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

Kamil Hupało,Sonja Leidenberger,Vladislav Ivanov,Lasse Topstad,Daniel Marquina,Kenny Meganck,Molly Victoria Czachur,Kristy Deiner,Torbjørn Ekrem,Markus Majaneva,Zuzana Čiamporová‐Zaťovičová,Lucas Sire,Andrea Desiderato,Gaute Kjærstad,Z A Danial Hariz ,Izabela Santos Mendes ,Mark I Stevens ,F Cĭampor ,Darío A Lijtmaer ,Benjamin W Price ,Lin X

doi:10.1002/edn3.152

Abstract

AbstractAs 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.

Highlights

Global biodiversity is imperiled with an estimated one million species at risk of extinction (IPBES, 2019)
Because the data collected here were digitized shortly after collection in the form of DNA sequences and available through Multiplex Barcode Research And Visualization Environment (mBRAVE), as a team of people from 14 different countries many of whom had never generated or analyzed environmental DNA (eDNA) information, we could collectively engage in learning about the biodiversity in the city of Trondheim from all over the world
The sampling strategy implemented in our study was based on a noninvasive eDNA metabarcoding sampling method, differing from the methodology used in the referenced studies which relies solely on single-specimen DNA barcoding (Laforest et al, 2013; Sobel et al, 2017; Telfer et al, 2015)

Summary

Introduction

Global biodiversity is imperiled with an estimated one million species at risk of extinction (IPBES, 2019). There is an urgent need to build consensus around action and reverse the impending loss of life from our planet. Many biodiversity observation programs exist to engage with the public (e.g., BioBlitz; Postles & Bartlett, 2018). When such surveys occur, the amount of equipment, resources, and time needed from experts to survey diversity across the tree of life quickly becomes intractable for many educators. Educational and outreach programs using rapid biodiversity surveys are often limited in their taxonomic breadth, are infrequent, and are offered mostly by larger organizations (Postles & Bartlett, 2018; Ruch et al, 2010)

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Conclusion