Special Issue "eDNA for Basic and Applied Sciences"

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Biodiversity Loss & Dynamics".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 4940

Special Issue Editors

Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
Interests: crustacean; insect and fish ecophysiology (growth, reproduction and stress responses); alien species
Special Issues, Collections and Topics in MDPI journals
Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
Interests: eDNA; aquatic invasive species; DNA barcoding and metabarcoding; conservation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

You are cordially invited to contribute to this Special Issue of Diversity entitled "eDNA for basic and applied sciences". The analysis of eDNA covers all habitats found on Earth and has enormous application potential as it is non-invasive. So far, research with eDNA has mainly investigated aquatic habitats and provided qualitative data (presence/absence applications) that offer new opportunities for wildlife monitoring. However, a growing body of work is also addressing quantitative aspects (abundance applications) and eDNA deserves to be expanded due to its versatility.

This Special Issue of Diversity calls for submissions on new studies that use eDNA analyses for their purposes.

Prof. Dr. Piero Giulio Giulianini
Dr. Chiara Manfrin
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • eDNA
  • monitoring
  • abundance
  • DNA barcoding
  • DNA metabarcoding

Published Papers (5 papers)

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Research

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Communication
Haplosporidium pinnae Detection from the Faeces of Pinna nobilis: A Quick and Noninvasive Tool to Monitor the Presence of Pathogen in Early-Stage or during Fan Mussel Mass Mortalities
Diversity 2023, 15(4), 477; https://doi.org/10.3390/d15040477 - 24 Mar 2023
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Abstract
Due to the increasing mass mortality of Pinna nobilis, mainly caused by the protozoan Haplosporidium pinnae along the Mediterranean Sea, it is necessary to develop rapid and effective methods to detect the pathogen. The present study describes the development and validation of [...] Read more.
Due to the increasing mass mortality of Pinna nobilis, mainly caused by the protozoan Haplosporidium pinnae along the Mediterranean Sea, it is necessary to develop rapid and effective methods to detect the pathogen. The present study describes the development and validation of a species-specific assay based on hydrolysis probe chemistry to detect H. pinnae DNA from faeces and pseudofaeces of P. nobilis. During a study campaign in the Gulf of Trieste (Italy) in the spring and summer of 2022, 18 samples (10 faeces and 8 pseudofaeces) were collected. DNA was isolated from all samples and the presence of H. pinnae was tested by amplifying a small portion of 18S rDNA using qPCR. The newly developed assay detected positive H. pinnae in the faeces of the fan mussel in the spring, while no evidence of an outbreak of H. pinnae was found in the summer. In addition, the method proved to be noninvasive and can be used to monitor suspected H. pinnae infections in the early stages when bivalves are still vital. Furthermore, fecal analysis allows the monitoring of P. nobilis without dissecting tissues. The presented assay can also be used to routinely monitor the progress of mass mortalities caused by H. pinnae and to screen for the pathogen in live fan mussels and other environmental matrices, such as water, sediment, and faeces from other species that can host the protozoan. Full article
(This article belongs to the Special Issue eDNA for Basic and Applied Sciences)
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Article
Investigating the Potential Utility of Environmental DNA to Provide a Relative Abundance Index for the Depleted Teleost, Mulloway, Argyrosomus japonicus
Diversity 2023, 15(3), 322; https://doi.org/10.3390/d15030322 - 22 Feb 2023
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Abstract
Non-invasive, low-cost methods for censusing depleted fish populations are being prioritised among many jurisdictions worldwide. Collecting environmental DNA (eDNA) could offer one such option for augmenting fish population assessments. However, candidate species need to be carefully selected because species-specific DNA shedding and decay [...] Read more.
Non-invasive, low-cost methods for censusing depleted fish populations are being prioritised among many jurisdictions worldwide. Collecting environmental DNA (eDNA) could offer one such option for augmenting fish population assessments. However, candidate species need to be carefully selected because species-specific DNA shedding and decay rates are affected by many biotic and abiotic factors that may influence relative abundance estimates. In this study, we sought to ascertain if the eDNA of a depleted Australian teleost, mulloway, Argyrosomus japonicus, reflects its weight under controlled aquaria conditions. With four experiments, we investigated the relationships between mulloway eDNA concentrations and their weight tank−1 as a function of: (1) time post-tank establishment; (2) water temperatures (within the species’ tolerance range); (3) stocking densities; and (4) among individual, similar-sized fish. The concentrations of eDNA in tanks stabilised after six days, and a positive relationship was found between fish weight and eDNA concentration, despite some variability in shedding rates by similar-sized fish. There was also a positive effect of water temperature on eDNA concentrations, which reinforces the need to control for such abiotic factors. We conclude that there is strong utility in applying eDNA concentrations as an index of relative abundance for mulloway under controlled conditions, which justifies future field-based investigations. Full article
(This article belongs to the Special Issue eDNA for Basic and Applied Sciences)
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Article
Cuticular Swabs and eDNA as Non-Invasive Sampling Techniques to Monitor Aphanomyces astaci in Endangered White-Clawed Crayfish (Austropotamobius pallipes Complex)
Diversity 2023, 15(2), 279; https://doi.org/10.3390/d15020279 - 15 Feb 2023
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Abstract
In endangered crayfish conservation projects, it is paramount to map the distribution of the causative agent of crayfish plague, Aphanomyces astaci, in native populations. Considering the inapplicability of the destructive cuticular sampling protocol for monitoring endangered populations, we explored the use of [...] Read more.
In endangered crayfish conservation projects, it is paramount to map the distribution of the causative agent of crayfish plague, Aphanomyces astaci, in native populations. Considering the inapplicability of the destructive cuticular sampling protocol for monitoring endangered populations, we explored the use of non-invasive sampling techniques to detect this pathogen with molecular assays. In the present study, we exploited environmental DNA (testing increasing water volumes combined with different filter porosities) and cuticular swabs to collect A. astaci DNA. In addition, we evaluated the impact of the storage method on DNA preservation during field activities. After the first evaluations performed on both highly infected Austropotamobius pallipes and carrier Procambarus clarkii specimens in laboratory conditions, these sampling techniques were applied to wild populations of white-clawed crayfish. Our findings highlight better results with the filtration of 5 L of water with filters of 2.7 µm porosity for eDNA analysis and demonstrate that cuticular swabbing is equally effective as the World Organisation of Animal Health’s protocol. Storage in absolute ethanol proved to be the best solution to preserve swabs and filter samples for up to a week at room temperature. In conclusion, we suggest an integration of both sampling methods when monitoring A. astaci for conservation purposes. Full article
(This article belongs to the Special Issue eDNA for Basic and Applied Sciences)
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Article
Detection of the Endangered Stone Crayfish Austropotamobius torrentium (Schrank, 1803) and Its Congeneric A. pallipes in Its Last Italian Biotope by eDNA Analysis
Diversity 2022, 14(3), 205; https://doi.org/10.3390/d14030205 - 10 Mar 2022
Cited by 2 | Viewed by 1812
Abstract
The stone crayfish, Austropotamobius torrentium, is a European freshwater crayfish. Although this species is relatively widespread throughout the continent, it is undergoing significant declines throughout its range. However, as the decline rates have not been quantified in detail, this species is classified [...] Read more.
The stone crayfish, Austropotamobius torrentium, is a European freshwater crayfish. Although this species is relatively widespread throughout the continent, it is undergoing significant declines throughout its range. However, as the decline rates have not been quantified in detail, this species is classified as data deficient by the IUCN Red List of Threatened Species. The present study describes the development and validation of two species-specific assays based on hydrolysis probe chemistry for the detection of A. torrentium and A. pallipes environmental DNA (eDNA) in water samples collected in the Julian Alps of Italy (Friuli Venezia Giulia). The eDNA-based method was applied to 14 sites within the Danubian Slizza basin, known to be inhabited by A. torrentium, but with insufficient information on their distribution. In addition, one station in the Tagliamento River basin was sampled to test the performance of the A. pallipes probe. The presence of A. torrentium is confirmed at 6 out of 15 sites. At four of these sites, A. torrentium is detected for the first time. In contrast, the presence of A. torrentium was not detected at two sites already known to harbour the species. Finally, the presence of A. pallipes was confirmed in the station belonging to the Tagliamento basin. The methodology described, which allows the distinction between the two species, paves the way for the parallel detection of the stone crayfish and the white-clawed crayfish (A. pallipes) through eDNA analysis. Full article
(This article belongs to the Special Issue eDNA for Basic and Applied Sciences)
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Review

