scholarly journals Evolution of a high-throughput environmental DNA sampling platform

2021 ◽  
Vol 4 ◽  
Author(s):  
Austen Thomas ◽  
Caren Goldberg
Keyword(s):  
Environmental Dna ◽  
Spatial Distance ◽  
Water Volume ◽  
Barriers To Entry ◽  
Data Logging ◽  
Sampling System ◽  
Pilot Studies ◽  
Custom Made ◽  
Filtration Apparatus ◽  
Pressure Water

With the rise of environmental DNA as a surveillance tool for aquatic species, a need has also arisen for professionally engineered research tools specifically designed for eDNA applications. We created the first portable, purpose-built eDNA sampling system in the form of a backpack smart-pump filtration apparatus and custom made eDNA filter packets for each sample. The eDNA-Sampler (previously ANDe) enables both point-location sampling and mobile sampling over a spatial distance, with the ability to standardize filtration parameters (e.g. flow rate, pressure, water volume, etc.). In this presentation we will describe the evolution of the eDNA sampling backpack and associated components, each designed to help streamline the eDNA sampling process and increase sampling efficiency. We have optimized the platform for mobile sampling by integrating GPS and data logging capabilities, in addition to modifying the chemistry of the eDNA filter packets to minimize the effort required for sample preservation. Results will be presented from a series of pilot studies in which the eDNA-Sampler capabilities were evaluated. Combined, the innovations described herein should help remove barriers to entry for potential eDNA practitioners and also improve overall eDNA data quality.

scholarly journals What’s the potential for environmental DNA (eDNA) to assess stygofauna and trogolofauna: pilot studies from Western Australia

2018 ◽  
Vol 1 ◽  
Author(s):  
Nicole White ◽  
Michelle Guzik ◽  
Steven Cooper ◽  
Andrew Austin ◽  
Michael Bunce
Keyword(s):  
Western Australia ◽  
Environmental Dna ◽  
Proof Of Concept ◽  
Field Sampling ◽  
Fecal Matter ◽  
Collection Method ◽  
Pilot Studies ◽  
Community Assemblage ◽  
Reference Databases ◽  
Biological Organisms

Biological organisms living in any environment can expel DNA into their surroundings through fecal matter, mucus, shed skin, gametes, etc. Here we examine the utility of metabarcoding from a variety of environmental DNA (eDNA) substrates collected from the Pilbara region, Western Australia, to assess the feasibility for both stygo- and troglofauna detection. With metabarcoding, we confirm eDNA from both stygo- and troglofauna is detectable via molecules. In addition, our proof-of-concept and validation of using an eDNA approach was confirmed when both traditional morphological and metabarcoding assessments were compared. The metabarcoding results from the eDNA substrates are very encouraging when compared to the results of traditional morphological assessments, although highlighted the need for comprehensive DNA reference databases to be accessible for metabarcoding comparisons in order to obtain species identifications and community assemblage profiles. Furthermore, our results indicate a standardised field sampling collection method is warranted in order to maximise the success of subterranean eDNA detection from environmental substrates. eDNA data collected suggest metabarcoding approaches will become a powerful part of the toolkit to study subterranean fauna.

scholarly journals Environmental DNA for conservation

2021 ◽  
pp. 157-176
Author(s):  
Antoinette J. Piaggio
Keyword(s):  
Wildlife Conservation ◽  
Empirical Studies ◽  
Sampling Site ◽  
Environmental Dna ◽  
Successful Implementation ◽  
Pilot Studies ◽  
Sampling Schemes ◽  
Non Invasive ◽  
Elusive Species ◽  
Negative Impacts

Detection and monitoring of wildlife species of concern is a costly and time-consuming challenge that is critical to the management of such species. Tools such as lures and traps can cause unnecessary stress or other health impacts to sensitive species. Development and refinement of tools that provide means to detect rare and elusive species without requiring contact with them reduce such impacts. Further, the potential of detection after the target species has moved on from a sampling site could allow for higher potential for detection of rare species. The ability to amplify DNA from environmental samples (e.g. water, soil, air, and other substrates) has provided a non-invasive method for detection of rare or elusive species while reducing negative impacts to wildlife. Like other non-invasive methods, such as cameras, there are methodological pitfalls associated with environmental DNA (eDNA) sampling to consider. Each study system will provide unique challenges to adequate eDNA sampling. Thus, pilot studies are critical for successful implementation of a larger-scale detection and monitoring study. This chapter will describe the benefits and challenges of using eDNA, detail types of eDNA sampling, and provide guidance on designing appropriate study design and sampling schemes. Empirical studies using eDNA applied to wildlife conservation efforts will be highlighted and discussed.

scholarly journals How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?

