Environmental DNA (eDNA) Monitoring of Noble Crayfish Astacus astacus in Lentic Environments Offers Reliable Presence-Absence Surveillance – But Fails to Predict Population Density

Noble crayfish is the most widespread native freshwater crayfish species in Europe. It is threatened in its entire distribution range and listed on the International Union for Concervation Nature- and national red lists. Reliable monitoring data is a prerequisite for implementing conservation measures, and population trends are traditionally obtained from catch per unit effort (CPUE) data. Recently developed environmental DNA (eDNA) tools can potentially improve the effort. In the past decade, eDNA monitoring has emerged as a promising tool for species surveillance, and some studies have established that eDNA methods yield adequate presence-absence data for crayfish. There are also high expectations that eDNA concentrations in the water can predict biomass or relative density. However, eDNA studies for crayfish have not yet been able to establish a convincing relationship between eDNA concentrations and crayfish density. This study compared eDNA and CPUE data obtained the same day and with high sampling effort, and evaluated whether eDNA concentrations can predict relative density of crayfish. We also compared two analytical methods [Quantitative real-time PCR (qPCR) and digital droplet PCR (ddPCR)], and estimated the detection probability for eDNA monitoring compared to trapping using occupancy modeling. In all lakes investigated, we detected eDNA from noble crayfish, even in lakes with very low densities. The eDNA method is reliable for presence-absence monitoring of noble crayfish, and the probability of detecting noble crayfish from eDNA samples increased with increasing relative crayfish densities. However, the crayfish eDNA concentrations were consistently low and mostly below the limit of quantification, even in lakes with very high crayfish densities. The hypothesis that eDNA concentrations can predict relative crayfish density was consequently not supported. Our study underlines the importance of intensified sampling effort for successful detection of very low-density populations, and for substantiating presumed absence, inferred from negative results. Surprisingly, we found a higher likelihood of eDNA detection using qPCR compared to ddPCR. We conclude that eDNA monitoring cannot substitute CPUE data, but is a reliable supplement for rapid presence-absence overviews. Combined with eDNA analyses of alien crayfish species and diseases such as crayfish plague, this is a cost-efficient supplement offering a more holistic monitoring approach for aquatic environments and native crayfish conservation.

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Environmental DNA monitoring of noble crayfish Astacus astacus: Comparison and refining of methodology

ARPHA Conference Abstracts ◽

10.3897/aca.4.e65010 ◽

2021 ◽

Vol 4 ◽

Author(s):

David Strand ◽

Stein Johnsen ◽

Frode Fossøy ◽

Johannes Rusch ◽

Brett Sandercock ◽

...

Keyword(s):

