R. Cruz-Cano, M. Kolb, R. A. Saldaña-Vázquez, L. Bretón-Deval, N. Cruz-Cano, A. Aldama-Cervantes
{"title":"Existing evidence on the use of environmental DNA as an operational method for studying rivers: a systematic map and thematic synthesis","authors":"R. Cruz-Cano, M. Kolb, R. A. Saldaña-Vázquez, L. Bretón-Deval, N. Cruz-Cano, A. Aldama-Cervantes","doi":"10.1186/s13750-024-00325-6","DOIUrl":null,"url":null,"abstract":"Environmental DNA (eDNA) is the DNA that can be extracted from an environmental sample, enabling the monitoring of whole biological communities across a large number of samples, at a potentially lower cost, which can significantly benefit river conservation. A systematic mapping protocol was designed to investigate the use of eDNA in rivers, specifically in terms of research topics, geographic and taxonomic biases, as well as information gaps. Furthermore, the potential research opportunities of eDNA in rivers and possible paths to find this kind of information on available platforms are identified. A published systematic map protocol was applied, consisting of a search for published articles and gray literature in two bibliographic databases and one search engine. All search results were submitted to a 2-stage screening for relevance and pertinence in accordance with pre-defined eligibility criteria. Data extraction and codification regarding country of study, year, taxonomic group, sequencing platform, and type of technique employed resulted in a publicly available database. From 7372 studies initially obtained by the search, 545 met the inclusion criteria spanning a period from 2003 to 2022. The five countries with most studies are: USA (134), Japan (61), China (54), Brazil (29) and the UK (25). The most used fragments to analyze DNA are 16S and COI, whilst 26S and 23S are the least used. Only 84 (15%) of the studies reported hypervariable regions, among which the most used are V4 and V5. Regarding taxonomic groups, fishes are most often studied (176), followed by bacteria (138) and virus (52), while fungi is the least studied group (3). Concerning data availability, 229 (42%) studies provided access to sequencing data. This study presents a comprehensive analysis of the available evidence regarding the implementation of the eDNA methods in rivers. The findings indicate that since the year 2003, this approach has been applied to aquatic lotic systems, and their recent increase can be attributed to the development of Next-Generation-Sequencing technologies and their reduced costs. However, there is a bias towards high-income countries, particularly USA and Europe. Widespread use and applications of this approach at a global level would allow for the generation of a large amount of information that can be compared between countries to understand if responses of aquatic systems follow similar patterns worldwide.","PeriodicalId":48621,"journal":{"name":"Environmental Evidence","volume":"42 1","pages":""},"PeriodicalIF":3.4000,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Environmental Evidence","FirstCategoryId":"93","ListUrlMain":"https://doi.org/10.1186/s13750-024-00325-6","RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"ENVIRONMENTAL SCIENCES","Score":null,"Total":0}
引用次数: 0
Abstract
Environmental DNA (eDNA) is the DNA that can be extracted from an environmental sample, enabling the monitoring of whole biological communities across a large number of samples, at a potentially lower cost, which can significantly benefit river conservation. A systematic mapping protocol was designed to investigate the use of eDNA in rivers, specifically in terms of research topics, geographic and taxonomic biases, as well as information gaps. Furthermore, the potential research opportunities of eDNA in rivers and possible paths to find this kind of information on available platforms are identified. A published systematic map protocol was applied, consisting of a search for published articles and gray literature in two bibliographic databases and one search engine. All search results were submitted to a 2-stage screening for relevance and pertinence in accordance with pre-defined eligibility criteria. Data extraction and codification regarding country of study, year, taxonomic group, sequencing platform, and type of technique employed resulted in a publicly available database. From 7372 studies initially obtained by the search, 545 met the inclusion criteria spanning a period from 2003 to 2022. The five countries with most studies are: USA (134), Japan (61), China (54), Brazil (29) and the UK (25). The most used fragments to analyze DNA are 16S and COI, whilst 26S and 23S are the least used. Only 84 (15%) of the studies reported hypervariable regions, among which the most used are V4 and V5. Regarding taxonomic groups, fishes are most often studied (176), followed by bacteria (138) and virus (52), while fungi is the least studied group (3). Concerning data availability, 229 (42%) studies provided access to sequencing data. This study presents a comprehensive analysis of the available evidence regarding the implementation of the eDNA methods in rivers. The findings indicate that since the year 2003, this approach has been applied to aquatic lotic systems, and their recent increase can be attributed to the development of Next-Generation-Sequencing technologies and their reduced costs. However, there is a bias towards high-income countries, particularly USA and Europe. Widespread use and applications of this approach at a global level would allow for the generation of a large amount of information that can be compared between countries to understand if responses of aquatic systems follow similar patterns worldwide.
期刊介绍:
Environmental Evidence is the journal of the Collaboration for Environmental Evidence (CEE). The Journal facilitates rapid publication of evidence syntheses, in the form of Systematic Reviews and Maps conducted to CEE Guidelines and Standards. We focus on the effectiveness of environmental management interventions and the impact of human activities on the environment. Our scope covers all forms of environmental management and human impacts and therefore spans the natural and social sciences. Subjects include water security, agriculture, food security, forestry, fisheries, natural resource management, biodiversity conservation, climate change, ecosystem services, pollution, invasive species, environment and human wellbeing, sustainable energy use, soil management, environmental legislation, environmental education.