2021 ◽  
Author(s):  
Salome Stauffer ◽  
Meret Jucker ◽  
Thomas Keggin ◽  
Virginie Marques ◽  
Marco Andrello ◽  
...  
Keyword(s):  
False Negative ◽  
Dynamic Environment ◽  
Environmental Dna ◽  
Water Volume ◽  
Marine Biodiversity ◽  
Marine Environments ◽  
Tropical Regions ◽  
Paired Samples ◽  
Promising Tool ◽  
Accumulation Curves

Quantifying the diversity of species in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, the reliability of biodiversity detection from eDNA samples can be low in marine environments because eDNA density is low and certainly patchy in this vast, heterogenous and dynamic environment. So, the number of sampling replicates and filtered volume necessary to obtain accurate estimates of biodiversity in rich tropical marine environments using eDNA metabarcoding is still unknown. Here, we used a paired sampling design of 30L per replicate on 68 reef transects from 8 sites in three tropical regions and identified fish Molecular Taxonomic Units (MOTUs) using a 12S marker. We quantified local biodiversity variation as MOTU richness, compositional turnover and compositional nestedness between replicated pairs of seawater samples. We report strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non-overlapping assemblages rather than subsets of one-another. As a result, localised diversity accumulation curves showed that even 6 replicates (180L) in the same location underestimated local diversity (for an area <1km). However, sampling of regional diversity using ~25 replicates in variable locations (often covering 10s of km) achieved saturation of biodiversity accumulation curves. Our results demonstrate high variability of diversity estimates perhaps arising from heterogeneous and local distribution of eDNA distribution in seawater or highly skewed frequencies of eDNA traces. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes of local assemblages. Future biomonitoring efforts could be strongly undermined by a high level of false-negative detections under low replication protocols. We reveal the need to increase replicates or increase sampled water volume to better inform management of marine biodiversity using eDNA.

Measured and simulated analysis of a model rocket

2018 ◽  
Vol 233 (4) ◽  
pp. 1397-1411
Author(s):  
William Brown ◽  
Michael Wiesneth ◽  
Thomas Faust ◽  
Nghia Huynh ◽  
Carlos Montalvo ◽  
...  
Keyword(s):  
Simulation Software ◽  
Data Logging ◽  
Rigid Body Dynamic ◽  
Custom Made ◽  
Global Positioning ◽  
Open Source Software Package ◽  
Standard Set ◽  
The Cost ◽  
Simulated Analysis ◽  
Body Dynamic

A comparison between two types of sensors and two types of simulation software are investigated here for a student built rocket. Many students use an open source software package called OpenRocket which uses empirical aerodynamics based on the shape of the rocket. This software is compared to the standard set of rigid body dynamic equations using coefficients for the aerodynamics based on windtunnel and computational fluid dynamics tests. During experimentation two sensors are used and price and resolution is compared. The first sensor is a turn-key sensor called the TeleMega which has many features such as telemetry and on board data logging. In an effort to reduce costs, the Arduino Mega platform has been augmented with a custom made shield capable of measuring Global Positioning System (GPS), angular velocity, and attitude information with on board data logging as well. Although this sensor has limited functionality, the cost is substantially reduced. It is shown that all sensors and simulation software have their strengths and weaknesses with appropriate usage for each.

scholarly journals eDNA Sampler: A fully integrated environmental DNA sampling system

2018 ◽  
Vol 9 (6) ◽  
pp. 1379-1385 ◽  
Author(s):  
Austen C. Thomas ◽  
Jesse Howard ◽  
Phong L. Nguyen ◽  
Tracie A. Seimon ◽  
Caren S. Goldberg
Keyword(s):  
Environmental Dna ◽  
Sampling System ◽  
Fully Integrated ◽  
Dna Sampling

scholarly journals Fishing in the Water: Effect of Sampled Water Volume on Environmental DNA-Based Detection of Macroinvertebrates

2015 ◽  
Vol 50 (1) ◽  
pp. 305-312 ◽  
Author(s):  
Elvira Mächler ◽  
Kristy Deiner ◽  
Fabienne Spahn ◽  
Florian Altermatt
Keyword(s):  
Environmental Dna ◽  
Water Volume ◽  
Water Effect

scholarly journals The Karabo distributed control system

2019 ◽  
Vol 26 (5) ◽  
pp. 1448-1461 ◽  
Author(s):  
Steffen Hauf ◽  
Burkhard Heisen ◽  
Steve Aplin ◽  
Marijan Beg ◽  
Martin Bergemann ◽  
...  
Keyword(s):  
Control System ◽  
Data Analysis ◽  
Data Acquisition ◽  
Distributed Control ◽  
Situational Awareness ◽  
Integrated Control ◽  
Distributed Control System ◽  
Data Logging ◽  
Custom Made ◽  
Control Feedback

The Karabo distributed control system has been developed to address the challenging requirements of the European X-ray Free Electron Laser facility, including complex and custom-made hardware, high data rates and volumes, and close integration of data analysis for distributed processing and rapid feedback. Karabo is a pluggable, distributed application management system forming a supervisory control and data acquisition environment as part of a distributed control system. Karabo provides integrated control of hardware, monitoring, data acquisition and data analysis on distributed hardware, allowing rapid control feedback based on complex algorithms. Services exist for access control, data logging, configuration management and situational awareness through alarm indicators. The flexible framework enables quick response to the changing requirements in control and analysis, and provides an efficient environment for development, and a single interface to make all changes immediately available to operators and experimentalists.

