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 Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Reference Database ◽  
Chloroplast Gene ◽  
Coastal Plants ◽  
Reference Databases ◽  
Targeted Capture ◽  
Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

Blockchain Integration Into Supply Chain Operations

2021 ◽  
pp. 329-350
Author(s):  
Yigit Sever ◽  
Pelin Angin
Keyword(s):  
Supply Chain ◽  
Supply Chains ◽  
Global Supply Chains ◽  
Central Authority ◽  
Proof Of Concept ◽  
Pilot Studies ◽  
Blockchain Technology ◽  
History Of ◽  
Trusted Data

Following the globalization initiated by containerization of logistics, supply chains might be due another revolution by the integration of the disruptive blockchain technology that addresses the current issues with the management of complex global supply chains. Blockchains are distributed digital ledgers that require no central authority to operate while offering a tamper-proof and transparent history of each transaction from the very beginning. Distributed nature of these ledgers ensure that every participant of the supply chain has access to trusted data. The industry has already begun experimenting with blockchain integration into their operations. For the majority of the organizations, however, these experiments stay in proof-of-concept stages or small pilot studies. In this chapter, the authors discuss the supply chain characteristics that make blockchain integration favorable, lay the groundwork for how blockchain can be used for supply chain operations and how it has been used so far.

scholarly journals Combining Multiple Markers in Environmental DNA Metabarcoding to Assess Deep-Sea Benthic Biodiversity

2021 ◽  
Vol 8 ◽  
Author(s):  
Jun Liu ◽  
Haibin Zhang
Keyword(s):  
Deep Sea ◽  
Okinawa Trough ◽  
Environmental Dna ◽  
Rrna Gene ◽  
28S Rrna ◽  
Eukaryotic Diversity ◽  
The Okinawa Trough ◽  
Marine Diversity ◽  
Deep Sea Sediments ◽  
Reference Databases

Environmental DNA (eDNA) metabarcoding is an emerging tool to estimate diversity by combining DNA from the environmental samples and the high-throughput sequencing. Despite its wide use in estimating eukaryotic diversity, many factors may bias the results. Maker choice and reference databases are among the key issues in metabarcoding analyses. In the present study, we compared the performance of a novel 28S rRNA gene marker designed in this study and two commonly used 18S rRNA gene markers (V1-2 and V9) in estimating the eukaryotic diversity in the deep-sea sediments. The metabarcoding analyses based on the sediment surveys of the Okinawa Trough found that more eukaryotic taxa were discovered by 18S V9 than 28S and 18S V1-2, and that 18S V9 also performed better in metazoan recovery than the other two markers. Although a broad range of taxa were detected by the three metabarcoding markers, only a small proportion of taxa were shared between them even at the phylum level. The non-metric multidimensional scaling (NMDS) analysis also supported that communities detected by the three markers were distinct from each other. In addition, different communities were resolved by different reference databases (NCBI nt vs. SILVA) for the two 18S markers. Combining the three markers, annelids were found to be the most abundant (44.9%) and diverse [179 operational taxonomic units (OTUs)] metazoan group in the sediments of the Okinawa Trough. Therefore, multiple independent markers are recommended to be used in metabarcoding analyses during marine diversity surveys, especially for the poorly understood deep-sea sediments.

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 eDNAir: proof of concept that animal DNA can be collected from air sampling

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11030
Author(s):  
Elizabeth L. Clare ◽  
Chloe K. Economou ◽  
Chris G. Faulkes ◽  
James D. Gilbert ◽  
Frances Bennett ◽  
...  
Keyword(s):  
Sampling Methods ◽  
Air Sampling ◽  
Research Programme ◽  
Environmental Dna ◽  
Aquatic Systems ◽  
Ecological Research ◽  
Proof Of Concept ◽  
Confined Space ◽  
Substantial Interest

Environmental DNA (eDNA) is one of the fastest developing tools for species biomonitoring and ecological research. However, despite substantial interest from research, commercial and regulatory sectors, it has remained primarily a tool for aquatic systems with a small amount of work in substances such as soil, snow and rain. Here we demonstrate that eDNA can be collected from air and used to identify mammals. Our proof of concept successfully demonstrated that eDNA sampled from air contained mixed templates which reflect the species known to be present within a confined space and that this material can be accessed using existing sampling methods. We anticipate this demonstration will initiate a much larger research programme in terrestrial airDNA sampling and that this may rapidly advance biomonitoring approaches. Lastly, we outline these and potential related applications we expect to benefit from this development.

