scholarly journals Seasonal variation in environmental DNA detection in sediment and water samples

PLoS ONE ◽  
2018 ◽  
Vol 13 (1) ◽  
pp. e0191737 ◽  
Author(s):  
Andrew S. Buxton ◽  
Jim J. Groombridge ◽  
Richard A. Griffiths
Keyword(s):  
Seasonal Variation ◽  
Water Samples ◽  
Dna Detection ◽  
Environmental Dna

Laboratory experiments for the detection of environmental DNA of crayfish: Examining the potential

2015 ◽  
Vol 21 (1) ◽  
pp. 159-163 ◽  
Author(s):  
Chester R. Figiel ◽  
Sandra Bohn
Keyword(s):  
Water Samples ◽  
Dna Detection ◽  
Environmental Dna ◽  
Sampling Period ◽  
Sediment Samples ◽  
Target Dna ◽  
Invasive Crayfish ◽  
In The Wild ◽  
Species Specific ◽  
Crayfish Species

Abstract We examined methods for detecting environmental DNA of the invasive white river crayfish Procambarus zonangulus. In a laboratory experiment, we investigated detection capability in benthic sediment samples and in water samples in six flow-through tanks. Additionally we determined whether crayfish density (low = 0.67 or high = 2.69 crayfish·m-2) or crayfish time in tanks influenced DNA detectability (collection of samples on Days 2, 5, 8 and 15). Species-specific primers and probes were designed for P. zonangulus and their specificity was tested against other crayfish species. Limits of detection and quantification were specified for the target DNA sequence by means of quantitative PCR amplifications on dilution series of known amounts of P. zonangulus DNA. We detected crayfish DNA in 14 of the 24 benthic sediment samples and in two of the 24 water samples. DNA detection was found in benthic sediment samples in at least two tanks at every sampling period, while DNA detection was found in water samples only on Day 8. Crayfish DNA was detected in benthic sediment and water samples independently of crayfish density. Crayfish at both densities were observed to ‘explore’ all areas of the tank and move irrespective of diurnal time or conspecific presence. These behavior patterns were observed throughout the 15 day experiment and likely resulted in the positive detections, especially in benthic sediment samples. We believe that these methods could benefit monitoring of invasive crayfish species, although there is no doubt that further optimization and more research is needed to evaluate these techniques in the wild.

scholarly journals Effects of preservation strategies on environmental DNA detection and quantification using ddPCR

2021 ◽  
Author(s):  
Quentin Mauvisseau ◽  
David Halfmaerten ◽  
Sabrina Neyrinck ◽  
Alfred Burian ◽  
Rein Brys
Keyword(s):  
Dna Detection ◽  
Environmental Dna ◽  
Detection And Quantification

scholarly journals Hydrogeochemistry and surface water quality assessment of IB valley coalfield area, India

2021 ◽  
Vol 11 (9) ◽  
Author(s):  
Bishnu Prasad Sahoo ◽  
Himanshu Bhushan Sahu ◽  
Dhruti Sundar Pradhan
Keyword(s):  
Water Quality ◽  
Heavy Metal ◽  
Seasonal Variation ◽  
Surface Water ◽  
Water Samples ◽  
Nickel Aluminum ◽  
Acid Mine ◽  
Significant Seasonal Variation ◽  
Cadmium Selenium ◽  
High Degree

AbstractCoal mining and ancillary activities have the potential to cause water pollution characterized by acid mine drainage, acid mine leachates, extreme pH conditions and heavy metal contaminations. In the present work, 33 water samples in premonsoon and 34 water samples in monsoon were collected from the surface water bodies of Ib Valley coalfield, India for hydrogeochemical analysis. In premonsoon, pH, TSS, Turbidity, DO, BOD, COD, Magnesium, Cadmium, Selenium, Nickel, Aluminum and in monsoon, pH, TSS, Turbidity, DO, BOD, COD, Iron, Cadmium, Selenium, Nickel and Aluminum were nonconforming to the permissible limit set by the Bureau of Indian Standards, World Health Organisation and Ministry of Environment, Forest and Climate Change, Government of India. The average BOD/COD ratio of less than 0.6 in both seasons indicated Ib valley coalfield water was not fairly biodegradable. The analysis of variance (ANOVA) revealed that significant seasonal variation (p < 0.05) was observed in the hydro-chemical parameters viz. TSS, turbidity, redox potential, acidity, total hardness, bicarbonate alkalinity, chloride, sulfate, nitrate, sodium, calcium, magnesium, iron, cadmium, chromium and magnesium during the entire sampling period. Whereas, no significant seasonal variation (p > 0.05) was observed in pH, EC, TDS, DO, BOD, residual chlorine, COD, oil and grease, fluoride, potassium, zinc, copper, selenium, nickel, aluminum, boron, silica, temperature, salinity, cyanide and phenol. Water Quality Index revealed that 39.39% and 35.29% samples belong to poor water quality category in premonsoon and monsoon, respectively. As per Heavy Metal Pollution Index, Degree of Contamination (Cd) and Heavy metal evaluation index, medium degree of pollution were exhibited by 51.52%, 30.30% and 45.45% samples in premonsoon and 20.59%, 35.29% and 26.47% samples in monsoon. Whereas, 5.88%, 2.94% and 5.88% samples were having high degree of pollution in monsoon and 15.15% samples caused high degree of pollution with respect to Cd in premonsoon. However, EC, Na%, PI, SAR and RSC values suggested that the water can be used for irrigation. Water type of the region had been found to be Ca–Mg–Cl–SO4 by Piper diagram.

