Assessment of benthic invertebrate diversity and river ecological status along an urbanized gradient using environmental DNA metabarcoding and a traditional survey method

Author(s):  
Fenfen Ji ◽  
Dingyi Han ◽  
Liang Yan ◽  
Saihong Yan ◽  
Jinmiao Zha ◽  
...  
Water ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 331
Author(s):  
Sofia Duarte ◽  
Barbara R. Leite ◽  
Maria João Feio ◽  
Filipe O. Costa ◽  
Ana Filipa Filipe

Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs.


2020 ◽  
Vol 30 (0) ◽  
pp. 125-132
Author(s):  
Shusaku HIRAKAWA ◽  
Jun NAKAJIMA ◽  
Masaya MATSUKI ◽  
Takaoki KOGA ◽  
Koichiro HATA ◽  
...  

2021 ◽  
Vol 4 ◽  
Author(s):  
Denis Caudron ◽  
Lucie Galland ◽  
Melanie Taquet ◽  
Valentin Vasselon

A wild river is a living river, which is at baseline, well-preserved, and which runs freely and is home to a rich biodiversity in its high quality waters and on its banks. In Europe there are very few rivers which could be considered “wild”, which function at a high ecological level, since wild rivers, in the true sense of the term, no longer exist. Based on the fact that these rivers remain threatened, and that the existing tools (technical, regulatory, and financial) are insufficient and not adapted to ensure their preservation over the long term, the Wild Rivers project was founded in 2007, through a meeting of environmental defenders, scientists, fishermen, managers of land and river natural resources, and elected officials, all of whom were anxious to save the last of the French rivers which were still preserved, with a human impact that would be compatible with the conservation of the ecosystem. In 2014 the “Wild Rivers Site” label was created in France, as a conservation tool for rivers, both voluntary and non-regulatory, which allows the support necessary to enable the territorial players to preserve their rivers in harmony with the activity in the surrounding valleys. It also identifies and highlights these unique watercourses. The Valserine in the Ain region was the first river to obtain the Wild Rivers Site label. Today 28 rivers in France are labelled “Wild Rivers Sites” and the 22 management structures of these rivers are members of the Wild Rivers Site Network. To obtain the label, a river must fulfill two sets of criteria 1. The criteria grid: The watercourse must obtain a mark over 70/100. The grid is composed of 47 criteria evaluating the quality of the area, of which 12 are eliminatory, 8 are unrated, and 9 are under a bonus/penalty scheme 2. The program of actions taken by local players: The local managers must put in place a system of governance built around actions to be taken over a period of years, shared among them, and ambitious, going beyond the regulatory objectives of the European Directive Framework. It allows for the restoration of penalty points and the establishment of innovative conservation activities. The Wild Rivers Sites are also an open air laboratory for the development and use of innovative methods in order to provide new information on aquatic environments, and to improve their management and conservation. Numerous steps have already been taken within the network, such as the Ecosystem Services Study (Costa and Hernandez 2019); on the study of the genetic makeup of the brown trout population. Recently, the use of genetic study using environmental DNA to complete biodiversity inventories has also been deployed to study benthic diatoms (DNA of Diatoms Project 2020-2022). This project seeks to use DNA metabarcoding to respond to a number of objectives: i) inventory of the species of diatoms and their community structure in these watercourses which are generally seldom studied; ii) complete ecological status studies; iii) develop new genetic metrics and taxonomies adapted to the conservation of wild river watercourses. It is in this spirit that the Wild Rivers program was developed, and has received numerous positive responses on the behalf of watercourse management in France. Thanks to this impetus, work has been conducted to extend this conservation label to water sources in other countries (Switzerland, Ireland, Spain), with the future plan of building a European network dedicated to the conservation of Wild Rivers.


Author(s):  
Yoshihisa AKAMATSU ◽  
Takayoshi TSUZUKI ◽  
Ryota YOKOYAMA ◽  
Yayoi FUNAHASHI ◽  
Munehiro OHTA ◽  
...  

Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac

Chapter 10 “Environmental DNA for functional diversity” discusses the potential of environmental DNA to assess functional diversity. It first focuses on DNA metabarcoding and discusses the extent to which this approach can be used and/or optimized to retrieve meaningful information on the functions of the target community. This knowledge usually involves coarsely defined functional groups (e.g., woody, leguminous, graminoid plants; shredders or decomposer soil organisms; pathogenicity or decomposition role of certain microorganisms). Chapter 10 then introduces metagenomics and metatranscriptomics approaches, their advantages, but also the challenges and solutions to appropriately sampling, sequencing these complex DNA/RNA populations. Chapter 10 finally presents several strategies and software to analyze metagenomes/metatranscriptomes, and discusses their pros and cons.


Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac

Environmental DNA (eDNA), i.e. DNA released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on the distribution or feeding habits of species. It has therefore great potential for applications in ecology and biodiversity management. However, this research field is fast-moving, involves different areas of expertise and currently lacks standard approaches, which calls for an up-to-date and comprehensive synthesis. Environmental DNA for biodiversity research and monitoring covers current methods based on eDNA, with a particular focus on “eDNA metabarcoding”. Intended for scientists and managers, it provides the background information to allow the design of sound experiments. It revisits all steps necessary to produce high-quality metabarcoding data such as sampling, metabarcode design, optimization of PCR and sequencing protocols, as well as analysis of large sequencing datasets. All these different steps are presented by discussing the potential and current challenges of eDNA-based approaches to infer parameters on biodiversity or ecological processes. The last chapters of this book review how DNA metabarcoding has been used so far to unravel novel patterns of diversity in space and time, to detect particular species, and to answer new ecological questions in various ecosystems and for various organisms. Environmental DNA for biodiversity research and monitoring constitutes an essential reading for all graduate students, researchers and practitioners who do not have a strong background in molecular genetics and who are willing to use eDNA approaches in ecology and biomonitoring.


2021 ◽  
Author(s):  
José Luis Mena ◽  
Hiromi Yagui ◽  
Vania Tejeda ◽  
Emilio Bonifaz ◽  
Eva Bellemain ◽  
...  

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