scholarly journals Influence of Preservation Methods, Sample Medium and Sampling Time on eDNA Recovery in a Neotropical River

2018 ◽  
Author(s):  
Naiara Guimarães Sales ◽  
Owen Simon Wangensteen ◽  
Daniel Cardoso Carvalho ◽  
Stefano Mariani
Keyword(s):  
Water Samples ◽  
Fish Assemblages ◽  
Environmental Dna ◽  
Cost Effective ◽  
Southeastern Brazil ◽  
Similar Amount ◽  
Biodiversity Monitoring ◽  
Sediment Samples ◽  
Preservation Methods ◽  
Sampling Event

ABSTRACTEnvironmental DNA (eDNA) has rapidly emerged as a promising biodiversity monitoring technique, proving to be a sensitive and cost-effective method for species detection. Despite the increasing popularity of eDNA, several questions regarding its limitations remain to be addressed. We investigated the effect of sampling medium and time, and preservation methods, on fish detection performance based on eDNA metabarcoding of neotropical freshwater samples. Water and sediment samples were collected from 11 sites along the Jequitinhonha River, Southeastern Brazil; sediment samples were stored in ethanol, while the same amounts of water per sample (3L) were stored in a cool box with ice, as well as by adding the cationic surfactant Benzalkonium chloride (BAC). Sediment and water samples yielded a similar amount of fish MOTUs (237 vs 239 in the first sampling event, and 153 vs 142 in the second sampling event). Water stored in ice provided better results than those preserved in BAC (239 and 142 vs 194 and 71 MOTUs). While documenting the effectiveness of eDNA surveys as practical tools for fish biodiversity monitoring in poorly accessible areas, we showed that keeping water samples cooled results in greater eDNA recovery and taxon detection than by adding cationic surfactants as sample preservatives. Furthermore, by comparing two sets of samples collected from the same locations at a three-week interval, we highlight the importance of conducting multiple sampling events when attempting to recover a realistic picture of fish assemblages in lotic systems.

An eDNA approach to detect eastern hellbenders (Cryptobranchus a. alleganiensis) using samples of water

2012 ◽  
Vol 39 (7) ◽  
pp. 629 ◽  
Author(s):  
Zachary H. Olson ◽  
Jeffrey T. Briggler ◽  
Rod N. Williams
Keyword(s):  
Water Samples ◽  
Effective Means ◽  
Environmental Dna ◽  
Cost Effective ◽  
Negative Control ◽  
Specificity And Sensitivity ◽  
Genetic Sampling ◽  
Conservation Concern ◽  
Species Specific ◽  
Eastern Hellbender

Context Environmental DNA, or eDNA, methods are a novel application of non-invasive genetic sampling in which DNA from organisms is detected via sampling of water or soil, typically for the purposes of determining the presence or absence of an organism. eDNA methods have the potential to revolutionise the study of rare or endangered taxa. Aims We evaluated the efficacy of eDNA sampling to detect populations of an amphibian of conservation concern, the eastern hellbender (Cryptobranchus a. alleganiensis), indirectly from their aquatic environments. Methods We developed species-specific primers, validated their specificity and sensitivity, and assessed the utility of our methods in silico and in laboratory trials. In the field, we collected water samples from three sites with known densities of hellbenders, and from one site where hellbenders do not occur. We filtered water samples, extracted DNA from filters, and assayed the extraction products for hellbender DNA by using polymerase chain reaction (PCR) and gel electrophoresis. Key results Our methods detected hellbenders at densities approaching the lowest of reported natural densities. The low-density site (0.16 hellbenders per 100 m2) yielded two positive amplifications, the medium-density site (0.38 hellbenders per 100 m2) yielded eight positive amplifications, and the high-density site (0.88 hellbenders per 100 m2) yielded 10 positive amplifications. The apparent relationship between density and detection was obfuscated when river discharge was considered. There was no amplification in any negative control. Conclusion eDNA methods may represent a cost-effective means by which to establish broad-scale patterns of occupancy for hellbenders. Implications eDNA can be considered a valuable tool for detecting many species that are otherwise difficult to study.

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 The current state of DNA barcoding of macroalgae in the Mediterranean Sea: presently lacking but urgently required

2020 ◽  
Vol 63 (3) ◽  
pp. 253-272 ◽  
Author(s):  
Angela G. Bartolo ◽  
Gabrielle Zammit ◽  
Akira F. Peters ◽  
Frithjof C. Küpper
Keyword(s):  
Mediterranean Sea ◽  
Dna Barcoding ◽  
Environmental Dna ◽  
Cost Effective ◽  
Indigenous Species ◽  
Biodiversity Monitoring ◽  
Current State ◽  
Dna Libraries ◽  
The Mediterranean ◽  
Non Indigenous Species