Additions to the host range of Phytophthora cinnamomi in the jarrah (Eucalyptus marginata) forest of Western Australia

2001 ◽  
Vol 49 (2) ◽  
pp. 193 ◽  
Author(s):  
K. L. McDougall ◽  
G. E. St J. Hardy ◽  
R. J. Hobbs
Keyword(s):  
Host Range ◽  
Western Australia ◽  
Phytophthora Cinnamomi ◽  
Separate Study ◽  
Perennial Species ◽  
Wild Populations ◽  
Field Sampling ◽  
Eucalyptus Marginata ◽  
Pathogenicity Tests ◽  
Interpretation Of Results

Pathogenicity tests with Phytophthora cinnamomi were conducted on 25 perennial species from the jarrah (Eucalyptus marginata) forest of Western Australia. Most species tested had been found in a separate study to be scarce on sites affected by Phytophthora cinnamomi but frequently found in unaffected vegetation. Some species that were known to be field-tolerant of P. cinnamomi and some that were highly susceptible to infection were included in the study for comparison. Phytophthora cinnamomi was recorded from 13 of 17 species not previously known to be susceptible. Phytophthora cinnamomi was subsequently isolated from dead plants of two of these 13 species in the field. The interpretation of results from the glasshouse trials was difficult for some species because of inconsistent patterns of death and P. cinnamomi isolation in the glasshouse trials. Phytophthora cinnamomi probably causes decline in wild populations of Stylidium amoenum, based on the ease of field and glasshouse isolation of P. cinnamomi and the scarcity of this forb on dieback sites. It may also contribute to decline in populations of Boronia fastigiata, Hybanthus floribundus, Labichea punctata, Scaevola calliptera and Stylidium junceum, although further field sampling is required to confirm this.

Local habitat features explain the distribution of the imperiled grass pickerel (Esox americanus vermiculatus)

2019 ◽  
Vol 97 (5) ◽  
pp. 479-487
Author(s):  
J.E. Colm ◽  
N.E. Mandrak ◽  
B.L. Tufts
Keyword(s):  
Fish Community ◽  
Agricultural Land ◽  
Sampling Methods ◽  
Habitat Preferences ◽  
Field Sampling ◽  
Community Assemblage ◽  
Habitat Features ◽  
Community Data ◽  
Local Habitat ◽  
Habitat Variables

We investigated patterns of grass pickerel (Esox americanus vermiculatus Lesueur, 1846) distribution in three watersheds in Ontario, Canada, using site- and reach-scale habitat variables and fish community assemblage data to determine why this species occurs sporadically throughout watersheds despite abundant seemingly suitable, but unoccupied, habitat. Habitat and fish community data were collected using conventional field sampling methods, and reach-scale habitat data were compiled with the aid of a geographic information system. We found that occupied sites had lower baseflow indices and reach slopes but higher conductivity and agricultural land uses than unoccupied sites. More grass pickerel were detected when conductivity, channel cover, and wetlands in the floodplain were highest and bank slopes lowest; this is consistent with habitat preferences described elsewhere in its range. Habitat features at the site scale appeared more important than reach-scale features suggesting that grass pickerel may be using small habitat patches. This study identifies habitat elements important to grass pickerel and offers insights into management implications.

scholarly journals An efficient and robust laboratory workflow and tetrapod database for larger scale eDNA studies

2018 ◽  
Author(s):  
Jan Axtner ◽  
Alex Crampton-Platt ◽  
Lisa A. Hörig ◽  
Azlan Mohamed ◽  
Charles C.Y. Xu ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Environmental Dna ◽  
Taxonomic Assignment ◽  
Bioinformatic Pipeline ◽  
Assignment Method ◽  
Reference Databases ◽  
Reference Sequences ◽  
Taxonomic Groups ◽  
Annotation Errors ◽  
Technical Replication

