University of Oulu

Hupało, K, Majaneva, M, Czachur, MV, et al. An urban Blitz with a twist: rapid biodiversity assessment using aquatic environmental DNA. Environmental DNA. 2021; 3: 200– 213. https://doi.org/10.1002/edn3.152

An urban Blitz with a twist : rapid biodiversity assessment using aquatic environmental DNA

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Author: Hupało, Kamil1; Majaneva, Markus2,3; Czachur, Molly Victoria4;
Organizations: 1Aquatische Ökosystemforschung, University Duisburg-Essen, Essen, Germany
2Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
3Norwegian Institute for Nature Research (NINA), Trondheim, Norway
4Evolutionary Genomics Group, Stellenbosch University, Stellenbosch, South Africa
5Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS Université de Tours, Tours, France
6Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
7Department of Zoology, Stockholm University, Stockholm, Sweden
8Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Buenos Aires, Argentina
9Department of Ecology and Genetics, University of Oulu, Oulu, Finland
10Department of Biology and Bioinformatics, School of Bioscience, University of Skövde, Skövde, Sweden
11Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
12Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, UFMG, Belo Horizonte, Brazil
13Conservation Genetics Lab, Programa de Pós-graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, PUC Minas, Belo Horizonte, Brazil
14Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Brazil
15Department of Functional Ecology, Alfred Wegener Institute & Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
16Tromsø Museum, University of Tromsø – The Arctic University of Norway, Tromsø, Norway
17Barcoding Facility for Organisms and Tissues of Policy Concern (BopCo), Royal Museum for Central Africa, Tervuren, Belgium
18Centre for Global Sustainability Studies (CGSS), Hamzah Sendut Library, Universiti Sains Malaysia, Penang, Malaysia
19College of Life Sciences, Nankai University, Tianjin, China
20Natural History Museum, London, UK
21Biological and Earth Sciences, South Australian Museum, Adelaide, SA, Australia
22School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
23Department of Environmental Systems Science, ETH Zurich, Zürich, Switzerland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 2 MB)
Persistent link: http://urn.fi/urn:nbn:fi-fe2021071241344
Language: English
Published: John Wiley & Sons, 2021
Publish Date: 2021-07-12
Description:

Abstract

As global biodiversity declines, there is an increasing need to create an educated and engaged society. Having people of all ages participate in measuring biodiversity where they live helps to create awareness. Recently, the use of environmental DNA (eDNA) for biodiversity surveys has gained momentum. Here, we explore whether sampling eDNA and sequencing it can be used as a means of rapidly surveying urban biodiversity for educational purposes. We sampled 2 × 1 L of water from each of 15 locations in the city of Trondheim, Norway, including a variety of freshwater, marine, and brackish habitats. DNA was extracted, amplified in triplicate targeting the barcoding fragment of COI gene, and sequenced. The obtained data were analyzed on the novel mBRAVE platform, an online open-access software and computing resource. The water samples were collected in 2 days by two people, and the laboratory analysis was completed in 5 days by one person. Overall, we detected the presence of 506 BINs identified as belonging to 435 taxa, representing at least 265 putative species. On average, only 5.4% of the taxa were shared among six replicates per site. Based on the observed diversity, three distinct clusters were detected and related to the geographic distribution of sites. There were some taxa shared between the habitats, with a substantial presence of terrestrial biota. Here we propose a new form of BioBlitz, where with noninvasive sampling effort combined with swift processing and straightforward online analyses, hundreds of species can be detected. Thus, using eDNA analysis of water is useful for rapid biodiversity surveys and valuable for educational purposes. We show that rapid eDNA surveys, combined with openly available services and software, can be used as an educational tool to raise awareness about the importance of biodiversity.

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Series: Environmental DNA
ISSN: 2637-4943
ISSN-E: 2637-4943
ISSN-L: 2637-4943
Volume: 3
Issue: 1
Pages: 200 - 213
DOI: 10.1002/edn3.152
OADOI: https://oadoi.org/10.1002/edn3.152
Type of Publication: A1 Journal article – refereed
Field of Science: 1181 Ecology, evolutionary biology
Subjects:
Funding: WILEY; VWR Foundation; Helse Sør-Øst Genomics Core Facility at Oslo University Hospital; Illumina
Copyright information: © 2020 The Authors. Environmental DNA published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
  https://creativecommons.org/licenses/by/4.0/