AbstractThis review article explores the state of DNA barcoding of macroalgae in the Mediterranean Sea. Data from the Barcode of Life Data System (BOLD) were utilised in conjunction with a thorough bibliographic review. Our findings indicate that from around 1124 records of algae in the Mediterranean Sea, only 114 species have been barcoded. We thus conclude that there are insufficient macroalgal genetic data from the Mediterranean and that this area would greatly benefit from studies involving DNA barcoding. Such research would contribute to resolving numerous questions about macroalgal systematics in the area and address queries related to biogeography, especially those concerned with non-indigenous species. It could also possibly result in the development and application of better, cost-effective biodiversity monitoring programmes emanating from UN conventions and EU Directives. One possible way of achieving this is to construct DNA libraries via sequencing and barcoding, subsequently enabling better cost-effective biodiversity monitoring through environmental DNA metabarcoding.

scholarly journals Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals:

2018 ◽  
Author(s):  
Allan D McDevitt ◽  
Naiara Guimaraes Sales ◽  
Samuel S Browett ◽  
Abbie Sparnenn ◽  
Stefano Mariani ◽  
...  
Keyword(s):  
Fish Assemblages ◽  
Fish Communities ◽  
Environmental Dna ◽  
Cost Effective ◽  
Aquatic Habitats ◽  
Dna Metabarcoding ◽  
Canal Systems ◽  
Rapid Tool ◽  
Fish Monitoring

Environmental DNA (eDNA) metabarcoding has revolutionized biomonitoring of aquatic habitats. Man-made canal systems are among the least-studied environments in terms of biodiversity in Britain. Here we focus on a case study along an English canal comparing eDNA metabarcoding with two types of electrofishing techniques (wade-and-reach and boom-boat). In addition to corroborating data obtained by electrofishing, eDNA provided a wider snapshot of fish assemblages. Given the semi-lotic nature of canals, we encourage the use of eDNA as a fast and cost-effective tool to detect and monitor whole fish communities.

ANALYSIS OF ACCUMULATION AND DISTRIBUTION OF LEAD IN THE SYSTEM WATER-BOTTOM SEDIMENTS IN THE BACH DANG ESTUARY (VIETNAM)

2017 ◽  
pp. 62-66
Author(s):  
Truong Van Tuan ◽  
Irina Vladimirovna Volkova
Keyword(s):  
Bottom Sediment ◽  
Bottom Sediments ◽  
Water Samples ◽  
Suspended Solids ◽  
Natural Habitat ◽  
Bottom Layer ◽  
Sediment Samples ◽  
Natural Breeding ◽  
System Water ◽  
Water Bottom

Research was held in the estuary of the river Bach Dang (Dongbay community, Rakhtay district, Hai Phong, Vietnam) in June, 2012 - May, 2013. Concentration of lead was studied in water, suspended solids and bottom sediment. Clam beach (natural breeding environment of Meretrix lyrata ) was inspected regularly, every month. Water samples were taken 6 times from the bottom layer 10 cm down the bottom, once per 3 hours in each of 12 investigated zones. Bottom sediment samples were taken at the depth 2 cm. The findings show that lead accumulates mainly in suspended solids (23.3 mg/kg) and in bottom sediment (14.31 mg/kg), in water it is in small quantities (0.003 mg/kg). Analysis of bottom sediment samples taken in different places showed that they have even leadcontent, lead is distributed uniformly, localization of contaminations is not found. The results obtained can be assumed as the basis for investigating lead accumulation and its excretion by clam Meretrix lyrata organisms in the natural habitat.

scholarly journals The Assessment of the Sewage and Sludge Contamination by Phthalate Acid Esters (PAEs) in Eastern Europe Countries

2021 ◽  
Vol 13 (2) ◽  
pp. 529
Author(s):  
Olga Anne ◽  
Tatjana Paulauskiene
Keyword(s):  
Water Samples ◽  
Raw Materials ◽  
Phthalate Esters ◽  
Gas Chromatography Mass Spectrometry ◽  
Sediment Samples ◽  
Toxicological Effects ◽  
Sources Of Pollution ◽  
Eastern European Countries ◽  
Acid Esters ◽  
Phthalate Acid Esters

Phthalate acid esters (PAEs) are widely used as raw materials for industries that are well known for their environmental contamination and toxicological effects as “endocrine disruptors”. The determining of PAE contamination was based on analysis of dimethyl phthalate (DMP), diethyl phthalate (DEP), dipropyl phthalate (DPP), dibutyl phthalate (DBP), diisobutyl phthalate (DiBP), dicyclohexyl phthalate (DCHP) and di(2-ethylhexyl) phthalate (DEHP) in wastewater and sediment samples collected from city sewer systems of Lithuania and Poland, and Denmark for comparison. The potential PAE sources as well as their concentrations in the wastewater were analyzed and discussed. The intention of the study was to determine the level and key sources of pollution by phthalates in some Eastern European countries and to reveal the successful managerial actions to minimize PAEs taken by Denmark. Water and sludge samples were collected in 2019–2020 and analyzed by gas chromatography-mass spectrometry. The highest contamination with phthalates in Lithuania can be attributed to DEHP: up to 63% of total PAEs in water samples and up to 94% of total PAEs in sludge samples, which are primarily used as additive compounds to plastics but do not react with them and are gradually released into the environment. However, in water samples in Poland, the highest concentration belonged to DMP—up to 210 μg/L, while the share of DEHP reached 15 μg/L. The concentrations of priority phthalate esters in the water samples reached up to 159 μg/L (DEHP) in Lithuania and up to 1.2 μg/L (DEHP) in Denmark. The biggest DEHP concentrations obtained in the sediment samples were 95 mg/kg in Lithuania and up to 6.6 mg/kg in Denmark. The dominant compounds of PAEs in water samples of Lithuania were DEHP > DEP > DiBP > DBP > DMP. DPP and DCHP concentrations were less than 0.05 μg/L. However, the distribution of PAEs in the water samples from Poland was as follows: DMP > DEHP > DEP > DBP, and DiBP, as well as DPP and DCHP, concentrations were less than 0.05 μg/L. Further studies are recommended for adequate monitoring of phthalates in wastewater and sludge in order to reduce or/and predict phthalates’ potential risk to hydrobiots and human health.

