scholarly journals An experimental comparison of composite and grab sampling of stream water for metagenetic analysis of environmental DNA

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5871 ◽  
Author(s):  
Robert S. Cornman ◽  
James E. McKenna ◽  
Jennifer Fike ◽  
Sara J. Oyler-McCance ◽  
Robin Johnson
Keyword(s):  
Water Samples ◽  
Stream Water ◽  
Environmental Dna ◽  
Experimental Comparison ◽  
Grab Sampling ◽  
Detection Rates ◽  
Composite Sampling ◽  
Lowest Common Ancestor ◽  
The Impact ◽  
Composite Samples

Use of environmental DNA (eDNA) to assess distributions of aquatic and semi-aquatic macroorganisms is promising, but sampling schemes may need to be tailored to specific objectives. Given the potentially high variance in aquatic eDNA among replicate grab samples, compositing smaller water volumes collected over a period of time may be more effective for some applications. In this study, we compared eDNA profiles from composite water samples aggregated over three hours with grab water samples. Both sampling patterns were performed with identical autosamplers paired at two different sites in a headwater stream environment, augmented with exogenous fish eDNA from an upstream rearing facility. Samples were filtered through 0.8 μm cellulose nitrate filters and DNA was extracted with a cetyl trimethylammonium bromide procedure. Eukaryotic and bacterial community profiles were derived by amplicon sequencing of 12S ribosomal, 16S ribosomal, and cytochrome oxidase I loci. Operational taxa were assigned to genus with a lowest common ancestor approach for eukaryotes and to family with the RDP Classifier software for prokaryotes. Eukaryotic community profiles were more consistent with composite sampling than grab sampling. Downstream, rarefaction curves suggested faster taxon accumulation for composite samples, and estimated richness was higher for composite samples as a set than for grab samples. Upstream, composite sampling produced lower estimated richness than grab samples, but with overlapping standard errors. Furthermore, a bimodal pattern of richness as a function of sequence counts suggested the impact of clumped particles on upstream samples. Bacterial profiles were insensitive to sample method, consistent with the more even dispersion expected for bacteria compared with eukaryotic eDNA. Overall, samples composited over 3 h performed equal to or better than triplicate grab sampling for quantitative community metrics, despite the higher total sequencing effort provided to grab replicates. On the other hand, taxon-specific detection rates did not differ appreciably and the two methods gave similar estimates of the ratio of the common fish genera Salmo and Coregonus at each site. Unexpectedly, Salmo eDNA dropped out substantially faster than Coregonus eDNA between the two sites regardless of sampling method, suggesting that differential settling affects the estimation of relative abundance. We identified bacterial patterns that were associated with eukaryotic diversity, suggesting potential roles as biomarkers of sample representativeness.

scholarly journals The Impact of Sampling Type, Frequency and Scale of Collection System on SARS-CoV-2 Quantification Fidelity

2021 ◽  
Author(s):  
Andrea D. George ◽  
Devrim Kaya ◽  
Blythe A. Layton ◽  
Kestrel Bailey ◽  
Christine Kelly ◽  
...  
Keyword(s):  
False Negative ◽  
Treatment Plant ◽  
High Flow ◽  
Low Flow ◽  
Grab Sampling ◽  
Flow Rates ◽  
Composite Sampling ◽  
Neighborhood Scale ◽  
The Impact ◽  
Composite Samples