Dna Extraction ◽

Brown Trout ◽

Detection Probability ◽

Environmental Dna ◽

Northern Pike ◽

Freshwater Crayfish ◽

Astacus Astacus ◽

European Perch ◽

Detection Frequency ◽

Noble Crayfish

During the past decade, environmental DNA (eDNA) methodology has become an important non-invasive tool to monitor aquatic micro- and macro-organisms, including freshwater crayfish. In Europe, noble crayfish Astacus astacus is the most widespread native freshwater crayfish. However, the species is threatened in its entire distribution range. It is therefore included on the International Union for Conservation Nature (IUCN) red list, and on several national red lists. Reliable monitoring is essential for implementation of conservation measures. For crayfish, traditional population trends have been obtained from catch per unit effort (CPUE) data. In order to successfully apply and use eDNA monitoring for noble crayfish, or any species, it is a prerequisite to know the strengths and weaknesses of the applied methods and how they perform compared to traditional methodology. Sampling strategy and analysis methodology also depends on choice of species to be monitored, and which questions to be answered. Further, refinement of the employed methods may improve the detection probability for eDNA monitoring. Here we report the results from 1) a recently published study on noble crayfish eDNA monitoring (Johnsen et al. 2020) and 2) an ongoing study comparing and optimising the methods used for monitoring noble crayfish. 1) We compared eDNA monitoring (transects with ten 5L samples) with traditional trapping (transects with 50 traps) for noble crayfish in lentic habitats, in order to evaluate detection probability and if eDNA concentration correlates with relative density of crayfish. We also compared two commonly used analytical methods [quantitative real-time PCR (qPCR) and droplet digital PCR (ddPCR)] for eDNA monitoring. We found that qPCR outperformed ddPCR in detection frequency (Fig. 1), most likely due to some inhibition in the ddPCR analysis. eDNA monitoring provided reliable presence/absence data for noble crayfish, even in lakes with very low crayfish densities. Detection frequency increased with increasing CPUE (Fig. 1). However, we did not observe any correlation between relative crayfish densities and eDNA concentrations of crayfish. eDNA concentrations were consistently very low, even in lakes with very high crayfish densities. For lakes with very low crayfish densities, we estimated that ~5 samples (5L samples) are needed for 95 % detection likelihood, while for lakes with high densities 2 samples were needed. 2) We compared two eDNA sampling strategies (sampling from bottom or the surface), commonly used for crayfish or fish in Norway to investigate how both strategies perform. The sampled filters were divided and two DNA extraction protocols were evaluated (CTAB based vs Column based). We found that the DNA yield was higher from the column based DNA extraction protocol, and that eDNA concentrations from fish (brown trout Salmon trutta, northern pike Esox lucius and European perch Perca fluviatilis) were significantly higher than for crayfish. For crayfish and brown trout, there was little difference between detection probability for bottom and surface samples, while for northern pike and European perch the detection probability was higher for the bottom samples. Currently, we are analysing eDNA samples collected with glass fibre filters and NatureMetrix filters for noble crayfish in both lentic and lotic habitats and the preliminary results will be presented. We conclude that eDNA monitoring cannot substitute CPUE monitoring for freshwater crayfish, but it offers reliable presence-absence data, provided sufficient sampling efforts. Thus, it is suitable for large scale monitoring of threatened crayfish and combined with eDNA analysis of alien crayfish and diseases such as crayfish plague, this is a cost-efficient supplement offering a more holistic approach for aquatic environments and native crayfish conservation. Furthermore, the synergy effect of using collected eDNA samples from different projects to monitor additional species is substantial.

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Environmental DNA concentrations are correlated with regional biomass of Atlantic cod in oceanic waters

Communications Biology ◽

10.1038/s42003-019-0696-8 ◽

2019 ◽

Vol 2 (1) ◽

Cited By ~ 9

Author(s):

Ian Salter ◽

Mourits Joensen ◽

Regin Kristiansen ◽

Petur Steingrund ◽

Poul Vestergaard

Keyword(s):

Gadus Morhua ◽

Atlantic Cod ◽

Environmental Dna ◽

Sampling Effort ◽

Trawl Survey ◽

Catch Per Unit Effort ◽

Fish Stocks ◽

Powerful Approach ◽

Commercially Important ◽

Positive Correlations

AbstractEnvironmental DNA (eDNA) has emerged as a powerful approach for studying marine fisheries and has the potential to negate some of the drawbacks of trawl surveys. However, successful applications in oceanic waters have to date been largely focused on qualitative descriptions of species inventories. Here we conducted a quantitative eDNA survey of Atlantic cod (Gadus morhua) in oceanic waters and compared it with results obtained from a standardized demersal trawl survey. Detection of eDNA originating from Atlantic cod was highly concordant (80%) with trawl catches. We observed significantly positive correlations between the regional integrals of Atlantic cod biomass (kg) and eDNA quantities (copies) (R2 = 0.79, P = 0.003) and between sampling effort-normalised Catch Per Unit Effort (kg hr−1) and eDNA concentrations (copies L−1) (R2 = 0.71, P = 0.008). These findings extend the potential application of environmental DNA to regional biomass assessments of commercially important fish stocks in the ocean.

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Comparative transcriptome analysis of noble crayfish and marbled crayfish immune response to Aphanomyces astaci challenges

10.1101/2021.05.25.445163 ◽

2021 ◽

Author(s):

Ljudevit Luka Boštjančić ◽

Caterina Francesconi ◽

Christelle Rutz ◽

Lucien Hoffbeck ◽

Laetitia Poidevin ◽

...

Keyword(s):

Invasive Disease ◽

Freshwater Crayfish ◽

Post Challenge ◽

Aphanomyces Astaci ◽

Resistant Species ◽

High Virulence ◽

Noble Crayfish ◽

Immune Related Genes ◽

Marbled Crayfish ◽

Crayfish Species

Introduction of invasive North American crayfish species and their pathogen Aphanomyces astaci has significantly contributed to the decline of European freshwater crayfish populations. In this study, noble crayfish, a susceptible native European species, and marbled crayfish, an invasive disease-resistant species, were challenged with haplogroup A (low virulence) and haplogroup B (high virulence) strain of A. astaci. Hepatopancreatic tissue was isolated 3 and 21 days post-challenge. Our results revealed strong up-regulation in expression levels of the prophenoloxidase cascade immune-related genes in the haplogroup B challenged noble crayfish 3 days post-challenge. In the marbled crayfish, we observed an up-regulation of immune system relevant genes (DSCAM, AP, ALFs, CTLs and hemocyanin) 3 days post-challenge. This response highlights the marbled crayfish capability of building the immune tolerance. Furthermore, we successfully characterised several novel immune related gene groups in both crayfish species, contributing to our current understanding of crayfish immune related genes landscape.

