"Who's Afraid of Edna O'Brien?" asks an early interviewer inConversations with Edna O'Brien. With over fifty years of published novels, biographies, plays, telecasts, short stories, and more, it is ...hard not to be intimidated by her. An acclaimed and controversial Irish writer, O'Brien (b. 1932) saw her early works, starting in 1960 withThe Country Girls, banned and burned in Ireland, but often read in secret. Her contemporary work continues to spark debates on the rigors and challenges of Catholic conservatism and the struggle for women to make a place for themselves in the world without anxiety and guilt. The raw nerve of emotion at the heart of her lyrical prose provokes readers, challenges politicians, and proves difficult for critics to place her.
In these interviews, O'Brien finds her own critical voice and moves interviewers away from a focus on her life as the "once infamous Edna" toward a focus on her works. Parallels between Edna O'Brien and her literary muse and mentor, James Joyce, are often cited in interviews such as Phillip Roth's description ofThe Country Girlsas "rural Dubliners." While Joyce is the centerpiece of O'Brien's literary pantheon, allusions to writers such as Shakespeare, Chekhov, Beckett, and Woolf become a medium for her critical voice. Conversations with contemporary writers Phillip Roth and Glenn Patterson reveal Edna O'Brien's sense of herself as a contemporary writer. The final interview included here, with BBC personality William Crawley at Queen's University, Belfast, is a synthesis of her acceptance and fame as an Irish writer and an Irish woman and an affirmation of her literary authority.
Multiple studies have demonstrated environmental (e)DNA detections of rare and invasive species. However, invasive species managers struggle with using eDNA results because detections might not ...indicate species presence. We evaluated whether eDNA methods have matured to a point where they can be widely applied to aquatic invasive species management. We have found that eDNA methods meet legal standards for being admissible as evidence in most courts, suggesting eDNA method reliability is not the problem. Rather, we suggest the interface between results and management needs attention since there are few tools for integrating uncertainty into decision-making. Solutions include decision-support trees based on molecular best practices that integrate the temporal and spatial trends in eDNA positives relative to human risk tolerance.
We consider whether eDNA methods have matured to a point where they can go from research to widespread application and be incorporated into aquatic invasive species management.Under the Daubert standard of scientific evidence, eDNA is arguably a sufficiently mature and reliable technique.However, invasive species managers struggle with using eDNA since it is uncertain if detections indicate species presence and the costs of acting can be high.eDNA based, decision support tools for invasive species management are lacking.Manuals on best practices, decision support trees for the interpretation of results, education and training of managers and stakeholders, and communication protocols are necessary outputs before widespread incorporation of eDNA into invasive species management.Many of these outputs are coming into place, which will allow eDNA to better support invasive species management.
Eukaryotic communities in groundwater may be particularly sensitive to disturbance because they are adapted to stable environmental conditions and often have narrow spatial distributions. Traditional ...methods for characterising these communities, focussing on groundwater-inhabiting macro and meiofauna (stygofauna), are challenging because of limited taxonomic knowledge and expertise (particularly in less-explored regions), and the time and expense of morphological identification. The primary objective of this study was to evaluate the vulnerability of eukaryote communities in shallow groundwater to mine water discharge containing elevated concentrations of magnesium (Mg) and sulfate (SO4). The study was undertaken in a shallow sand bed aquifer within a wet-dry tropical setting. The aquifer, featuring a saline mine water gradient primarily composed of elevated Mg and SO4, was sampled from piezometers in the creek channel upstream and downstream of the mine water influence during the dry season when only subsurface water flow was present. Groundwater communities were characterised using both morphological assessments of stygofauna from net samples and environmental DNA (eDNA) targeting the 18S rDNA and COI mtDNA genes. eDNA data revealed significant shifts in community composition in response to mine waters, contrasting with findings from traditional morphological composition data. Changes in communities determined using eDNA data were notably associated with concentrations of SO42−, Mg2+, Na+, and water levels in the piezometers. This underscores the importance of incorporating molecular approaches in impact assessments, as relying solely on traditional stygofauna sampling methods in similar environments may lead to inaccurate conclusions about the responses of the assemblage to studied impacts.