With the rapid onset of the COVID-19 pandemic, wastewater-based epidemiology (WBE) sampling methodologies for SARS-CoV-2 were often implemented quickly and may not have taken the unique drainage catchment characteristics into account. One question of debate is the relevance of grab versus composite samples when surveying for SARS-CoV-2 at various catchment scales. This study assessed the impact of grab versus composite sampling on the detection and quantification of SARS-CoV-2 in catchment basins with flow rates ranging from high-flow (wastewater treatment plant influent), to medium-flow (neighborhood-scale micro-sewershed), to low-flow (city block-scale micro-sewershed) and down to ultra-low flow (building scale). At the high-flow site, grab samples were reasonably comparable to 24-h composite samples with the same non-detect rate (0%) and SARS-CoV-2 concentrations that differed by 32% on the Log10 scale. However, as the flow rates decreased, the percentage of false-negative grab samples increased up to 44% and the SARS-CoV-2 concentrations of grab samples varied by up to 1-2 orders of magnitude compared to their respective composite sample concentrations. At the ultra-low-flow site, increased sampling frequencies down to every 5 min led to composite samples with higher fidelity to the SARS-CoV-2 load. Thus, composite sampling is superior to grab sampling, especially as flow decreases.

scholarly journals Transect sampling promotes higher detection rates compared to discrete sampling for environmental DNA applications

2021 ◽  
Vol 4 ◽  
Author(s):  
Thiago Sanches
Keyword(s):  
Detection Probability ◽  
Environmental Dna ◽  
Common Species ◽  
Fish Population ◽  
Probability Of Detection ◽  
Detection Rates ◽  
Indirect Measure ◽  
Real Distribution ◽  
Transect Sampling ◽  
The Impact

The use of environmental DNA (eDNA) to monitor species in aquatic environments has rapidly increased over the past decade. eDNA has consistently outperformed other methods of detection, yet eDNA relies on an indirect measure to estimate the real distribution of a species. Therefore, understanding the environmental factors that disperse eDNA is of major importance. Here we modeled the use of transect sampling for eDNA studies and also model the impact of river advection on detection radius and the expected probability of detection. Our model suggests that transect sampling: 1) increases the detection probability for both rare and common species, thus reducing the frequency of false negatives, 2) diminishes the standard deviation of the detection probability, which in most cases means higher reproducibility of eDNA studies, 3) better estimates systemwide trends of fish population distinguishing zones of multiple fishes from zones where few fishes are present, and 4) diminishes the effects of eddies and river velocity on the detection probability and detection radius. We propose the use of transect sampling as an alternative method of eDNA sampling with benefits that surpass the disadvantages of not being able to pinpoint the exact fish location. Our model also suggests that even short transects (less than 100 m) can yield considerable benefits compared to point sampling.

scholarly journals Environmental DNA Based Surveillance for the Highly Invasive Carpet Sea Squirt Didemnum vexillum: A Targeted Single-Species Approach

2021 ◽  
Vol 8 ◽  
Author(s):  
Iveta Matejusova ◽  
Jennifer Graham ◽  
Fiona Bland ◽  
Jean-Pierre Lacaze ◽  
Guillaume Herman ◽  
...  
Keyword(s):  
Water Samples ◽  
Native Species ◽  
Limit Of Detection ◽  
Sampling Site ◽  
Monitoring Program ◽  
Environmental Dna ◽  
Qpcr Assay ◽  
Didemnum Vexillum ◽  
Sampling Points ◽  
The Impact

The presence and diversity of marine non-native species, the number of new invasions, and the impact on native communities and habitats are important metrics used to assess the health of marine ecosystems. Monitoring for marine non-native species, using traditional approaches such as rapid assessment surveys (RASs), requires taxonomic expertise and may still fail to detect rare or inconspicuous species. This study reports a validation process for a quantitative PCR (qPCR) assay based on the cytochrome oxidase 1 gene, designed to detect highly invasive tunicate Didemnum vexillum by targeting environmental DNA (eDNA) present in water samples. The D. vexillum qPCR assay showed high sensitivity, with the threshold limit of detection (LOD) and modeled LOD3 (based on triplicate qPCR reactions) estimated as 9.187 and 1.117 copies reaction–1, respectively and the limit of quantification (LOQ) was calculated as 18 copies reaction–1. Analyses of water samples collected from selected Pacific oyster farms and recreational marinas in Scotland showed 100% concordance between the historical data on presence of D. vexillum from RASs and detection of D. vexillum eDNA. Consistency of detection of D. vexillum eDNA among different sampling points within each infected sampling site varied, ranging between 100% positive throughout the site to some sampling points testing “negative” or only as “suspected” for D. vexillum. Sites with lower within-site detection consistency included sites with a low density of D. vexillum as reported by RASs or were sites undergoing D. vexillum management. The present pilot monitoring program demonstrates the potential to generate important data on presence of D. vexillum. This program will be scaled up across large geographic regions and used in the first instance to focus and target the traditional RASs to D. vexillum eDNA-positive sites in a cost-effective way, with an aim to verify the species presence by visual observation and direct Sanger sequencing of positive qPCR products.