scholarly journals Physico-chemical attributes of water of Hakaluki Haor, Sylhet, Bangladesh

2016 ◽  
Vol 3 (2) ◽  
pp. 67-72
Author(s):  
Md Tajul Islam ◽  
M Mahfuzur Rahman ◽  
Hassan Mahmud
Keyword(s):  
Water Quality ◽  
Seasonal Variation ◽  
Water Samples ◽  
Water Quality Assessment ◽  
Inorganic Pollutants ◽  
Chemical Parameters ◽  
Ph Values ◽  
Physico Chemical ◽  
Significant Seasonal Variation ◽  
Chemical Attributes

Water quality assessment has been carried out in the Hakaluki Haor of greater Sylhet district during May, 2013 to February, 2014. Water samples were collected from 5 spots during 4 seasons and a total of 15 physico-chemical parameters were studied. Significant seasonal variation was observed in all seasons among physico-chemical parameters. pH values varied from 5.9 - 7.1, water temperature varied from 23.7 – 26.7OC, transference varied from 23-53 cm, TSS varied from 18.1-192 mg/l, TDS varied 25-193.5 mg/l, EC varied from 30-680 ?s/cm , DO content of water varied from 4.6 - 5.6mg/l, BOD varied from 0.2-2.614 mg/l, COD varied from 38-312 mg/l, NO3-N varied from 0.1-30.4 mg/l, NH3 varied from 0.9-2.18 mg/l, alkalinity varied from 12-42 mg/l and PO4 varied from 0.9 -13.4 (mg/l). Agricultural and inorganic pollutants have been observed as the main causes of the Haor water pollution.Jahangirnagar University J. Biol. Sci. 3(2): 67-72, 2014 (December)

scholarly journals A Simple Technique for the Identification of Environmental DNA (eDNA ) in the Water Samples

2021 ◽  
pp. 77-80
Author(s):  
Chitra K. Y.
Keyword(s):  
Water Samples ◽  
Large Scale ◽  
Dna Isolation ◽  
Simple Technique ◽  
Environmental Dna ◽  
Water Bodies ◽  
Easy Method ◽  
Selective Staining ◽  
Generation Sequencing ◽  
Dark Pink

The environmental DNA(eDNA) is the DNA that is shed by the organisms in their environment by different ways viz. , mucous, faeces, skin, eggs, sperms and also when these organisms die due to natural death or disease. The eDNA will persist for several days. Identification of eDNA is a useful method of determining the organisms present in an aquatic environment like amphibians, reptiles, fishes , insects and larval forms of some of these organisms. By analysing the e-DNA it is possible to monitor the species distribution in water bodies like lakes and ponds simply by collecting a sample of water. The technique can be applied for the survey of the water bodies on a large scale for the genomic, taxonomic as well as pollutional studies. The DNA isolation procedures that are available are laborious and time consuming. Therefore, during the present study, a simplified method was devised i. e. , isolation of eDNA with ethanol after which Feulgen stain was applied to identify and confirm it, as it is an easy method before proceeding to work with the isolated eDNA using other techniqnies for further studies. The Feulgen method is used for the selective staining and the localisation of the DNA in the tissues but is adopted during the present study for the water samples for quick identification of eDNA. The smear of eDNA stained with Feulgen showed dark pink or magenta colour under the microscope where it was concentrated but stained lightly when dispersed and fragmented as observed in the present study. Further studies of the isolated eDNA are in progress in our laboratory for quantifying and sequencing eDNA using latest techniques like next generation sequencing for the identification of fish species in the lakes.

scholarly journals Environmental DNA (eDNA) metabarcoding surveys extend the range of invasion for non-indigenous freshwater species in Eastern Europe.