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•Morphological and molecular (eDNA) methods were used to assess mine water impacts on groundwater eukaryote communities.•Eukaryote community composition shifted with increasing SO42−, Mg2+ & Na+ concentrations in groundwater.•Traditional methods of stygofauna sampling did not show changes in communities that were associated with mine water impacts.
Accelerating global urbanization is leading to drastic losses and restructuring of biodiversity. Although it is crucial to understand urban impacts on biodiversity to develop mitigation strategies, ...there is a dearth of knowledge on the functional structure of fish assemblages spanning the entire city-scale spectrum of urbanization intensity. Here, using environmental DNA sampled from 109 water sites in Beijing, we investigated the taxonomic and functional diversity patterns of fish assemblages across the city and uncovered community-, trait-, and species-level responses to various environmental stressors. By ranking sampling sites into three disturbance levels according to water physiochemical and landcover conditions, we found that both native and non-native fish taxonomic and functional α-diversity decreased significantly with elevating disturbance, as strong disturbance led to the disappearance of many species. However, the quantitative taxonomic and functional β-diversity components of native and non-native fish showed distinct patterns; assemblage turnover dominated native fish β-diversity and decreased with increasing disturbance, whereas species/trait richness differences dominated non-native fish β-diversity and increased with disturbance intensity particularly in lotic waters. RLQ and fourth-corner analyses revealed that fish size, fecundity, diet, and reproductive behaviors were significantly correlated with water quality, with pollution-tolerant, larger-sized native and omnivorous non-native fishes being urban winners, which indicates strong trait-dependent environmental filtering. Potential ecological indicator species were identified based on the sensitivity of fish responses to pollution loads; these were mostly small native species, and many have bivalve-dependent reproduction. Our results demonstrate that, along with native fish assemblage simplification and homogenization, urban stressors exert profound impacts on community trait composition, highlighting the need to consider both biodiversity loss and functional reorganization in combating disturbance of aquatic ecosystems under global urbanization. Furthermore, correlations between cropland cover and water nutrient level suggested that the management of agricultural runoff might be critically important for safeguarding urban water quality.
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•Fish assemblages across Beijing were investigated using eDNA.•Disturbance intensity was delineated based on water quality and landcover.•Severe disturbance reduced native fish taxonomic and functional α- and β-diversity.•Water quality strongly filtered fish traits.•Cropland runoff should be managed to preserve water ecosystems.
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•Rockfish are culturally and economically important requiring marine protection.•Many rockfish species overlap geographically making environmental DNA surveys hard.•qPCR-based eDNA ...assays were successfully designed for target rockfish species.•eDNA metabarcoding detected significantly more species than SCUBA diving surveys.•Combining eDNA and conventional methods strengthen rockfish biodiversity monitoring.
The rocky reefs of British Columbia’s (BC) coast are a productive ecosystem, home to 38 rockfish species (Genus: Sebastes) that are culturally and economically important. Quantitatively assessing rockfish populations is vital to support conservation and stock assessment needs. Self-contained underwater breathing apparatus (SCUBA) diving surveys are a commonly used monitoring method in BC. However, this resource-intensive approach is challenging, particularly for cryptic or deeper species. Herein, we compared environmental DNA (eDNA) detection methods with SCUBA diving surveys to capture overall rockfish biodiversity. We employed two eDNA methods: 1) a targeted quantitative real-time polymerase chain reaction (qPCR) approach to monitor species of particular importance to First Nations collaborators and decision makers, and 2) a metabarcoding approach for assessing community composition using the previously published MiSebastes assay. Both approaches are confounded by the little DNA sequence divergence among species and high sequence variation within species. Overcoming these challenges using a whole mitochondrial approach with the mtGrasp and unikseq pipelines, we generated highly useful eDNA tools. We found that eDNA methods were highly comparable to dive surveys, as both methods indicated a similar ecological reality, including species detections and distributions. Though there are certain species that cannot be distinguished by the MiSebastes assay, eDNA metabarcoding still detected more rockfish species overall. Both eDNA methods show potential for use alongside conventional methods for scalable incorporation into community-based monitoring programs.