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Evaluating and predicting impacts of Australian redclaw crayfish Cherax quadricarinatus and Louisiana red swamp crayfish Procambarus clarkii invasions

10.21504/10962/191137 ◽

2021 ◽

Author(s):

◽

Takudzwa Comfort Madzivanzira

Keyword(s):

Southern Africa ◽

Conservation Management ◽

Procambarus Clarkii ◽

Ecological Impacts ◽

Freshwater Crayfish ◽

Catch Per Unit Effort ◽

Cherax Quadricarinatus ◽

Unit Effort ◽

Crayfish Species ◽

Probability Of Capture

Freshwater crayfish have become one of the most widely introduced freshwater taxa globally. Crayfish introductions have not spared the African continent, which, apart from Madagascar, is naturally devoid of native freshwater crayfish. These introductions are of concern because invasive crayfish have generally been shown to cause strong impacts on recipient ecosystems outside Africa. This study therefore set out to compile up-to-date information regarding crayfish introductions in Africa, their pathways and distributions and to improve our understanding of the nature and magnitude of their environmental impacts. A systematic review revealed that nine crayfish species have been introduced into the continent with five of those, Astacus astacus, Cherax quadricarinatus, Faxonius limosus, Procambarus clarkii and Procambarus virginalis, having established naturalised populations in fourteen African countries (Chapter 2). The main driver of these crayfish introductions was to provide socio-economic benefits but there is limited evidence of success. The thesis further documents attempts made to address crayfish knowledge gaps in Africa, including standardisation of C. quadricarinatus sampling gear (Chapter 3), determination of the distribution of C. quadricarinatus in the recently invaded Upper Zambezi Basin (Chapter 4), and predicting ecological and socioeconomic impacts of two crayfish species that are spreading rapidly in Southern Africa, namely, C. quadricarinatus and P. clarkii (Chapters 5 – 8). To standardise C. quadricarinatus sampling methods in Africa, two methods used in Southern Africa were compared and the Promar® collapsible trap baited with dry pellets was recommended as the best approach for C. quadricarinatus abundance studies due to the high catch per unit effort (CPUE), probability of capture and the suitability of dry dog food as a standard bait. This standard approach was used for crayfish surveys in the Zambezi Basin to comprehensively determine the spread and establishment of C. quadricarinatus across the basin. The establishment of C. quadricarinatus in the Barotse Floodplain, Upper Zambezi Floodplains freshwater ecoregion was confirmed. Although the probability of capture and catch per unit effort (CPUE) of C. quadricarinatus in the Barotse floodplain were similar to that of older invasions in the basin (Lake Kariba and Kafue River), morphometric differences among C. quadricarinatus populations sampled from these invaded regions were detected. Although crayfish were not detected in other regions, for example, the Okavango Floodplains ecoregions, C. quadricarinatus have the potential to spread at a downstream and upstream rate of 49 and 12 km·year-1, impacting native biota therein. To evaluate the potential for ecological impacts, the consumer-resource dynamics of C. quadricarinatus and P. clarkii were described in comparison to a native trophic analogue, the freshwater crab of the Potamonautes genus, preying on various native taxa ubiquitous to African aquatic and terrestrial ecosystems. The use of functional response (FR) and consumption experiments in this study showed the potential impacts of the two crayfish species on native resources and on resources that support livelihoods in invaded ecosystems. This in most cases was a result of their high attack parameter, which also resulted in high functional responses ratios (FRRs) compared to native crabs. The crayfish FR, FRRs and consumption rates were mostly enhanced under the high temperature treatments. The FRs and consumption results were then combined with the field biomasses of crayfish and crabs to calculate the relative impact potential (RIP) to successfully predict the degree of impact caused by crayfish species relative to crabs. Crayfish species consistently displayed RIP scores > 1 relative to the native crab irrespective of region, which were higher for the summer than the winter season, suggesting greater impact of the invaders compared to the native species. This study further estimated the socioeconomic losses due to catch spoilage by C. quadricarinatus which are up to 1500 t per year in the invaded Kafue River Basin, which translates to an annual income loss of US$ 2 million. Information provided in this study is vital for conservation management and to compel policymakers to develop appropriate conservation management tools within regulatory frameworks, which could stop or minimise the spread of crayfish species and protect Africa from further losing aquatic biodiversity.

