eDNA‑based detection of the invasive crayfish Pacifastacus leniusculus in streams with a LAMP assay using dependent replicates to gain higher sensitivity

Occurrence
Latest version published by National Museum of Natural History, Luxembourg on Nov 14, 2022 National Museum of Natural History, Luxembourg
Publication date:
14 November 2022
License:
CC0 1.0

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Data as a DwC-A file download 340 records in English (49 KB) - Update frequency: not planned
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Description

The records in this dataset were collected and evaluated for the following publication: Porco, D., Hermant, S., Purnomo, C.A. et al. eDNA-based detection of the invasive crayfish Pacifastacus leniusculus in streams with a LAMP assay using dependent replicates to gain higher sensitivity. Sci Rep 12, 6553 (2022). https://doi.org/10.1038/s41598-022-10545-w

Abstract of the publication: LAMP assays are becoming increasingly popular in the feld of invasive species detection but are still underused in eDNA-based monitoring. Here, we propose a LAMP assay designed to detect the North American crayfsh species Pacifastacus leniusculus in water samples from streams. The presence of P. leniusculus was detected through this new LAMP assay in all but one of the nine sites sampled. No correlation was found between ddPCR absolute concentration measurements and the number of LAMP-positive technical replicates. However, we showed that using dependent technical replicates could signifcantly enhance the detection sensitivity of the LAMP assay. Applied to other assays, it could improve sensitivity and thus allow for a more efcient use of eDNA-based LAMP assays for invasive species detection in aquatic ecosystems.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 340 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Porco D (2022): eDNA‑based detection of the invasive crayfish Pacifastacus leniusculus in streams with a LAMP assay using dependent replicates to gain higher sensitivity. v1.10. National Museum of Natural History, Luxembourg. Dataset/Occurrence. https://gbif.mnhn.lu/ipt/resource?r=edna_pacifastacus_leniusculus_2022&v=1.10

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is National Museum of Natural History, Luxembourg. To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: ea16e238-4e23-41fb-9eee-c1ea4f0caa63.  National Museum of Natural History, Luxembourg publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF Luxembourg.

Keywords

Occurrence

Contacts

David Porco
  • Originator
  • Point Of Contact
researcher
National Museum of Natural History, Luxembourg
25 Rue Münster
L-2160 Luxembourg
LU
Paul Braun
  • Metadata Provider
  • Point Of Contact
Digital Curator
National Museum of Natural History, Luxembourg
25 Rue Münster
L-2160 Luxembourg
LU

Geographic Coverage

Luxembourg

Bounding Coordinates South West [49.425, 5.691], North East [50.198, 6.537]

Temporal Coverage

Start Date / End Date 2021-10-07 / 2021-10-11

Project Data

DNADIVE aims at developing a toolbox for the molecular monitoring of invasive crayfish in the streams of Luxembourg. Three exotic species (Orconectes limosus, Pacifastacus leniusculus and Astacus leptodactylus) and a native one (Astacus astacus) will be targeted for the project. This molecular toolbox will encompass several techniques of detection comprising (1) a simple amplification method easily performed in a laboratory with few elements, (2) a digital droplet amplification (ddPCR) which is a more elaborated lab method that can allow for a higher detection sensitivity and a possible quantification of DNA that could be related through the proxy of biomass and abundance to the size of the populations detected and (3) an isotherm amplification method (iPCR) i.e. a simple, cost effective approach which will allow for a field detection usable by non-trained agents. The results will enable the development of a predictive species distribution model for the target species and to infer their impact on freshwater communities through the comparison with previous sampling campaigns.This set of methods has the high potential to efficiently contribute to early detection and routine monitoring of the invasive crayfish species in Luxembourg, thus allowing for a timely and efficient decision-making and appropriate management.

Title eDNA Detection for crayfish InvasiVE species in streams of Luxembourg: development of a molecular toolbox
Identifier fnr_6a3662d14403588d48664fb09ec37a0b
Funding National Research Fund Luxembourg 2, Avenue de l'Universite (Maison du Savoir B.P. 1777) L-1017 Luxembourg, 4365 Esch-sur-Alzette Grant Number: fnr_6a3662d14403588d48664fb09ec37a0b

The personnel involved in the project:

David Porco

Additional Metadata

Alternative Identifiers ea16e238-4e23-41fb-9eee-c1ea4f0caa63
https://gbif.mnhn.lu/ipt/resource?r=edna_pacifastacus_leniusculus_2022