Environmental DNA (eDNA) analysis from water samples is a promising new method to identify both targeted species and whole communities of aquatic organisms. However, the current literature regarding ...eDNA shedding rates primarily focuses on fish and most decay rate constants are reported for warm sunlit waters. Here, we conducted experiments to investigate how eDNA shedding differs between animal forms and how long eDNA can persist in waters of varying temperature and light conditions. We designed quantitative PCR assays for one fish (mummichog, Fundulus heteroclitus), one crustacean (grass shrimp, Palaemon spp.), and two scyphomedusae (moon jelly, Aurelia aurita and nettle, Chrysaora spp.) to estimate eDNA shedding and decay rates. We found that shedding rates were highly variable for all organisms, but grass shrimp had the lowest shedding rate. We quantified eDNA decay rate constants at 6, 15, and 23°C and found that decay rate constants of mummichog and grass shrimp were larger at higher temperatures, while those of scyphomedusae did not show clear temperature dependence. We also found that higher‐order decay models with tails fit the data better than first‐order log‐linear models, suggesting temporal variability in eDNA decay rates. Results indicate that different animal forms shed different types of eDNA, impacting both shedding and decay rates. These findings fill critical knowledge gaps regarding variation in eDNA shedding and decay across animal forms under a range of realistic marine temperature conditions. These data will be useful for interpreting field studies that utilize eDNA to investigate ocean habitats that are otherwise difficult to access.
We conducted mesocosm experiments using a fish, a crustacean, and two scyphomedusae to investigate how environmental DNA (eDNA) shedding differs between animal forms and how long eDNA can persist in waters of different temperature and light conditions. We found that shedding rates were highly variable for all organisms, but grass shrimp had the lowest eDNA shedding rate and that decay rate constants of mummichog and grass shrimp were larger at higher temperatures, while those of scyphomedusae did not show clear temperature dependence. These findings fill critical knowledge gaps regarding variation in shedding and decay of eDNA across different animal forms under a range of realistic marine temperature and light conditions.
•eDNA can be transported on several kilometers in lotic environments.•Dilution and dispersion show effect on eDNA relative abundance after 100 m.•eDNA metabarcoding can locally document community ...composition in large rivers.
Protection of freshwater fish diversity is a global conservation priority in face of its alarming decline in the last decades. A crucial step to protect freshwater fish diversity is the production of prompt and precise evaluation of community composition and spatial distribution. Metabarcoding of environmental DNA (eDNA metabarcoding) generally surpasses traditional methods for documenting diversity and community composition in aquatic environments. Nevertheless, empirical evidence evaluating how eDNA transportation in water affect community composition and structure via eDNA metabarcoding data remains scarce. Using a brown trout (Salmo trutta) cage transplant experiment in the St. Lawrence River (Canada), a large fluvial system, we tested the detection and relative abundance of species’ eDNA along 15 sampling locations. We detected brown trout eDNA in five localities up to 5,000 m from the cage, but only one sampling location situated 10 m downstream and in the direct line of the cage was affected at the community composition level. This locality showed a relative abundance of brown trout eDNA of 13.1%, while the four others showed a relative abundance under 1.0%. K-means cluster analysis confirmed the impact of brown trout eDNA on community composition by separating this locality from all others. Based on species loading of a redundancy analysis, we showed that this different k-means group was associated with the high relative abundance of brown trout. No evidence of transport effect of brown trout eDNA on fish community composition was observed in any other sampling locations. Together, our results support the view that eDNA metabarcoding can be both a conveyor belt of biodiversity information and a precise tool to study the composition and structure of fish communities in river.
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•Filtration-based eDNA sampling has many drawbacks.•Passive eDNA samplers were tested in biodiverse natural waters.•The two sampling methods yielded comparable fish ...biodiversity.•Passive samplers were superior in capturing a rare species.•Passive eDNA samplers show strong potential for eDNA biomonitoring.
