scholarly journals The amount of environmental DNA increases with freshwater crayfish density and over time

2021 ◽  
Author(s):  
Daniela Sint ◽  
Bernhard Kolp ◽  
Oskar Rennstam Rubbmark ◽  
Leopold Füreder ◽  
Michael Traugott
Keyword(s):  
Environmental Dna ◽  
Freshwater Crayfish ◽  
Over Time

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

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.

scholarly journals Molecular Analysis of Shower Curtain Biofilm Microbes

2004 ◽  
Vol 70 (7) ◽  
pp. 4187-4192 ◽  
Author(s):  
Scott T. Kelley ◽  
Ulrike Theisen ◽  
Largus T. Angenent ◽  
Allison St. Amand ◽  
Norman R. Pace
Keyword(s):  
Microbial Communities ◽  
Biofilm Formation ◽  
Environmental Dna ◽  
Rrna Genes ◽  
Opportunistic Pathogens ◽  
Microbial Biofilms ◽  
Potential Source ◽  
Household Environment ◽  
Soap Scum ◽  
Over Time

ABSTRACT Households provide environments that encourage the formation of microbial communities, often as biofilms. Such biofilms constitute potential reservoirs for pathogens, particularly for immune-compromised individuals. One household environment that potentially accumulates microbial biofilms is that provided by vinyl shower curtains. Over time, vinyl shower curtains accumulate films, commonly referred to as “soap scum,” which microscopy reveals are constituted of lush microbial biofilms. To determine the kinds of microbes that constitute shower curtain biofilms and thereby to identify potential opportunistic pathogens, we conducted an analysis of rRNA genes obtained by PCR from four vinyl shower curtains from different households. Each of the shower curtain communities was highly complex. No sequence was identical to one in the databases, and no identical sequences were encountered in the different communities. However, the sequences generally represented similar phylogenetic kinds of organisms. Particularly abundant sequences represented members of the α-group of proteobacteria, mainly Sphingomonas spp. and Methylobacterium spp. Both of these genera are known to include opportunistic pathogens, and several of the sequences obtained from the environmental DNA samples were closely related to known pathogens. Such organisms have also been linked to biofilm formation associated with water reservoirs and conduits. In addition, the study detected many other kinds of organisms at lower abundances. These results show that shower curtains are a potential source of opportunistic pathogens associated with biofilms. Frequent cleaning or disposal of shower curtains is indicated, particularly in households with immune-compromised individuals.

scholarly journals The amount of environmental DNA increases with freshwater crayfish density and over time

2021 ◽  
Vol 4 ◽  
Author(s):  
Corinna Wallinger ◽  
Daniela Sint ◽  
Bernhard Kolp ◽  
Leopold Füreder ◽  
Michael Traugott
Keyword(s):  
Invasive Species ◽  
Native Species ◽  
Laboratory Experiments ◽  
High Sensitivity ◽  
Environmental Dna ◽  
Freshwater Crayfish ◽  
Population Densities ◽  
Non Invasive ◽  
Crayfish Population ◽  
The Relationship

eDNA analysis is ideally suited to monitor the occurrence of endangered or invasive species because of its non-invasive nature and high sensitivity. European freshwater crayfish are threatened across the whole continent. Classical crayfish monitoring is challenging and time consuming due to their nocturnal activity and hidden lifestyle. Therefore, eDNA-based monitoring of native as well as invasive species seems to be of great benefit for the conservation of the native species and it has indeed been increasingly applied in recent years. Nevertheless, comparably little is known on the relationship between eDNA concentration and crayfish population densities, a prerequisite for estimating population size based on eDNA measurements. Here, we performed laboratory experiments to investigate the relationship between the concentration of crayfish eDNA and population densities - measured as crayfish size and biomass. There was a strong correlation between the two measurements. Moreover, the amount of eDNA increased at least during the first three days after crayfish stocking in the aquarium. The experiments also indicate, that crayfish activity might have a strong influence on the eDNA signal strength. Our findings will significantly contribute to an optimization of the monitoring of freshwater crayfish via the analysis of eDNA and therefore be important for the conservation of these threatened species.

