 2022): e14428. http://dx.doi.org/10.7717/peerj.14428.
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The Amur or Siberian tiger Panthera tigris altaica (Temminck, 1844) is currently restricted to a small region of its original geographical range in northwestern Asia and is considered ‘endangered’ by the IUCN Red List of Threatened Species. This solitary, territorial, and large top predator is in major need of genomic resources to inform conservation management strategies. This study formally tested if complete mitochondrial genomes of P. tigris altaica can be assembled from non-enriched metagenomic libraries generated from scat eDNA samples using the Illumina sequencing platform and open-access bioinformatics pipelines. The mitogenome of P. tigris altaica was assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 322.7x to 17.6x in four different scat eDNA samples. A nearly complete mitochondrial genome (101x) was retrieved from a fifth scat eDNA sample. The complete or nearly complete mitochondrial genomes of P. tigris altaica were AT-rich and composed of 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Synteny observed in all assembled mitogenomes was identical to that reported before for P. tigris altaica and other felids. A phylogenomic analysis based on all PCGs demonstrated that the mitochondrial genomes assembled from scat eDNA reliably identify the sequenced samples as belonging to P. tigris and distinguished the same samples from closely and distantly related congeneric species. This study demonstrates that it is viable to retrieve accurate whole and nearly complete mitochondrial genomes of P. tigris altaica (and probably other felids) from scat eDNA samples without library enrichment protocols and using open-access bioinformatics workflows. This new genomic resource represents a new tool to support conservation strategies (bio-prospecting and bio-monitoring) in this iconic cat.
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Suryobroto, Bambang, Ahmad Abdul Jabbar, and Puji Rianti. "Application of Environmental DNA (eDNA) Metabarcoding Method to Identify Threatened Sulawesi Mammal Based on 12S rRNA Gene." HAYATI Journal of Biosciences 29, no. 1 (December 28, 2021): 114–21. http://dx.doi.org/10.4308/hjb.29.1.114-121.
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Species detection and identification is a crucial steps in biodiversity assessment. Traditional methods are often invasive and resource intensive. The number of studies demonstrating successful of eDNA metabarcoding approach in species identification has increased rapidly in recent years. Some of large terrestrial mammals have reportedly utilize natural salt licks as a source of minerals in the diet and its genetic material left in the environment can be used to identify species from this site. An eDNA metabarcoding protocol had been carried out to identify Sulawesi mammals from Adudu natural salt-licks, Nantu Wildlife Reserve, Gorontalo. Environmental DNA were extracted from water samples, Amplicon libraries were prepared by PCR amplification and Illumina MiSeq high throughput sequencing. Reads processing and taxonomic assignment carried out in two bioinformatics packages, PipeCraft-1.0 and OBITools-2.11. Two endangered Sulawesi mammals species had been identified, i.e. lowland anoa (Bubalus depressicornis) and babirusa (Babyrousa babyrussa). The accuracy of mammal species identification using eDNA metabarcoding is affected by rigorous experimental procedures, DNA marker reliability, and availability of reference sequence database.
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KITLV, Redactie. "Bookreviews." New West Indian Guide / Nieuwe West-Indische Gids 83, no. 1-2 (January 1, 2009): 121–86. http://dx.doi.org/10.1163/13822373-90002463.