2021 ◽  
Author(s):  
Gert-Jan Jeunen ◽  
Tatsiana Lipinskaya ◽  
Helen Gajduchenko ◽  
Viktoriya Golovenchik ◽  
Michail Moroz ◽  
...  
Keyword(s):  
Surface Water ◽  
Water Samples ◽  
False Negative ◽  
Simultaneous Detection ◽  
Environmental Dna ◽  
Reference Database ◽  
Indigenous Species ◽  
Freshwater Species ◽  
Traditional Approaches ◽  
Surface Water Samples

Active environmental DNA (eDNA) surveillance through species-specific amplification has shown increased sensitivity in the detection of non-indigenous species (NIS) compared to traditional approaches. When many NIS are of interest, however, active surveillance decreases in cost- and time-efficiency. Passive surveillance through eDNA metabarcoding takes advantage of the complex DNA signal in environmental samples and facilitates the simultaneous detection of multiple species. While passive eDNA surveillance has previously detected NIS, comparative studies are essential to determine the ability of eDNA metabarcoding to accurately describe the range of invasion for multiple NIS versus alternative approaches. Here, we surveyed twelve sites, covering nine rivers across Belarus for NIS with three different techniques, i.e., an ichthyological, hydrobiological, and eDNA survey, whereby DNA was extracted from 500 mL surface water samples and amplified with two 16S rRNA primer assays targeting the fish and macro-invertebrate biodiversity. Nine non-indigenous fish and ten non-indigenous sediment-living macro-invertebrates were detected by traditional surveys, while seven NIS eDNA signals were picked up, including four fish, one aquatic and two sediment-living macro-invertebrates. Passive eDNA surveillance extended the range of invasion further north for two invasive fish and identified a new NIS for Belarus, the freshwater jellyfish Craspedacusta sowerbii. False-negative detections for the eDNA survey could be attributed to (i) preferential amplification of aquatic over sediment-living macro-invertebrates from surface water samples and (ii) an incomplete reference database. The evidence provided in this study recommends the implementation of both molecular-based and traditional approaches to maximize the probability of early detection of non-native organisms.

scholarly journals Detection of fish pathogen Saprolegnia parasitica in environmental DNA samples by droplet digital PCR

2021 ◽  
Vol 4 ◽  
Author(s):  
Dora Pavić ◽  
Anđela Miljanović ◽  
Uršula Prosenc-Zmrzljak ◽  
Rok Košir ◽  
Dorotea Grbin ◽  
...  
Keyword(s):  
Water Samples ◽  
Genomic Dna ◽  
Environmental Dna ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Economic Losses ◽  
Internal Transcribed Spacer Region ◽  
Saprolegnia Parasitica ◽  
Oomycete Pathogen ◽  
Total Dna

Oomycetes are fungal-like microorganisms parasitic towards a large number of plant and animal species. Genera from order Saprolegniales, such as Saprolegnia and Aphanomyces, cause devastating infections of freshwater animals. Saprolegnia parasitica is a widely distributed oomycete pathogen that causes saprolegniosis, a disease responsible for significant economic losses in aquaculture, as well as declines of natural populations of fish and other freshwater organisms. Despite its negative impact, no monitoring protocol for S. parasitica has been established to date. Thus, we aimed to develop a droplet digital PCR (ddPCR) assay for the detection and quantification of S. parasitica in environmental DNA samples. Saprolegnia parasitica-specific primers were designed to target internal transcribed spacer region 2 (ITS 2), based on the alignment of ITS sequences of S. parasitica and a range of Saprolegnia spp., as well as other oomycetes. The specificity of primers was tested using genomic DNA of S. parasitica (as positive control) and DNA of non–S. parasitica oomycete isolates, as well as trout/crayfish DNA (as negative control). The primers specifically amplified a segment of the ITS region of oomycete pathogen S. parasitica, while no amplification (i.e. no positive droplets) was obtained for closely related Saprolegnia spp. (e.g. Saprolegnia sp. 1 and S. ferax) and other more distantly related oomycetes. Next, the limit of detection (LOD) of the assay was established by using serial dilutions of the S. parasitica genomic DNA. The determined sensitivity of the assay was high: LOD was 15 fg of pathogen’s genomic DNA per µL of the reaction mixture. Assay performance was further assessed with environmental DNA samples isolated from water from the trout farms and natural environments, as well as (ii) biofilm from the host surface (swab samples). Water samples were collected from 21 different locations in Croatia, while swab samples were collected from S. parasitica host/carrier species: (i) skin and eggs of the rainbow trout (Oncorhynchus mykiss Walbaum, 1792) and brown trout (Salmo trutta Linnaeus, 1758), and (ii) cuticle of signal crayfish (Pacifastacus leniusculus Dana, 1852) and narrow clawed crayfish (Pontastacus leptodactylus Eschscholtz, 1823). Samples were classified into agent levels A0 to A6, depending of the number of S. parasitica ITS copies per ng of total DNA. Saprolegnia parasitica was detected in 76 % of water samples (16/21) and the range of pathogen’s ITS copies in positive samples was between 0.02 and 14 copies/ng of total DNA (agent levels A1 to A3). Regarding the swab samples, S. parasitica load was significantly higher in diseased trout than in those with healthy appearance: 9375 vs 3.28 S. parasitica copies/ng of total swab DNA (average agent level A6 vs. A2, respectively). Despite the fact that none of the sampled crayfish had signs of infection, the pathogen was detected in all tested cuticle swabs. Swabs of P. leniusculus, a known S. parasitica host, had significantly higher S. parasitica load than swabs of P. leptodactylus, S. parasitica carrier: 390 vs 83 S. parasitica copies/ng (agent level A5 vs. A4, respectively). In conclusion, our results demonstrate the applicability of the newly developed ddPCR assay in monitoring and early detection of S. parasitica in aquaculture facilities and natural freshwater environments. This would help in a better understanding of S. parasitica ecology and its effects on the host populations.