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

2020 ◽  
Vol 8 ◽  
Author(s):  
Stein I. Johnsen ◽  
David A. Strand ◽  
Johannes C. Rusch ◽  
Trude Vrålstad
Keyword(s):  
Relative Density ◽  
Environmental Dna ◽  
Sampling Effort ◽  
Freshwater Crayfish ◽  
Catch Per Unit Effort ◽  
Limit Of Quantification ◽  
Red Lists ◽  
Negative Results ◽  
Noble Crayfish ◽  
Crayfish Species

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.

scholarly journals No evidence that crayfish carcasses produce detectable environmental DNA (eDNA) in a stream enclosure experiment

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9333 ◽  
Author(s):  
Amanda N. Curtis ◽  
Eric R. Larson
Keyword(s):  
Procambarus Clarkii ◽  
Extraction Procedure ◽  
Poor Performance ◽  
Environmental Dna ◽  
Field Studies ◽  
Enclosure Experiment ◽  
Field Samples ◽  
Over Time ◽  
Imperiled Species

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.

scholarly journals Environmental DNA detection of the giant freshwater crayfish ( Astacopsis gouldi )

2021 ◽  
Author(s):  
Alejandro Trujillo‐Gonzalez ◽  
Rheyda Hinlo ◽  
Sam Godwin ◽  
Leon A. Barmuta ◽  
Anne Watson ◽  
...  
Keyword(s):  
Dna Detection ◽  
Environmental Dna ◽  
Freshwater Crayfish

Bloom Story: reconstructing historical cyanobacterial communities in six contrasting New Zealand lakes

2021 ◽  
Author(s):  
Maïlys Picard ◽  
Xavier Pochon ◽  
Andrew Rees ◽  
Jamie Howarth ◽  
Marc Schallenberg ◽  
...  
Keyword(s):  
New Zealand ◽  
Dna Analysis ◽  
Anthropogenic Activities ◽  
Sediment Cores ◽  
Geographic Location ◽  
Environmental Dna ◽  
Digital Pcr ◽  
Cyanobacterial Blooms ◽  
Key Drivers ◽  
Over Time

<p>Anthropogenic nutrient enrichment, hydrological modifications, and introduced species are contributing to an increase in the frequency and intensity of cyanobacterial blooms. This study aimed to document the evolution of cyanobacterial assemblages over time and explore the drivers of cyanobacterial blooms. Environmental DNA was extracted from sediment cores dating back approximately 1,000-years collected from six New Zealand lakes (Rotoehu, Pounui, Wairarapa, Paringa, Johnson, Hayes). Samples were analysed using cyanobacterial 16S rRNA metabarcoding and droplet digital PCR. Picocyanobacteria had the highest relative abundance. Marked shifts in species composition were observed over time but species varied between lakes. Marked shifts in total abundance (from ddPCR data) were observed through time in all lakes, and the metabarcoding data revealed these abundances to be bloom-forming taxa only in impacted lakes. Historical cyanobacterial communities seemed to be mostly influenced by anthropogenic activities and the geographic location of the lakes. Comparison with other paleolimnological proxies suggests land-use and non-native fish as key drivers in species and abundance shifts. Sedimentary environmental DNA analysis can complement traditional paleo-approaches, and provide novel information on microbial communities, and new insights into causes and consequences of cyanobacterial blooms.</p>

Social transmission bias and the cultural evolution of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
David Hirshleifer ◽  
Siew Hong Teoh
Keyword(s):  
Cultural Evolution ◽  
Social Transmission ◽  
Cognitive Approach ◽  
Economic Problems ◽  
Economic Attitudes ◽  
The Social ◽  
Economic Beliefs ◽  
Over Time

AbstractEvolved dispositions influence, but do not determine, how people think about economic problems. The evolutionary cognitive approach offers important insights but underweights the social transmission of ideas as a level of explanation. The need for asocialexplanation for the evolution of economic attitudes is evidenced, for example, by immense variations in folk-economic beliefs over time and across individuals.

Articulatory Generalization in Two Word-Medial, Ambisyllabic Contexts

1988 ◽  
Vol 19 (3) ◽  
pp. 251-258 ◽  
Author(s):  
Virginia I. Wolfe ◽  
Suzanne D. Blocker ◽  
Norma J. Prater
Keyword(s):  
Common View ◽  
Perceptual Salience ◽  
The Common ◽  
Unitary Concept ◽  
Over Time

Articulatory generalization of velar cognates /k/, /g/ in two phonologically disordered children was studied over time as a function of sequential word-morpheme position training. Although patterns of contextual acquisition differed, correct responses to the word-medial, inflected context (e.g., "picking," "hugging") occurred earlier and exceeded those to the word-medial, noninflected context (e.g., "bacon," "wagon"). This finding indicates that the common view of the word-medial position as a unitary concept is an oversimplification. Possible explanations for superior generalization to the word-medial, inflected position are discussed in terms of coarticulation, perceptual salience, and the representational integrity of the word.

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