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Review
Detection of Fish Pathogens in Freshwater Aquaculture Using eDNA Methods
Diversity 2022, 14(12), 1015; https://doi.org/10.3390/d14121015 - 22 Nov 2022
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Abstract
Organisms release their nucleic acid in the environment, including the DNA and RNA, which can be used to detect their presence. eDNA/eRNA techniques are being used in different sectors to identify organisms from soil, water, air, and ice. The advancement in technology led [...] Read more.
Organisms release their nucleic acid in the environment, including the DNA and RNA, which can be used to detect their presence. eDNA/eRNA techniques are being used in different sectors to identify organisms from soil, water, air, and ice. The advancement in technology led to easier detection of different organisms without impacting the environment or the organism itself. These methods are being employed in different areas, including surveillance, history, and conservation. eDNA and eRNA methods are being extensively used in aquaculture and fisheries settings to understand the presence of different fish species and pathogens in water. However, there are some challenges associated with the reliability of results because of the degradation of nucleic acid by several factors. In aquaculture, there are several diseases and parasites detected with these methods. In this review, we discuss different aquaculture diseases and parasites detected with eDNA/eRNA approach and the fate of these nucleic acids when subjected to different water quality and environmental parameters. This review intends to help the researcher with the potential of eDNA/eRNA-based detection of pathogens in aquaculture; this will be useful to predict a potential outbreak before it occurs. Along with that, this paper intends to help people understand several factors that degrade and can hamper the detection of these nucleic acids. Full article
(This article belongs to the Special Issue eDNA for Basic and Applied Sciences)
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