scholarly journals Validation of river typologies using molecular information from diatoms

2021 ◽  
Vol 4 ◽  
Author(s):  
Andreia Mortágua ◽  
Marco Teixeira ◽  
Manuela Sales ◽  
Maria Feio ◽  
Salomé Almeida
Keyword(s):  
Water Framework Directive ◽  
Reference Conditions ◽  
Ecological Indicators ◽  
Molecular Data ◽  
Reference Database ◽  
Depth Information ◽  
Morphological Identification ◽  
Body Type ◽  
Dna Metabarcoding ◽  
Total Environment

The European Water Framework Directive (2000/60/EC) includes biological assessment of water bodies that has been implemented for many years. Indicator organisms such as diatoms respond to geological and hydrological features of rivers by modifying their structure. Therefore, when implementing the WFD, it was necessary to establish type-specific reference conditions to be able to measure the deviations of sampled communities due to anthropogenic impact.HTS-related eDNA metabarcoding has been developed to complement or even replace traditional approaches for its rapid, low-cost and highly accurate identification of communities for assessment of rivers’ ecological status (e.g. Mortágua et al., 2019; Pérez-Burillo et al. 2020) and proved to provide even more in-depth information about biological elements. The use of this information without assignment to species is being addressed once it eliminates the limiting factor of the reference database incompleteness and may provide new ecological information (e.g. Feio et al., 2020; Rivera et al., 2020). Since WFD requires the establishment of reference conditions for each water body type, for eDNA methods’ implementation it will be essential to review, confirm or reformulate, and perhaps create new typologies. Hereupon, the aim of this study is to analyze diatom communities from different typologies of Portuguese rivers resulting from DNA metabarcoding data and compare it with current typology system. To do so, we will verify the consistency of biological groups included in each type, validate the molecular data, analyze the correspondence of OTU/ISU/ESV to environmental characteristics of rivers. A total of 154 sampling sites were selected from central Portugal and northern Portugal in 2017 and 2019. The biofilm was collected for morphological identification and DNA sequencing of diatoms. Reference sites were selected for 4 river types (mountain, littoral, small and medium-large northern rivers) based on a set of pressure information (water quality, hydromorphology, land use and riparian zones). Diatom inventories were obtained from molecular and morphological analysis. DNA sequences were treated using Mothur software which processed two bioinformatic strategies in order to obtain the final ISU and OTU tables, while ESVs were treated with DADA2 package from R. Identification and counting of diatom valves took place under the light microscope concerning the morphological approach. We expect results to validate the molecular data for each typology either when assigning to species or not, and to understand whether it is necessary to establish new typologies for future use of the molecular approach in ecological assessment of rivers. Directive, W. F. (2000). Water Framework Directive. Journal reference OJL, 327, 1-73. Feio, M. J., Serra, S. R., Mortágua, A., Bouchez, A., Rimet, F., Vasselon, V., & Almeida, S. F. P. (2020). A taxonomy-free approach based on machine learning to assess the quality of rivers with diatoms. Science of the Total Environment, 722, 137900. https://doi.org/10.1016/j.scitotenv.2020.137900 Mortágua, A., Vasselon, V., Oliveira, R., Elias, C., Chardon, C., Bouchez, A., ... & Almeida, S. F. P. (2019). Applicability of DNA metabarcoding approach in the bioassessment of Portuguese rivers using diatoms. Ecological indicators, 106, 105470. https://doi.org/10.1016/j.ecolind.2019.105470 Pérez-Burillo, J., Trobajo, R., Vasselon, V., Rimet, F., Bouchez, A., & Mann, D. G. (2020). Evaluation and sensitivity analysis of diatom DNA metabarcoding for WFD bioassessment of Mediterranean rivers. Science of the Total Environment, 727, 138445. https://doi.org/10.1016/j.scitotenv.2020.138445 Rivera, S. F., Vasselon, V., Bouchez, A., & Rimet, F. (2020). Diatom metabarcoding applied to large scale monitoring networks: Optimization of bioinformatics strategies using Mothur software. Ecological indicators, 109, 105775. https://doi.org/10.1016/j.ecolind.2019.105775

scholarly journals Assessing pollution of aquatic environments with diatoms’ DNA metabarcoding: experience and developments from France water framework directive networks

