scholarly journals Assessing ecological status in karstic lakes through the integration of phytoplankton functional groups, morphological approach and environmental DNA metabarcoding

2021 ◽  
Vol 131 ◽  
pp. 108166
Author(s):  
Nikola Hanžek ◽  
Marija Gligora Udovič ◽  
Katarina Kajan ◽  
Gábor Borics ◽  
Gábor Várbíró ◽  
...  
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.


2019 ◽  
Vol 3 ◽  
Author(s):  
Vasselon Valentin ◽  
Rimet Frédéric ◽  
Domaizon Isabelle ◽  
Monnier Olivier ◽  
Reyjol Yorick ◽  
...  

Ecological status assessment of watercourses is based on the calculation of quality indices using pollution sensitivity of targeted biological groups, including diatoms. The determination and quantification of diatom species is generally based on microscopic morphological identification, which requires expertise and is time-consuming and costly. In Europe, this morphological approach is legally imposed by standards and regulatory decrees by the Water Framework Directive (WFD). Over the past decade, a DNA-based molecular biology approach has newly been developed to identify species based on genetic criteria rather than morphological ones (i.e. DNA metabarcoding). In combination with high throughput sequencing technologies, metabarcoding makes it possible both to identify all species present in an environmental sample and to process several hundred samples in parallel. This article presents the results of two recent studies carried out on the WFD networks of rivers of Mayotte (2013–2018) and metropolitan France (2016–2018). These studies aimed at testing the potential application of metabarcoding for biomonitoring in the context of the WFD. We discuss the various methodological developments and optimisations that have been made to make the taxonomic inventories of diatoms produced by metabarcoding more reliable, particularly in terms of species quantification. We present the results of the application of this DNA approach on more than 500 river sites, comparing them with those obtained using the standardised morphological method. Finally, we discuss the potential of metabarcoding for routine application, its limits of application and propose some recommendations for future implementation in WFD.


2021 ◽  
Vol 33 ◽  
Author(s):  
Klivia Rilavia Paiva da Silva ◽  
José Etham de Lucena Barbosa ◽  
Lucineide Maria Santana ◽  
Luciana Gomes Barbosa

Abstract: Aim The study analyzed the potential use of the phytoplankton functional groups as an environmental bioindicator in aquatic ecosystems of Brazilian semiarid region. Methods Using data collected over five years of a natural lagoon and two reservoirs, we evaluate the relationship between functional groups and environmental conditions through the multivariate approach. The Q index was applied to assess ecological status in these ecosystems. Results In Panati, the temporary and natural lagoon, the partial habitat desiccation and presence of macrophytes reflected in the less nutrients concentrations and phytoplankton composition, with high biomass of coccoids Chlorophyceae, diatoms and desmids (functional groups J, MP and N, respectively). Taperoá and Soledade reservoirs presented high cyanobacteria contribution, however the biomass and contribution of cyanobacteria in Taperoá (SN, S1) were lower than in Soledade. In this reservoir, cyanobacteria were more abundant, alternating in dominance (LO, M, LM, SN, S1). According to tendencies revealed by Redundancy Analysis (RDA), the main driving abiotic factors on the phytoplankton functional groups were pH, nutrients and light availability. As expected, phytoplankton composition directly influenced the Q index result, showing mostly bad to tolerable conditions in Soledade, medium to good in Taperoá and good to excellent in Panati. Conclusions The Q index was a good tool to assess the water quality and ecological status in aquatic ecosystems from the Brazilian semiarid region, reflecting the influence of natural control mechanisms on the harmful cyanobacteria blooms in temporary ecosystems.


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.


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

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.


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