scholarly journals Validation of an eDNA-based method for the detection of wildlife pathogens in water

2020 ◽  
Vol 141 ◽  
pp. 171-184
Author(s):  
N Sieber ◽  
H Hartikainen ◽  
C Vorburger
Keyword(s):  
Water Samples ◽  
Pathogen Detection ◽  
Batrachochytrium Dendrobatidis ◽  
Tap Water ◽  
Pathogenic Fungus ◽  
Environmental Dna ◽  
Detection Sensitivity ◽  
Detection Rates ◽  
Filtration Step ◽  
Wildlife Pathogens

Monitoring the occurrence and density of parasites and pathogens can identify high infection-risk areas and facilitates disease control and eradication measures. Environmental DNA (eDNA) techniques are increasingly used for pathogen detection due to their relative ease of application. Since many factors affect the reliability and efficacy of eDNA-based detection, rigorous validation and assessment of method limitations is a crucial first step. We evaluated an eDNA detection method using in situ filtration of large-volume water samples, developed to detect and quantify aquatic wildlife parasites by quantitative PCR (qPCR). We assessed method reliability using Batrachochytrium dendrobatidis, a pathogenic fungus of amphibians and the myxozoan Tetracapsuloides bryosalmonae, causative agent of salmonid proliferative kidney disease, in a controlled experimental setup. Different amounts of parasite spores were added to tanks containing either clean tap water or water from a semi-natural mesocosm community. Overall detection rates were higher than 80%, but detection was not consistent among replicate samples. Within-tank variation in detection emphasises the need for increased site-level replication when dealing with parasites and pathogens. Estimated parasite DNA concentrations in water samples were highly variable, and a significant increase with higher spore concentrations was observed only for B. dendrobatidis. Despite evidence for PCR inhibition in DNA extractions from mesocosm water samples, the type of water did not affect detection rates significantly. Direct spiking controls revealed that the filtration step reduced detection sensitivity. Our study identifies sensitive quantification and sufficient replication as major remaining challenges for the eDNA-based methods for detection of parasites in water.

scholarly journals Tracing Copper Migration in the Tongling Area through Copper Isotope Values in Soils and Waters

2018 ◽  
Vol 15 (12) ◽  
pp. 2661 ◽  
Author(s):  
Jingwen Su ◽  
Ryan Mathur ◽  
Glen Brumm ◽  
Peter D’Amico ◽  
Linda Godfrey ◽  
...  
Keyword(s):  
Bronze Age ◽  
Water Samples ◽  
Copper Sulfide ◽  
Stream Water ◽  
Sulfide Minerals ◽  
Soil Samples ◽  
Copper Mining ◽  
Copper Isotope ◽  
The Impact ◽  
The Bronze Age

Copper mining in Tongling has occurred since the Bronze Age, and this area is known as one of the first historic places where copper has been, and is currently, extracted. Multiple studies have demonstrated, through concentrated work on soils and waters, the impact of mining in the area. Here we present copper isotope values of 13 ore samples, three tailing samples, 20 water samples (surface and groundwater), and 94 soil samples (15 different profiles ranging in depth from 0–2 m) from proximal to distal (up to 10 km) locations radiating from a tailings dam and tailings pile. Oxidation of the copper sulfide minerals results in isotopically heavier oxidized copper. Thus, copper sourced from sulfide minerals has been used to trace copper in mining and environmental applications. At Tongling, higher copper isotope values (greater than 1 per mil, which are interpreted to be derived from copper sulfide weathering) are found both in waters and the upper portions of soils (5–100 cm) within 1 km of the source tailings. At greater than 1 km, the soils do not possess heavier copper isotope values; however, the stream water samples that have low copper concentrations have heavier values up to 6.5 km from the source. The data suggest that copper derived from the mining activities remains relatively proximal in the soils but can be traced in the waters at greater distances.