2019 ◽  
Vol 3 ◽  
Author(s):  
Vasselon Valentin ◽  
Rimet Frédéric ◽  
Domaizon Isabelle ◽  
Monnier Olivier ◽  
Reyjol Yorick ◽  
...  
Keyword(s):  
Water Framework Directive ◽  
High Throughput Sequencing ◽  
Ecological Status ◽  
Aquatic Environments ◽  
Morphological Identification ◽  
The Past ◽  
Sequencing Technologies ◽  
Dna Metabarcoding ◽  
Morphological Approach ◽  
Status Assessment

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.

scholarly journals Composition of diatom communities on travertine barriers of the Una River (Bosnia and Herzegovina) obtained by DNA metabarcoding and morphological analysis

2021 ◽  
Vol 4 ◽  
Author(s):  
Jasmina Kamberović ◽  
Marija Gligora Udovič ◽  
Maria Kahlert ◽  
Kálmán Tapolczai ◽  
Zorana Lukić ◽  
...  
Keyword(s):  
Bosnia And Herzegovina ◽  
Analysis Data ◽  
Reference Database ◽  
Morphological Identification ◽  
Dna Metabarcoding ◽  
Morphological Approach ◽  
Diatom Communities ◽  
Identification Approach ◽  
Electron Microscopes ◽  
Scanning Electron Microscopes

The process of travertine formation and carbonate deposition in the rivers is unique, delicate, and depends on the activity of algae and mosses. Although diatoms have been used extensively in hydrobiological studies, the comparative analysis data on diatom communities of the travertine barriers in karstic rivers are still scarce. The study aimed to detect the diatom composition on travertine barriers in the Una River, the large karstic river in Bosnia and Herzegovina. An integrated classical morphological identification approach with metabarcoding was applied on eight samples across the river length profile. Morphological analyses were performed using both light and scanning electron microscopes. Subsequent DNA metabarcoding of the chloroplastic gene 312bp rbcL was done. The DADA2 pipeline was used for the bioinformatic treatment of the demultiplexed MiSeq reads to infer Amplicon Sequence Variants (ASVs). ASVs were taxonomically assigned using the Diat.barcode v7 reference database. A total of 126 species were identified using the morphological approach, while 133 ASVs were taxonomically assigned to 58 unique taxa with the molecular approach. Diatom community structures in terms of molecular and morphological approaches were congruent with 49 shared species. Species from genera Gomphonema, Navicula and Encyonema were less assigned in molecular analysis. The most abundant taxa in the Una River are alkaliphilous, belonging to the genera Gomphonema, Nitzshia and Navicula. Although specific for their extremely good chemical status, the travertine barriers of the Una River are largely inhabited with meso-eutraphentic taxa.

scholarly journals Land-use and agriculture in Denmark around year 1900 and the quest for EU Water Framework Directive reference conditions in coastal waters

AMBIO ◽  
2021 ◽  
Author(s):  
Bent T. Christensen ◽  
Birger F. Pedersen ◽  
Jørgen E. Olesen ◽  
Jørgen Eriksen
Keyword(s):  
Land Use ◽  
Water Framework Directive ◽  
Coastal Waters ◽  
Root Zone ◽  
Reference Conditions ◽  
Ecological Status ◽  
Agricultural Activity ◽  
Eu Water Framework Directive ◽  
Alternative Approach ◽  
The Eu

AbstractThe EU Water Framework Directive (WFD) aims to protect the ecological status of coastal waters. To establish acceptable boundaries between good and moderate ecological status, the WFD calls for reference conditions practically undisturbed by human impact. For Denmark, the nitrogen (N) concentrations present around year 1900 have been suggested to represent reference conditions. As the N load of coastal waters relates closely to runoff from land, any reduction in load links to agricultural activity. We challenge the current use of historical N balances to establish WFD reference conditions and initiate an alternative approach based on parish-level land-use statistics collected 1896/1900 and N concentrations in root zone percolates from experiments with year 1900-relevant management. This approach may be more widely applicable for landscapes with detailed historic information on agricultural activity. Using this approach, we find an average N concentration in root zone percolates that is close to that of current agriculture. Thus, considering Danish coastal waters to be practically unaffected by human activity around year 1900 remains futile as 75% of the land area was subject to agricultural activity with a substantial potential for N loss to the environment. It appears unlikely that the ecological state of coastal waters around year 1900 may serve as WFD reference condition.

scholarly journals Monitoring Scotland’s transitional water fish communities under the EU Water Framework Directive

2021 ◽  
Vol 27 (3) ◽  
pp. 48-67
Author(s):  
M. O’Reilly ◽  
J. Boyle ◽  
S. Nowacki ◽  
M. Elliott ◽  
R. Foster
Keyword(s):  
Water Framework Directive ◽  
Assessment Tool ◽  
Reference Conditions ◽  
Ecological Status ◽  
Fish Communities ◽  
High Status ◽  
Eu Water Framework Directive ◽  
Transitional Waters ◽  
Water Fish ◽  
The Eu