Environmental DNA (eDNA) technology has revolutionized biomonitoring, but challenges remain regarding water sample processing. The passive eDNA sampler (PEDS) represents a viable alternative to active, water filtration-based eDNA enrichment methods, but the effectiveness of PEDS for surveying biodiverse and complex natural water bodies is unknown. Here, we collected eDNA using filtration and glass fiber filter-based PEDS (submerged in water for 1 d) from 27 sites along the final reach of the Yangtze River and the coast of the Yellow Sea, followed by eDNA metabarcoding analysis of fish biodiversity and quantitative PCR (qPCR) for a critically endangered aquatic mammal, the Yangtze finless porpoise. We ultimately detected 98 fish species via eDNA metabarcoding. Both eDNA sampling methods captured comparable local species richness and revealed largely similar spatial variation in fish assemblages and community partitions between the river and sea sites. Notably, the Yangtze finless porpoise was detected only in the metabarcoding of eDNA collected by PEDS at five sites. Also, species-specific qPCR revealed that the PEDS captured porpoise eDNA at more sites (7 vs. 2), in greater quantities, and with a higher detection probability (0.803 vs. 0.407) than did filtration. Our results demonstrate the capacity of PEDS for surveying fish biodiversity, and support that continuous eDNA collection by PEDS can be more effective than instantaneous water sampling at capturing low abundance and ephemeral species in natural waters. Thus, the PEDS approach can facilitate more efficient and convenient eDNA-based biodiversity surveillance and rare species detection.
Summary
Environmental DNA (eDNA) analysis for detecting the presence of aquatic and terrestrial organisms is an established method, and the eDNA concentration of a species can reflect its ...abundance/biomass at a site. However, attempts to estimate the abundance/biomass of aquatic species using eDNA concentrations in large stream and river ecosystems have received little attention.
We determined the eDNA concentration and abundance/biomass of a stream fish, Plecoglossus altivelis, by conducting a snorkelling survey in the Saba River, Japan. Furthermore, we evaluated the relationship between eDNA concentrations and the estimated abundance/biomass of P. altivelis, and determined its spatial distribution within the river.
Across the three seasons from spring to autumn, we found significant correlations between the eDNA concentration of P. altivelis and its abundance/biomass at study sites within the river. We detected the eDNA at the sites where we found only feeding traces on stones (where P. altivelis was not directly observed), but not at sites without feeding traces. Additionally, we tested the optimal number of qPCR replicates needed for the eDNA evaluation of P. altivelis abundance and biomass; only a small number of replicates was required when the eDNA concentration was high.
Our findings suggest that eDNA analysis is a useful tool to estimate fish abundance/biomass as well as their spatial distribution in rivers.
The extracellular polymeric substances (EPS) construct the three-dimensional (3-D) structure of biofilms, but their respective roles are still not clear. Therefore, this study aimed to illuminate the ...role of key chemical components extracellular DNA (eDNA), extracellular proteins, and carbohydrates of EPS in biofilm formation of
Vibrio parahaemolyticus
. The correlations between each key chemical component and biofilm formation were first determined, showing that the biofilm formation of
V. parahaemolyticus
was strongly positively correlated with both eDNA and protein content (
P
< 0.01), but not with carbohydrates. Subsequently, individual DNase I or protease K treatment markedly reduced the initial adhesion and structural stability of the formed biofilms by hydrolyzing the eDNA or extracellular proteins, but did not induce significant dispersion of mature biofilms. However, the combination of DNase I and protease K treatment induced the obvious dispersion of the mature biofilms through the concurrent destruction of eDNA and extracellular proteins. The analysis at a structural level showed that the collapse of biofilms was mainly attributed to the great damage of the loop configuration of eDNA and the secondary structure of proteins caused by the enzyme treatment. Therefore, this study provides a deep understanding of the role of key chemical components of EPS in biofilm development of
V. parahaemolyticus
, which may give a new strategy to develop environmentally friendly methods to eradicate the biofilms in food industry.
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