Monitoring newt communities in urban area using eDNA metabarcoding

Newts are amphibians commonly present in small ponds or garden pools in urban areas. They are protected in many countries and their presence is monitored through visual observation and/or trapping. However, newts are not easy to spot as they are small, elusive and often hidden at the bottom of water...

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Autores principales:	Léo Charvoz, Laure Apothéloz-Perret-Gentil, Emanuela Reo, Jacques Thiébaud, Jan Pawlowski
Formato:	article
Lenguaje:	EN
Publicado:	PeerJ Inc. 2021
Materias:	eDNA Metabarcoding Newt Illumina Invasive Water Medicine R
Acceso en línea:	https://doaj.org/article/da7c3f72d7c04291bcf7278dd6115e3a
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id	oai:doaj.org-article:da7c3f72d7c04291bcf7278dd6115e3a
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spelling	oai:doaj.org-article:da7c3f72d7c04291bcf7278dd6115e3a2021-11-28T15:05:10ZMonitoring newt communities in urban area using eDNA metabarcoding10.7717/peerj.123572167-8359https://doaj.org/article/da7c3f72d7c04291bcf7278dd6115e3a2021-11-01T00:00:00Zhttps://peerj.com/articles/12357.pdfhttps://peerj.com/articles/12357/https://doaj.org/toc/2167-8359Newts are amphibians commonly present in small ponds or garden pools in urban areas. They are protected in many countries and their presence is monitored through visual observation and/or trapping. However, newts are not easy to spot as they are small, elusive and often hidden at the bottom of water bodies. In recent years, environmental DNA (eDNA) has become a popular tool for detecting newts, with a focus on individual species using qPCR assays. Here, we assess the effectiveness of eDNA metabarcoding compared to conventional visual surveys of newt diversity in 45 ponds within urban areas of Geneva canton, Switzerland. We designed newt-specific mitochondrial 16S rRNA primers, which assign the majority of amplicons to newts, and were able to detect four species known to be present in the region, including the invasive subspecies Lissotriton vulgaris meridionalis, native to the Italian peninsula, that has been introduced in the Geneva area recently. The obtained eDNA results were congruent overall with conventional surveys, confirming the morphological observations in the majority of cases (67%). In 25% of cases, a species was only detected genetically, while in 8% of cases, the observations were not supported by eDNA metabarcoding. Our study confirms the usefulness of eDNA metabarcoding as a tool for the effective and non-invasive monitoring of newt community and suggests its broader use for the survey of newt diversity in urban area at larger scales.Léo CharvozLaure Apothéloz-Perret-GentilEmanuela ReoJacques ThiébaudJan PawlowskiPeerJ Inc.articleeDNAMetabarcodingNewtIlluminaInvasiveWaterMedicineRENPeerJ, Vol 9, p e12357 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	eDNA Metabarcoding Newt Illumina Invasive Water Medicine R
spellingShingle	eDNA Metabarcoding Newt Illumina Invasive Water Medicine R Léo Charvoz Laure Apothéloz-Perret-Gentil Emanuela Reo Jacques Thiébaud Jan Pawlowski Monitoring newt communities in urban area using eDNA metabarcoding
description	Newts are amphibians commonly present in small ponds or garden pools in urban areas. They are protected in many countries and their presence is monitored through visual observation and/or trapping. However, newts are not easy to spot as they are small, elusive and often hidden at the bottom of water bodies. In recent years, environmental DNA (eDNA) has become a popular tool for detecting newts, with a focus on individual species using qPCR assays. Here, we assess the effectiveness of eDNA metabarcoding compared to conventional visual surveys of newt diversity in 45 ponds within urban areas of Geneva canton, Switzerland. We designed newt-specific mitochondrial 16S rRNA primers, which assign the majority of amplicons to newts, and were able to detect four species known to be present in the region, including the invasive subspecies Lissotriton vulgaris meridionalis, native to the Italian peninsula, that has been introduced in the Geneva area recently. The obtained eDNA results were congruent overall with conventional surveys, confirming the morphological observations in the majority of cases (67%). In 25% of cases, a species was only detected genetically, while in 8% of cases, the observations were not supported by eDNA metabarcoding. Our study confirms the usefulness of eDNA metabarcoding as a tool for the effective and non-invasive monitoring of newt community and suggests its broader use for the survey of newt diversity in urban area at larger scales.
format	article
author	Léo Charvoz Laure Apothéloz-Perret-Gentil Emanuela Reo Jacques Thiébaud Jan Pawlowski
author_facet	Léo Charvoz Laure Apothéloz-Perret-Gentil Emanuela Reo Jacques Thiébaud Jan Pawlowski
author_sort	Léo Charvoz
title	Monitoring newt communities in urban area using eDNA metabarcoding
title_short	Monitoring newt communities in urban area using eDNA metabarcoding
title_full	Monitoring newt communities in urban area using eDNA metabarcoding
title_fullStr	Monitoring newt communities in urban area using eDNA metabarcoding
title_full_unstemmed	Monitoring newt communities in urban area using eDNA metabarcoding
title_sort	monitoring newt communities in urban area using edna metabarcoding
publisher	PeerJ Inc.
publishDate	2021
url	https://doaj.org/article/da7c3f72d7c04291bcf7278dd6115e3a
work_keys_str_mv	AT leocharvoz monitoringnewtcommunitiesinurbanareausingednametabarcoding AT laureapothelozperretgentil monitoringnewtcommunitiesinurbanareausingednametabarcoding AT emanuelareo monitoringnewtcommunitiesinurbanareausingednametabarcoding AT jacquesthiebaud monitoringnewtcommunitiesinurbanareausingednametabarcoding AT janpawlowski monitoringnewtcommunitiesinurbanareausingednametabarcoding
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Monitoring newt communities in urban area using eDNA metabarcoding

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