AbstractBackgroundThe use of environmental DNA, ‘eDNA,’ for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the two most important risks of eDNA: sample contamination and taxonomic mis-assignment. These risks arise from the need for PCR amplification to detect the trace amounts of DNA combined with the necessity of using short target regions due to DNA degradation.FindingsOur high-throughput workflow minimises these risks via a four-step strategy: (1) technical replication with two PCR replicates and two extraction replicates; (2) using multi-markers (12S, 16S, CytB); (3) a ‘twin-tagging,’ two-step PCR protocol;(4) use of the probabilistic taxonomic assignment method PROTAX, which can account for incomplete reference databases.As annotation errors in the reference sequences can result in taxonomic mis-assignment, we supply a protocol for curating sequence datasets. For some taxonomic groups and some markers, curation resulted in over 50% of sequences being deleted from public reference databases, due to (1) limited overlap between our target amplicon and reference sequences; (2) mislabelling of reference sequences; (3) redundancy.Finally, we provide a bioinformatic pipeline to process amplicons and conduct PROTAX assignment and tested it on an ‘invertebrate derived DNA’ (iDNA) dataset from 1532 leeches from Sabah, Malaysia. Twin-tagging allowed us to detect and exclude sequences with non-matching tags. The smallest DNA fragment (16S) amplified most frequently for all samples, but was less powerful for discriminating at species rank. Using a stringent and lax acceptance criteria we found 162 (stringent) and 190 (lax) vertebrate detections of 95 (stringent) and 109 (lax) leech samples.ConclusionsOur metabarcoding workflow should help research groups increase the robustness of their results and therefore facilitate wider usage of e/iDNA, which is turning into a valuable source of ecological and conservation information on tetrapods.

scholarly journals Towards Understanding the Liver Fluke Transmission Dynamics on Farms: Detection of Liver Fluke Transmitting Snail and Liver Fluke-Specific Environmental DNA in Water Samples from an Irrigated Dairy Farm in Southeast Australia

2020 ◽  
Author(s):  
Vignesh Rathinasamy ◽  
Jaclyn Swan ◽  
Lily Tran ◽  
Jane Kelley ◽  
Chris Hosking ◽  
...  
Keyword(s):  
Water Samples ◽  
Liver Fluke ◽  
Dairy Farm ◽  
Environmental Dna ◽  
Snail Host ◽  
Control Measures ◽  
Water Bodies ◽  
Proof Of Concept ◽  
Fluke Infection ◽  
Liver Fluke Infection

Abstract Background Livestock production around the world is impacted by liver fluke (Fasciola spp.) infection resulting in serious economic losses to the beef, dairy and sheep industries with significant losses of about $90 million per annum in Australia. Liver fluke infection is predominantly controlled by anthelmintic treatment and Triclabendazole (TCBZ) is usually the drug of choice due its superior efficacy against early immature, immature and adult liver fluke stages; however, the widespread emergence of TCBZ resistance in livestock threatens liver fluke control. We are in the urgent need for alternative control measures to lower the exposure of livestock to liver fluke infection which would help to preserve the usefulness of current anthelmintic treatments. Our ability to understand the prevalence of intermediate snail hosts and infective liver fluke stages in the environment is crucial to implement alternative control measures for liver fluke control. However, identification of liver fluke and snails in the environment is hampered by lack of efficient diagnostic methods. Environmental DNA (eDNA) based identification of liver fluke and the intermediate snail host in the water bodies is a promising method to identify liver fluke and snail prevalence on farms. Our aim is to provide a proof of concept to use a molecular tool (quantitative PCR) to detect and quantify eDNA of liver fluke and snail in water bodies on Victorian farming properties for potential large-scale analysis of liver fluke and snail ecology in water bodies. Methods To demonstrate the identification of liver fluke and snail in water bodies, we used a multiplex quantitative PCR assay for the independent but simultaneous detection of eDNA released from snail (Austropeplea tomentosa) a crucial intermediate snail host for liver fluke transmission in South-east Australia and free-living liver fluke stages (Fasciola hepatica). We have collected water samples from an irrigation channel over a period of 11 months in 2016 at a dairy farm located at Maffra, Victoria, South-east Australia and used water samples from selected months (February, March, May, September, October, November and December) for eDNA assay. Results The multiplex qPCR assay effectively allows for the detection and quantification of eDNA released from liver fluke life stages and snails and we observed differential levels of liver fluke and snail specific eDNA in water at the time points analysed in this study. This assay was able to detect 14 fg and 50 pg of liver fluke and snail DNA in the presence of potential inhibitors from field collected water samples. Conclusion The successful detection of eDNA specific to liver fluke and snails from the field collected water samples provides a proof of concept for the use of this method as a monitoring tool to determine the prevalence of liver fluke and liver fluke-transmitting snails in irrigation regions to allow for understanding the liver fluke transmission zones on farms to implement effective control strategies.

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