scholarly journals Hydrochemical Assessment of Groundwater around Lapite Dumpsite for Irrigation Water Quality in Ibadan, Southwestern Nigeria

2021 ◽  
Vol 8 (2) ◽  
pp. 98-108
Author(s):  
Oluwatoyin Opeyemi Akintola ◽  
Gabriel Oladapo Adeyemi ◽  
Adewunmi Idayat Bodede ◽  
Oluwatoyin Adekoya ◽  
Kehinde O. Babatunde
Keyword(s):  
Water Quality ◽  
Irrigation Water ◽  
Water Samples ◽  
Stream Water ◽  
Magnesium Content ◽  
Resource Assessment ◽  
Irrigation Water Quality ◽  
Southwestern Nigeria ◽  
High Concentrations ◽  
The Impact

Due to the increase in population and industrialization growth, most countries in the world depend on groundwater to meet agriculture demands for food production. The increase in water contamination due to indiscriminate solid wastes has necessitated the assessment of water quality and its suitability for agricultural usage. Twenty four groundwater and ten stream water samples were randomly collected from the downslope and upslope side of the dumpsite for all the major physio-chemical parameters. The pH of water samples indicates slightly acidic to alkaline in nature. High concentrations of nitrate, total dissolved solids and electrical conductivity suggest the impact of the waste on the water resource. Assessment of irrigation water quality based on Sodium Adsorption Ratio (SAR), Soluble Sodium Percentage (SSP), Permeability Index (PI) and Magnesium content (MC) indicated that most of the water samples fall within the permissible standard for irrigation water. Thus, the water should be used with caution on crops for long time agricultural sustainability.

scholarly journals eDNA sampled from stream networks correlates with camera trap detection rates of terrestrial mammals

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arnaud Lyet ◽  
Loïc Pellissier ◽  
Alice Valentini ◽  
Tony Dejean ◽  
Abigail Hehmeyer ◽  
...  
Keyword(s):  
Large Scale ◽  
Stream Water ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Camera Trap ◽  
Camera Traps ◽  
Sufficient Information ◽  
Multiple Time ◽  
Detection Rates ◽  
Terrestrial Mammals

AbstractBiodiversity monitoring delivers vital information to those making conservation decisions. Comprehensively measuring terrestrial biodiversity usually requires costly methods that can rarely be deployed at large spatial scales over multiple time periods, limiting conservation efficiency. Here we investigated the capacity of environmental DNA (eDNA) from stream water samples to survey terrestrial mammal diversity at multiple spatial scales within a large catchment. We compared biodiversity information recovered using an eDNA metabarcoding approach with data from a dense camera trap survey, as well as the sampling costs of both methods. Via the sampling of large volumes of water from the two largest streams that drained the study area, eDNA metabarcoding provided information on the presence and detection probabilities of 35 mammal taxa, 25% more than camera traps and for half the cost. While eDNA metabarcoding had limited capacity to detect felid species and provide individual-level demographic information, it is a cost-efficient method for large-scale monitoring of terrestrial mammals that can offer sufficient information to solve many conservation problems.

