scholarly journals Development of environmental DNA surveillance for the threatened crucian carp (Carassius carassius)

2018 ◽  
Author(s):  
Lynsey R Harper ◽  
Nathan P Griffiths ◽  
Lori Lawson Handley ◽  
Carl D Sayer ◽  
Daniel S Read ◽  
...  
Keyword(s):  
Copy Number ◽  
Crucian Carp ◽  
Abiotic Factors ◽  
Environmental Dna ◽  
Carassius Carassius ◽  
Catch Per Unit Effort ◽  
Dna Copy Number ◽  
Species Detection ◽  
Biotic And Abiotic Factors ◽  
Macrophyte Cover

The crucian carp (Carassius carassius) is one of few fish species associated with small ponds in the UK. These populations contain genetic diversity not found in Europe and are important to conservation efforts for the species, which has declined across its range. Detection and monitoring of extant crucian carp populations are crucial for conservation success. Environmental DNA (eDNA) analysis could be very useful in this respect as a rapid, cost-efficient monitoring tool. We developed a species-specific quantitative PCR (qPCR) assay for eDNA surveillance of crucian carp to enable non-invasive, large-scale distribution monitoring. We compared fyke netting and eDNA at ponds with (N = 10) and without (N = 10) crucian carp for presence-absence detection and relative abundance estimation, specifically whether DNA copy number reflected catch-per-unit-effort (CPUE) estimate. We examined biotic and abiotic influences on eDNA detection and quantification, and compared qPCR to standard PCR. Notably, eDNA occurrence and detection probabilities in relation to biotic and abiotic factors were estimated using a hierarchical occupancy model. eDNA analysis achieved 90% detection for crucian carp (N = 10), failing in only one pond where presence was known. We observed an overall positive trend between DNA copy number and CPUE estimate, but this was not significant. Macrophyte cover decreased the probability of eDNA occurrence at ponds, whereas CPUE and conductivity had positive and negative influences on eDNA detection probability in qPCR replicates respectively. Conductivity also had a negative effect on DNA copy number, but copy number increased with temperature and percentage of macrophyte cover. PCR was comparable to qPCR for species detection and may provide semi-quantitative information. Our results demonstrate that eDNA could enable detection of crucian carp populations in ponds and benefit ongoing conservation efforts, but imperfect species detection in relation to biotic and abiotic factors and eDNA workflow requires further investigation. Nonetheless, we have established an eDNA framework for crucian carp and sources of imperfect detection which future investigations can build upon.

scholarly journals Effect of biotic and abiotic factors on the production and degradation of fish environmental DNA: An experimental evaluation

2021 ◽  
Author(s):  
Isabeau Caza‐Allard ◽  
Martin Laporte ◽  
Guillaume Côté ◽  
Julien April ◽  
Louis Bernatchez
Keyword(s):  
Experimental Evaluation ◽  
Abiotic Factors ◽  
Environmental Dna ◽  
Biotic And Abiotic Factors

scholarly journals Development and application of environmental DNA surveillance for the threatened crucian carp (Carassius carassius )

2018 ◽  
Vol 64 (1) ◽  
pp. 93-107 ◽  
Author(s):  
Lynsey R. Harper ◽  
Nathan P. Griffiths ◽  
Lori Lawson Handley ◽  
Carl D. Sayer ◽  
Daniel S. Read ◽  
...  
Keyword(s):  
Crucian Carp ◽  
Environmental Dna ◽  
Carassius Carassius ◽  
Crucian Carp Carassius Carassius

scholarly journals Effects of Microbial Activity and Environmental Parameters on the Degradation of Extracellular Environmental DNA from a Eutrophic Lake

2019 ◽  
Vol 16 (18) ◽  
pp. 3339 ◽  
Author(s):  
Nur Syahidah Zulkefli ◽  
Keon-Hee Kim ◽  
Soon-Jin Hwang
Keyword(s):  
Microbial Activity ◽  
Degradation Rate ◽  
Abiotic Factors ◽  
Environmental Parameters ◽  
Environmental Dna ◽  
Eutrophic Lake ◽  
Freshwater Ecosystems ◽  
Extracellular Dna ◽  
Biotic And Abiotic Factors ◽  
Positive Effects

Extracellular DNA (exDNA) pool in aquatic environments is a valuable source for biomonitoring and bioassessment. However, degradation under particular environmental conditions can hamper exDNA detectability over time. In this study, we analyzed how different biotic and abiotic factors affect the degradation rate of extracellular environmental DNA using 16S rDNA sequences extracted from the sediment of a eutrophic lake and Anabaena variabilis cultured in the laboratory. We exposed the extracted exDNA to different levels of temperature, light, pH, and bacterial activity, and quantitatively analyzed the concentration of exDNA during 4 days. The solution containing bacteria for microbial activity treatment was obtained from the lake sediment using four consecutive steps of filtration; two mesh filters (100 μm and 60 μm mesh) and two glass fiber filters (2.7 μm and 1.2 μm pore-sized). We found that temperature individually and in combination with bacterial abundance had significant positive effects on the degradation of exDNA. The highest degradation rate was observed in samples exposed to high microbial activity, where exDNA was completely degraded within 1 day at a rate of 3.27 day−1. Light intensity and pH had no significant effects on degradation rate of exDNA. Our results indicate that degradation of exDNA in freshwater ecosystems is driven by the combination of both biotic and abiotic factors and it may occur very fast under particular conditions.

scholarly journals Factors related to age-0 native fish catch per unit effort in the South Dakota Missouri River reservoirs.

2020 ◽  
Author(s):  
William Radigan ◽  
Mark Fincel
Keyword(s):  
South Dakota ◽  
Fish Species ◽  
Native Species ◽  
Abiotic Factors ◽  
Missouri River ◽  
Native Fish ◽  
Catch Per Unit Effort ◽  
Biotic And Abiotic Factors ◽  
Emerald Shiner ◽  
Lewis And Clark

The Missouri River in South Dakota was dammed in the 1950s and 1960s, altering the biotic and abiotic factors that potentially affect native species in the mainstem reservoirs. Little research has been conducted regarding what factors regulate age-0 CPUE (catch per unit effort) of native fish species since the damming occurred. Thus, we examined age-0 CPUE for thirteen native fish species in the four Missouri River mainstem reservoirs. We analyzed data from 1995-2015 in Lake Oahe, 2002-2016 in Lake Sharpe, 1998-2008 in Lake Francis Case, and 2000-2013 in Lewis and Clark Lake. Not all species were sampled in all reservoirs. We evaluated potential environmental (inflow, gauge height, peak flow, precipitation, air temperature) and biological (CPUE of other native species, non-native CPUE, predator CPUE) factors that have documented impacts on age-0 native fish CPUE. Significant relationships existed between age-0 native fish CPUE and both biotic and abiotic factors in all four reservoirs, but specific factors related to native fish CPUE were species and reservoir dependent. For all species examined in all reservoirs except age-0 Emerald Shiner Notropis atherinoides CPUE in Lewis and Clark Lake, age-0 CPUE was either stable or increasing. Age-0 Emerald Shiner CPUE in Lewis and Clark Lake was most supported by total age-0 non-native CPUE and adult White Bass Morone chrysops CPUE, and a positive relationship existed between age-0 Emerald Shiner CPUE and both factors. We believe our findings provide valuable insight into successful management of native fish populations.

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