scholarly journals A non-lethal method for detection of Bonamia ostreae in flat oyster (Ostrea edulis) using environmental DNA

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Louise von Gersdorff Jørgensen ◽  
Johan Wedel Nielsen ◽  
Mikkel Kehler Villadsen ◽  
Bent Vismann ◽  
Sussie Dalvin ◽  
...  
Keyword(s):  
Water Samples ◽  
Sea Water ◽  
Diagnostic Technique ◽  
Environmental Dna ◽  
Detection Methods ◽  
Ostrea Edulis ◽  
Breeding Programs ◽  
Bonamia Ostreae ◽  
Flat Oyster ◽  
Selection Of

Abstract Surveillance and diagnosis of parasitic Bonamia ostreae infections in flat oysters (Ostrea edulis) are prerequisites for protection and management of wild populations. In addition, reliable and non-lethal detection methods are required for selection of healthy brood oysters in aquaculture productions. Here we present a non-lethal diagnostic technique based on environmental DNA (eDNA) from water samples and demonstrate applications in laboratory trials. Forty oysters originating from Limfjorden, Denmark were kept in 30 ppt sea water in individual tanks. Water was sampled 6 days later, after which all oysters were euthanized and examined for infection, applying PCR. Four oysters (10%) were found to be infected with B. ostreae in gill and mantle tissue. eDNA purified from the water surrounding these oysters contained parasite DNA. A subsequent sampling from the field encompassed 20 oysters and 15 water samples from 5 different locations. Only one oyster turned out positive and all water samples proved negative for B. ostreae eDNA. With this new method B. ostreae may be detected by only sampling water from the environment of isolated oysters or isolated oyster populations. This non-lethal diagnostic eDNA method could have potential for future surveys and oyster breeding programs aiming at producing disease-free oysters.

scholarly journals Development of a quantitative PCR assay for detection of redside shiner (Richardsonius balteatus) from environmental DNA

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Marshal S. Hoy ◽  
Carl O. Ostberg
Keyword(s):  
Quantitative Pcr ◽  
Water Samples ◽  
Effective Means ◽  
Environmental Dna ◽  
Sympatric Species ◽  
Negative Control ◽  
Control Site ◽  
Qpcr Assay ◽  
Redside Shiner ◽  
Richardsonius Balteatus

Abstract Objective A quantitative PCR (qPCR) assay for the detection of redside shiner (Richardsonius balteatus) environmental DNA (eDNA) was designed as a side product of a larger project aimed at using eDNA to determine the presence and geographic extent of native and non-native fishes in the reservoirs and associated tributaries above the three mainstem dams (Ross, Diablo, Gorge) on the Skagit River, Washington, USA. The eDNA survey results can be used to help guide additional sampling efforts that include traditional sampling methods, such as electrofishing and netting. Results The redside shiner qPCR assay (RSSCOI_540-601) was validated by testing for sensitivity using redside shiner genomic DNA from three different populations and by testing for specificity against 30 potentially sympatric species. No non-target amplification was observed in our validation tests. We then evaluated the assay on field-collected water samples where there are known populations of redside shiner and a negative control site where the target species is known to be absent. The field-collected water samples tested positive at the redside shiner sites and tested negative at the negative control site. The assay could provide resource managers with an effective means for surveying and monitoring redside shiner populations.

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