scholarly journals The effect of silica desiccation under different storage conditions on filter-immobilized environmental DNA

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Michael J. Allison ◽  
Jessica M. Round ◽  
Lauren C. Bergman ◽  
Ali Mirabzadeh ◽  
Heather Allen ◽  
...  
Keyword(s):  
Silica Gel ◽  
Storage Temperature ◽  
Environmental Dna ◽  
Cost Effective ◽  
Storage Conditions ◽  
Systematic Evaluation ◽  
Silica Bead ◽  
Gel Beads ◽  
Polymerase Chain

Abstract Objective Silica gel beads have promise as a non-toxic, cost-effective, portable method for storing environmental DNA (eDNA) immobilized on filter membranes. Consequently, many ecological surveys are turning to silica bead filter desiccation rather than ethanol preservation. However, no systematic evaluation of silica bead storage conditions or duration past 1 week has been published. The present study evaluates the quality of filter-immobilized eDNA desiccated with silica gel under different storage conditions for over a year using targeted quantitative real-time polymerase chain reaction (qPCR)-based assays. Results While the detection of relatively abundant eDNA target was stable over 15 months from either ethanol- or silica gel-preserved filters at − 20 and 4 °C, silica gel out-performed ethanol preservation at 23 °C by preventing a progressive decrease in eDNA sample quality. Silica gel filter desiccation preserved low abundance eDNA equally well up to 1 month regardless of storage temperature (18, 4, or − 20 °C). However only storage at − 20 °C prevented a noticeable decrease in detectability at 5 and 12 months. The results indicate that brief storage of eDNA filters with silica gel beads up to 1 month can be successfully accomplished at a range of temperatures. However, longer-term storage should be at − 20 °C to maximize sample integrity.

Biodiversity monitoring using environmental DNA

2021 ◽  
Author(s):  
Naiara Rodríguez‐Ezpeleta ◽  
Lucie Zinger ◽  
Andrew Kinziger ◽  
Holly M. Bik ◽  
Aurélie Bonin ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Biodiversity Monitoring

Mobile-phone-based colourimetric analysis for determining nitrite content in water

2018 ◽  
Vol 15 (7) ◽  
pp. 403 ◽  
Author(s):  
Chanida Puangpila ◽  
Jaroon Jakmunee ◽  
Somkid Pencharee ◽  
Wipada Pensrisirikul
Keyword(s):  
Mobile Phone ◽  
Water Samples ◽  
Diazonium Salt ◽  
Field Measurements ◽  
Cost Effective ◽  
Environmental Water ◽  
Sulfanilic Acid ◽  
Calibration Graph ◽  
Nitrite Ion ◽  
Griess Reaction

Environmental contextA widespread pollutant in groundwater, rivers and lakes is nitrite, which is commonly determined batchwise by using colourimetry. The batchwise method, however, requires relatively large and expensive instrumentation, and hence is unsuitable for in-field measurements. This work introduces a simple and portable colourimetric analyser based on a mobile-phone camera for monitoring nitrite concentrations in environmental water samples. AbstractA cost-effective and portable colourimetric analyser installed on a mobile phone was used to measure nitrite in water samples in Chiang Mai City, Thailand. The colourimetric detection was based on the Griess reaction, in which nitrite ion reacts with sulfanilic acid under acidic conditions to produce a diazonium salt that further reacts with N-(1-naphthyl)-ethylenediamine dihydrochloride to form a red–violet azo dye. Under controlled conditions using a light-tight box with LED flash lights, images of the red–violet solution were captured using a built-in camera and further analysed by a program, Panalysis, on the mobile phone. The calibration graph was created by measuring the red colour intensity of a series of standard nitrite solutions from 0.09–1.8 mg N L−1. The calibration equation was then automatically stored for nitrite analysis. The results demonstrated good performance of the mobile phone analyser as an analytical instrument. The accuracy (RE <4%) and precision (RSD ≤ 1%, intra- and inter-day) were also obtained with a detection limit of 0.03 mg N L−1 and a sample throughput of 40 samples per hour. Our results establish this simple, inexpensive and portable device as a reliable in-field monitor of nitrite in environmental waters.

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