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Afro-Atlantic Dialogues: Anthropology in the Diaspora, edited by Kevin A. Yelvington (reviewed by Aisha Khan)Central Africans, Atlantic Creoles, and the Foundation of the Americas, 1585-1660, by Linda M. Heywood & John K. Thornton (reviewed by James H. Sweet)An Eye for the Tropics: Tourism, Photography, and Framing the Caribbean Picturesque, by Krista A. Thompson (reviewed by Carl Thompson)Taíno Indian Myth and Practice: The Arrival of the Stranger King, by William F. Keegan (reviewed by Frederick H. Smith) Historic Cities of the Americas: An Illustrated Encyclopedia, by David F. Marley (reviewed by Richard L. Kagan) Arming Slaves: From Classical Times to the Modern Age, edited by Christopher Leslie Brown & Philip D. Morgan (reviewed by James Sidbury)Sweet Negotiations: Sugar, Slavery, and Plantation Agriculture in Early Barbados, by Russell R. Menard (reviewed by Kenneth Morgan)Jamaica in 1850 or, The Effects of Sixteen Years of Freedom on a Slave Colony, by John Bigelow (reviewed by Jean Besson) Moral Capital: Foundations of British Abolitionism, by Christopher Leslie Brown (reviewed by Cassandra Pybus) Caribbean Journeys: An Ethnography of Migration and Home in Three Family Networks, by Karen Fog Olwig (reviewed by George Gmelch) Afro-Caribbean Immigrants and the Politics of Incorporation: Ethnicity, Exception, or Exit, by Reuel R. Rogers (reviewed by Kevin Birth) Puerto Rican Arrival in New York: Narratives of the Migration, 1920-1950, edited by Juan Flores (reviewed by Wilson A. Valentín-Escobar)The Conquest of History: Spanish Colonialism and National Histories in the Nineteenth Century, by Christopher Schmidt-Nowara (reviewed by Aline Helg)Gender and Slave Emancipation in the Atlantic World, edited by Pamela Scully & Diana Paton (reviewed by Bernard Moitt) Gender and Democracy in Cuba, by Ilja A. Luciak (reviewed by Florence E. Babb) The “New Man” in Cuba: Culture and Identity in the Revolution, by Ana Serra (reviewed by Jorge Duany) Lydia Cabrera and the Construction of an Afro-Cuban Cultural Identity, by Edna M. Rodríguez-Mangual (reviewed by Brian Brazeal) Worldview, the Orichas, and Santeria: Africa to Cuba and Beyond, by Mercedes Cros Sandoval (reviewed by Elizabeth Pérez)The 1812 Aponte Rebellion in Cuba and the Struggle against Atlantic Slavery, by Matt D. Childs (reviewed by Manuel Barcia) Caliban and the Yankees: Trinidad and the United States Occupation, by Harvey R. Neptune (reviewed by Selwyn Ryan) Claims to Memory: Beyond Slavery and Emancipation in the French Caribbean, by Catherine A. Reinhardt (reviewed by Dominique Taffin) The Grand Slave Emporium, Cape Coast Castle and the British Slave Trade, by William St. Clair (reviewed by Ray A. Kea) History of the Caribbean, by Frank Moya Pons (reviewed by Olwyn M. Blouet) Out of the Crowded Vagueness: A History of the Islands of St Kitts, Nevis & Anguilla, by Brian Dyde (reviewed by Karen Fog Olwig) Scoping the Amazon: Image, Icon, Ethnography, by Stephen Nugent (reviewed by Neil L. Whitehead)
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McNeil, James, Anneke DeLuycker, and Sarah Putman. "Using Environmental DNA to Connect Lab Science with Field Practice." American Biology Teacher 80, no. 4 (April 1, 2018): 285–89. http://dx.doi.org/10.1525/abt.2018.80.4.285.
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Experiential learning helps students make connections between different skill sets and allows them to engage in a deeper level of inquiry. To enhance the connection between field and laboratory practice for undergraduate students in our wildlife ecology curriculum, we developed an exercise using environmental DNA (eDNA) analysis. eDNA sampling involves extracting and amplifying the DNA from specific organisms from an environmental sample, rather than from the organisms themselves, and has been rapidly adopted by conservation practitioners around the world. In our activity, students collect water samples from a local pond and process them to detect the presence of American bullfrogs. Practicing this procedure not only introduces them to professional skills they may utilize in their careers, but also helps create context for how laboratory science and field work support each other and can be used to connect to larger issues of conservation, environmental studies, or ecology.