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Glutathione as a suitable biomarker in hepatopancreas, gills and muscle of three freshwater crayfish species

Archives of Biological Sciences ◽

10.2298/abs0801059k ◽

2008 ◽

Vol 60 (1) ◽

pp. 59-66 ◽

Cited By ~ 17

Author(s):

Tijana Kovacevic ◽

Slavica Borkovic ◽

S.Z. Pavlovic ◽

Svetlana Despotovic ◽

Zorica Saicic

Keyword(s):

Redox Status ◽

Danube River ◽

Freshwater Crayfish ◽

Total Glutathione ◽

Orconectes Limosus ◽

Noble Crayfish ◽

Stone Crayfish ◽

Morava River ◽

Glutathione Redox ◽

Crayfish Species

We determined the contents of total glutathione (tGSH), reduced glutathione (GSH), and oxidized glutathione (GSSG) and values of the glutathione redox index (GSH RI) in hepatopancreas, gills, and muscle of three freshwater crayfish species: noble crayfish (Astacus astacus) from the Southern Morava River, stone crayfish (Austropotamobius torrentium) from the Krajkovacka River, and spinycheek crayfish (Orconectes limosus) from the Danube River. The obtained data show strong tissue and species specifity of investigated parameters: tGSH, GSH, GSSG, and GSH RI in the hepatopancreas, gills, and muscle of the indicated crayfish species. Our work represents the first study of its kind and showed that the investigated parameters can be considered suitable biomarkers of the cellular glutathione redox status in of freshwater crayfish species.

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Crayfish arts: an evaluation into the efficacy of artificial refuge traps for monitoring lotic white-clawed crayfish Austropotamobius pallipes (Lereboullet, 1858) (Decapoda, Astacidae) populations

Crustaceana ◽

10.1163/15685403-00003772 ◽

2018 ◽

Vol 91 (3) ◽

pp. 297-309 ◽

Cited By ~ 1

Author(s):

James O’Connor ◽

Sakinah Brennan ◽

Jan-Robert Baars

Keyword(s):

Population Studies ◽

Sampling Effort ◽

Irish Population ◽

Effective Technique ◽

Austropotamobius Pallipes ◽

Population Structures ◽

Capture Method ◽

Crayfish Population ◽

Capture Techniques ◽

Crayfish Species

White-clawed crayfishAustropotamobius pallipes(Lereboullet, 1858) are one of five crayfish species indigenous to Europe, and the only crayfish species to occur in Ireland. With no known invasive species posing a risk, the Irish population is of considerable conservation importance, particularly in a European context. While there are a number of capture techniques described for crayfish population studies, many have a number of limitations associated with them. There is a need therefore to evaluate new and emerging techniques, so as to assess their efficacy for monitoringA. pallipespopulations. Artificial refuge traps (ARTs), an alternative passive capture method, were evaluated against three other widely used capture techniques during the summer months of 2015. Results indicate ARTs to be an effective technique for sampling crayfish, and suggest that, in combination with other capture methods, ARTs could depict accurate population structures, and reduce some of the sampling effort and bias associated with crayfish monitoring.

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Predicting harvest of non-native signal crayfish in lakes — a role for changing climate?

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2015-0241 ◽

2016 ◽

Vol 73 (5) ◽

pp. 785-792 ◽

Cited By ~ 3

Author(s):

Patrik Bohman ◽

Lennart Edsman ◽

Alfred Sandström ◽

Per Nyström ◽

Marika Stenberg ◽

...