Pengaruh Variasi Waktu Paparan Gelombang Ultrasonik dalam Mengurangi Jumlah Bakteri coliform pada Sampel Air Sungai Kahayan

2020 ◽  
Vol 4 (1) ◽  
pp. 9-13 ◽  
Author(s):  
Neny Kurniawati, Kerelius, Sunariyati ◽  
Luqman Hakim, Dyah Ayu Pramoda Wardani, Widya Krestina ◽  
Dwi Tyas Setiawan, Ferry Purwanto, Diah K. Fatmala
Keyword(s):  
Water Treatment ◽  
River Water ◽  
Ultrasonic Wave ◽  
Exposure Time ◽  
Water Samples ◽  
Sampling Technique ◽  
Wave Exposure ◽  
Test Results ◽  
Time Data ◽  
Grab Sampling

Abstrak – Penelitian ini bertujuan untuk mengkaji pengaruh waktu paparan gelombang ultrasonik terhadap pengurangan jumlah koloni bakteri coliform pada sampel air sungai Kahayan. Pengambilan sampel air sungai dilakukan dengan teknik Grab Sampling menggunakan alat Kemmerer Sampler. Sampel air yang didapatkan diberikan paparan gelombang ultrasonik secara langsung, tanpa merubah kondisi lingkungan awal. Waktu paparan divariasikan pada 1 jam, 2 jam, 3 jam, 4 jam, dan 5 jam dengan frekuensi 40 kHz untuk memperoleh data waktu optimum. Uji coliform dilakukan dengan metode MPN, dengan tahapan uji pendugaan, uji penegasan, dan perhitungan koloni. Hasil uji MPN 24 jam setelah paparan menunjukkan bahwa penggunaan ultrasonik sebagai antibateri dapat optimum ketika diberikan paparan dengan waktu 3 jam, dengan efisiensi  96%. Kata kunci: antibakteri, coliform, ultrasonik, water treatment, sungai Kahayan  Abstract – This study aims to examine the effect of ultrasonic wave exposure time on reducing the number of coliform bacterial colonies in the Kahayan river water samples. River water sampling is done using the Grab Sampling technique using the Kemmerer Sampler tool. The water samples obtained were given direct ultrasonic wave exposure, without changing the initial environmental conditions. The exposure time is varied in 1 hour, 2 hours, 3 hours, 4 hours and 5 hours with a frequency of 40 kHz to obtain optimum time data. Coliform test was carried out by the MPN method, with the stages of the estimation test, affirmation test, and colony calculation. The MPN test results 24 hours after exposure showed that the use of ultrasonic as an antibody can be optimum when given exposure with a time of 3 hours, with an efficiency of 96%.Keywords : antibakterial, coliform, ultrasonic, water treatment, Kahayan river

scholarly journals Spatial Variation of Water Chemistry in Aries River Catchment Western Romania

2021 ◽  
Vol 11 (14) ◽  
pp. 6592
Author(s):  
Ana Moldovan ◽  
Maria-Alexandra Hoaghia ◽  
Anamaria Iulia Török ◽  
Marius Roman ◽  
Ionut Cornel Mirea ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Water Quality ◽  
Water Chemistry ◽  
Water Samples ◽  
Mine Drainage ◽  
Pollution Indices ◽  
Mining Activities ◽  
River Catchment ◽  
High Concentrations ◽  
The Impact

This study aims to investigate the quality and vulnerability of surface water (Aries River catchment) in order to identify the impact of past mining activities. For this purpose, the pollution and water quality indices, Piper and Durov plots, as well vulnerability modeling maps were used. The obtained results indicate that the water samples were contaminated with As, Fe, Mn, Pb and have relatively high concentrations of SO42−, HCO3−, TDS, Ca, K, Mg and high values for the electrical conductivity. Possible sources of the high content of chemicals could be the natural processes or the inputs of the mine drainage. Generally, according to the pollution indices, which were correlated to high concentrations of heavy metals, especially with Pb, Fe and Mn, the water samples were characterized by heavy metals pollution. The water quality index classified the studied water samples into five different classes of quality, namely: unsuitable for drinking, poor, medium, good and excellent quality. Similarly, medium, high and very high vulnerability classes were observed. The Durov and Piper plots classified the waters into Mg-HCO3− and Ca-Cl− types. The past and present mining activities clearly change the water chemistry and alter the quality of the Aries River, with the water requiring specific treatments before use.

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