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Bernardino, Angelo F., Fabiano S. Pais, Louisi S. Oliveira, Fabricio A. Gabriel, Tiago O. Ferreira, Hermano M. Queiroz, and Ana Carolina A. Mazzuco. "Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA." PeerJ 7 (November 7, 2019): e8042. http://dx.doi.org/10.7717/peerj.8042.
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Mine tailing disasters have occurred worldwide and contemporary release of tailings of large proportions raise concerns of the chronic impacts that trace metals may have on the aquatic biodiversity. Environmental metabarcoding (eDNA) offers an as yet poorly explored opportunity for biological monitoring of impacted aquatic ecosystems from mine tailings and contaminated sediments. eDNA has been increasingly recognized to be an effective method to detect previously unrecognized small-sized Metazoan taxa, but their ecological responses to environmental pollution has not been assessed by metabarcoding. Here, we evaluated chronic effects of trace metal contamination from sediment eDNA of the Rio Doce estuary, 1.7 years after the Samarco mine tailing disaster, which released over 40 million m3 of iron tailings in the Rio Doce river basin. We identified 123 new sequence variants environmental taxonomic units (eOTUs) of benthic taxa and an assemblage composition dominated by Nematoda, Crustacea and Platyhelminthes; typical of other estuarine ecosystems. We detected environmental filtering on the meiofaunal assemblages and multivariate analysis revealed strong influence of Fe contamination, supporting chronic impacts from mine tailing deposition in the estuary. This was in contrast to environmental filtering of meiofaunal assemblages of non-polluted estuaries. Here, we suggest that the eDNA metabarcoding technique provides an opportunity to fill up biodiversity gaps in coastal marine ecology and may become a valid method for long term monitoring studies in mine tailing disasters and estuarine ecosystems with high trace metals content.
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Fu'adil Amin, Muhammad Hilman, Ji-Hyun Lee, Ah Ran Kim, Ju-Kyoung Kim, Chung-Il Lee, and Hyun-Woo Kim. "Development of a Quantitative PCR Assay for Four Salmon Species Inhabiting the Yangyangnamdae River Using Environmental DNA." Biology 10, no. 9 (September 11, 2021): 899. http://dx.doi.org/10.3390/biology10090899.
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A species-specific quantitative PCR (qPCR) assay using environmental DNA (eDNA) is a promising tool for both qualitative and quantitative analyses of target species directly from water samples. Despite its reliability, an eDNA-based qPCR assay pipeline has not yet developed to monitor salmon species inhabiting Korean waters, which have been rapidly decreasing. We designed species-specific primers for four Oncorhynchus species inhabiting the eastern coastal waters along the Korean Peninsula. These include primers for two native species (Oncorhynchus keta and O. masou) and two that were introduced (O. mykiss and O. kisutch). The limit of detection and limit of quantification for the four qPCR assays ranged from 4.11 to 10.38 copies and from 30 to 81 copies, respectively, indicating a high sensitivity and specificity across all four species. Following optimization, the qPCR assays were used for the quantitative analyses of the four Oncorhynchus species in the Yangyangnamdae River during the spawning and non-spawning seasons in the year 2019–2020, one of the main rivers where salmon migrate during the spawning season in Korea. The raw copy numbers in all of the examined samples were normalized by PCR inhibition rates to standardize and compare with other studies. Among the four Oncorhynchus species examined, the eDNA concentration of O. keta increased significantly (63.60-fold, p < 0.0001) during the spawning season (November) compared with that in the non-spawning season (March), suggesting that O. keta is the main salmon species migrating through the Yangyangnamdae River. In contrast, we did not detect any differences in eDNA concentration for the other three Oncorhynchus species between the spawning and non-spawning seasons, indicating that their presence does not alter during the year. Their eDNA concentration is also relatively low compared to O. keta, which suggests that small numbers of these three species are present in the river. Overall, these newly developed qPCR assays represent useful monitoring tools for the management of four salmon species in Korean waters.