Keyword(s):

Population Dynamics ◽

Water Temperature ◽

Temperature Data ◽

Adult Survival ◽

Winter Mortality ◽

Freshwater Crayfish ◽

Catch Per Unit Effort ◽

Signal Crayfish ◽

Cool Water ◽

Air Temperatures

The signal crayfish (Pacifastacus leniusculus) was introduced to Sweden in 1960, and it has a high commercial and recreational value, but it may also have negative effects on native ecosystems. To better predict how climate warming will affect population dynamics of this cool-water crayfish, we explored the role of temperature and density dependence as explanatory factors of the subsequent years’ catch rates of commercially sized signal crayfish in four Swedish lakes. We found air temperatures to be good proxies for water temperatures in all lakes, except during winter. We could only obtain water temperature data for Lake Vättern, and winter temperature data were therefore only included in the analysis of catch-per-unit-effort patterns in this lake. Our results indicate that increasing mean air temperatures will potentially affect the population dynamics of cool-water freshwater crayfish species such as the signal crayfish. Based on data from four lakes, it seems that the population dynamics of signal crayfish are lake-specific and could be affected by either recruitment during the juvenile stage, the survival and growth of adults, or both. Increased fluctuations in water temperature during winter may potentially influence adult survival. To better predict the effects of global warming on the dynamics of cool-water crayfish populations, we suggest that future studies should investigate recruitment in crayfish along temperature gradients and the influence of variations in water temperature on winter mortality.

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Evidence for multiple paternity in two species of Orconectes crayfish

Canadian Journal of Zoology ◽

10.1139/cjz-2014-0132 ◽

2014 ◽

Vol 92 (11) ◽

pp. 985-988 ◽

Cited By ~ 6

Author(s):

A.F. Kahrl ◽

R.H. Laushman ◽

A.J. Roles

Keyword(s):

Genetic Variation ◽

Life History ◽

Multiple Mating ◽

Natural Populations ◽

Multiple Paternity ◽

The Body ◽

Freshwater Crayfish ◽

Decapod Crustaceans ◽

Freshwater Habitats ◽

Crayfish Species

Multiple mating is expected to be common in organisms that produce large clutches as a mechanism by which sexual reproduction can enrich genetic variation. For freshwater crayfish, observation of multiple mating suggests the potential for high rates of multiple paternity, but genetic confirmation is largely lacking from natural populations. We studied paternity within wild-caught broods of two crayfish species in the genus Orconectes (Sanborn’s crayfish (Orconectes sanbornii (Faxon, 1884)) and the Allegheny crayfish (Orconectes obscurus (Hagen, 1870))). Although females have been observed mating with multiple males, this is the first genetic confirmation of multiple paternity in broods of these two species. Berried females were collected in the field and maintained in aquaria until their eggs hatched. We amplified and genotyped extracted DNA from maternal and hatchling tissue for several microsatellite loci. For both species, paternity reconstruction (GERUD 2.0) yielded 2–3 sires per brood and no single paternity clutches. We discuss these results from natural populations in light of the body of work on reproductive ecology of decapod crustaceans and in the context of changes in life history following the transition from marine to freshwater habitats.

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Airborne environmental DNA metabarcoding detects more diversity, with less sampling effort, than a traditional plant community survey

BMC Ecology and Evolution ◽

10.1186/s12862-021-01947-x ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Mark D. Johnson ◽

Mohamed Fokar ◽

Robert D. Cox ◽

Matthew A. Barnes

Keyword(s):

Plant Community ◽

Plant Communities ◽

Traditional Method ◽

Environmental Dna ◽

Single Species ◽

Community Survey ◽

Sampling Effort ◽

Sampling Campaign ◽

Dna Metabarcoding ◽

Human Health Impacts

Abstract Background Airborne environmental DNA (eDNA) research is an emerging field that focuses on the detection of species from their genetic remnants in the air. The majority of studies into airborne eDNA of plants has until now either focused on single species detection, specifically only pollen, or human health impacts, with no previous studies surveying an entire plant community through metabarcoding. We therefore conducted an airborne eDNA metabarcoding survey and compared the results to a traditional plant community survey. Results Over the course of a year, we conducted two traditional transect-based visual plant surveys alongside an airborne eDNA sampling campaign on a short-grass rangeland. We found that airborne eDNA detected more species than the traditional surveying method, although the types of species detected varied based on the method used. Airborne eDNA detected more grasses and forbs with less showy flowers, while the traditional method detected fewer grasses but also detected rarer forbs with large showy flowers. Additionally, we found the airborne eDNA metabarcoding survey required less sampling effort in terms of the time needed to conduct a survey and was able to detect more invasive species than the traditional method. Conclusions Overall, we have demonstrated that airborne eDNA can act as a sensitive and efficient plant community surveying method. Airborne eDNA surveillance has the potential to revolutionize the way plant communities are monitored in general, track changes in plant communities due to climate change and disturbances, and assist with the monitoring of invasive and endangered species.

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