scholarly journals Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach

2020 ◽  
Author(s):  
Isabel Cantera ◽  
Jean-Baptiste Decotte ◽  
Tony Dejean ◽  
Jérôme Murienne ◽  
Régis Vigouroux ◽  
...  
Keyword(s):  
General Pattern ◽  
Fish Fauna ◽  
Species Distributions ◽  
Environmental Dna ◽  
Spatial Distance ◽  
Community Similarity ◽  
River Systems ◽  
Detection Distance ◽  
Local Species ◽  
Species Similarity

AbstractEnvironmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remain limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA. Up to now, attempts to measure eDNA detection distance compared known species distributions to eDNA results, limiting therefore studies to a few intensively studied rivers. Here we developed a framework to measure the detection distance of eDNA in rivers based on the comparison of faunas across an increasing range of spatial extents, making it independent from knowledge on species distributions. We hypothesized that under short detection distance the similarity between fish faunas should peak between nearby sites, whereas under long detection distance each site should cumulate species from a large upstream area. Applying this framework to the fish fauna of two large and species rich Neotropical river basins (Maroni and Oyapock), we show that fish eDNA detection distance did not exceed a few kilometers. eDNA hence provided inventories of local species communities. Those results were validated by retrieving the distance decay of species similarity, a general pattern in ecology based on the decline of local species community similarity with spatial distance between them. We finally compared species distribution derived from eDNA to the known distribution of the species based on capture data, and this comparison also confirmed a global match between methods, testifying for a short distance of detection of the fauna by eDNA.

scholarly journals Calculation of Water Wheel Design Parameters for Micro Hydroelectric Power Station

2019 ◽  
Vol 97 ◽  
pp. 05042 ◽  
Author(s):  
Dilshod Kodirov ◽  
Obid Tursunov
Keyword(s):  
Water Flow ◽  
Power Plants ◽  
Low Pressure ◽  
Design Parameters ◽  
Water Volume ◽  
Hydroelectric Power Station ◽  
Hydroelectric Power ◽  
Water Flow Velocity ◽  
Pressure Water ◽  
Water Wheel

This paper is devoted to the issues such as modelling the design parameters and operating modes and improving the design of micro hydroelectric power plants operating in low-pressure water flow. Taking into consideration above-mentioned issues, it is possible to increase the efficiency of using low-pressure water energy systems. The main dimensions of the water wheel of a micro hydropower plant depend on the water flow velocity v, water volume Q, acting at a fixed point in time on the water wheel blade, and also on the depth of the water level H.

scholarly journals Refining sampling protocols for cavefishes and cave crayfishes to account for environmental variation

2021 ◽  
Vol 39 ◽  
pp. 79-105
Author(s):  
Joshua B. Mouser ◽  
Shannon K. Brewer ◽  
Matthew L. Niemiller ◽  
Robert Mollenhauer ◽  
Ronald A. Van Den Bussche
Keyword(s):  
Environmental Conditions ◽  
Detection Probability ◽  
Survey Methods ◽  
Environmental Dna ◽  
Sampling Bias ◽  
Water Velocity ◽  
Conservation Strategies ◽  
Water Volume ◽  
Factors Affecting ◽  
Sampling Protocols

Subterranean habitats represent focal habitats in many conservation strategies; however, these environments are some of the most difficult to sample. New sampling methods, such as environmental DNA (eDNA), show promise to improve stygobiont detection, but sources of sampling bias are poorly understood. Therefore, we determined the factors affecting detection probability using traditional visual surveys and eDNA surveys for both cavefishes and cave crayfishes and demonstrated how detection affects survey efforts for these taxa. We sampled 40 sites (179 visual and 183 eDNA surveys) across the Ozark Highlands ecoregion. We estimated the detection probability of cave crayfishes and cavefishes using both survey methods under varying environmental conditions. The effectiveness of eDNA or visual surveys varied by environmental conditions (i.e., water volume, prevailing substrate, and water velocity) and the target taxa. When sampling in areas with average water velocity, no flow, and coarse substrate, eDNA surveys had a higher detection probability (0.49) than visual surveys (0.35) for cavefishes and visual surveys (0.67) had a higher detection probability than eDNA surveys (0.40) for cave crayfishes. Under the same sampling conditions, 5 visual surveys compared to 10 eDNA surveys would be needed to confidently detect cave crayfishes and 9 visual surveys compared to 4 eDNA surveys for cavefishes. Environmental DNA is a complementary tool to traditional visual surveys; however, the limitations we identified indicate eDNA currently cannot replace visual surveys in subterranean environments. Although sampling designs that account for imperfect sampling are particularly useful, they may not be practical; thus, increasing sampling efforts to offset known detection bias would benefit conservation strategies.

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