The history of monitoring transitional water fish in Scotland is briefly outlined. The requirements of the EU Water Framework Directive are explained and how this applies to the monitoring of transitional water fish communities in Scotland is described. The development of a monitoring programme for Scotland is outlined, including sampling methods and strategies. Six transitional waters were selected as representative for Scotland covering three different types of transitional water. A multi-metric tool, the Transitional Water Fish Classification Index was used to assess the ecological status of the fish communities in these waters and the operation of the different metrics and the creation of appropriate reference conditions is explained. The assessment tool was applied to survey data from 2005 to 2018, although only the more recent data fully met the tool requirements. The species composition and abundances in the respective transitional waters were compared. The fully valid surveys were all classed as of Good or High status, indicating the fish communities in all the representative transitional waters appeared to be in good ecological health. The efficacy of the different metrics is considered and some issues with Metric 2, enumerating migratory species, are discussed at length. A new multi-metric tool, the Estuarine Multi-metric Fish Index, is briefly discussed and its introduction for the assessments in Scotland is recommended.

scholarly journals Diat.barcode: a DNA tool to decipher diatom communities for the evaluation environmental pressures

2021 ◽  
Vol 4 ◽  
Author(s):  
Frederic Rimet ◽  
Teofana Chonova ◽  
Gilles Gassiole ◽  
Maria Kahlert ◽  
François Keck ◽  
...  
Keyword(s):  
Taxonomic Diversity ◽  
R Package ◽  
Life Forms ◽  
Reference Database ◽  
Sequencing Data ◽  
Culture Collections ◽  
Environmental Pressures ◽  
Ecological Features ◽  
Dna Metabarcoding ◽  
Environmental Sequences

Diatoms (Bacillariophyta) are ubiquitous microalgae, which present a huge taxonomic diversity, changing in correlation with differing environmental conditions. This makes them excellent ecological indicators for various ecosystems and ecological problematics (ecotoxicology, biomonitoring, paleo-environmental reconstruction …). Current standardized methodologies for diatoms are based on microscopic determinations, which is time consuming and prone to identification uncertainties. DNA metabarcoding has been proposed as a way to avoid these flaws, enabling the sequencing of a large quantity of barcodes from natural samples. A taxonomic identity is given to these barcodes by comparing their sequences to a barcoding reference library. However, to identify environmental sequences correctly, the reference database should contain a representative number of reference sequences to ensure a good coverage of diatom diversity. Moreover, the reference database needs to be carefully taxonomically curated by experts, as its content has an obvious impact on species detection. Diat.barcode is an open-access library for diatoms linking diatom taxonomic identities to rbcL barcode sequences (a chloroplast marker suitable for species-level identification of diatoms), which has been maintained since 2012. Data are accumulated from three sources: (1) the NCBI nucleotide database, (2) unpublished sequencing data of culture collections and more recently (3) environmental sequences. Since 2017, an international network of experts in diatom taxonomy curate this library. The last version of the database (version 9.2), includes 8066 entries that correspond to more than 280 different genera and 1490 different species. In addition to the taxonomic information, morphological features (e.g. biovolumes, chloroplasts, etc.), life-forms (mobility, colony-type) and ecological features (taxa preferences to pollution) are given. The database can be downloaded from the website (www6.inrae.fr/carrtel-collection/Barcoding-database/) or directly through the R package diatbarcode. Ready-to-use files for commonly used metabarcoding pipelines (Mothur and DADA2) are also available.

scholarly journals Ichthyoplankton metabarcoding as a tool for studying fish reproductive dynamics

2021 ◽  
Vol 4 ◽  
Author(s):  
Daniel Teixeira ◽  
Heron Hilário ◽  
Gustavo Rosa ◽  
Guilherme Santos ◽  
Gilmar Santos ◽  
...  
Keyword(s):  
Fish Assemblages ◽  
Fish Larvae ◽  
Reference Sequence ◽  
12S Rrna ◽  
Morphological Identification ◽  
Rrna Gene ◽  
Fish Eggs ◽  
Migration Routes ◽  
Dna Metabarcoding ◽  
Primer Sets

The study of ichthyoplankton composition, abundance and distribution is paramount to understand the reproductive dynamics of local fish assemblages. The analysis of these parameters allows the identification of spawning sites, nursery areas and migration routes. However, due to the lack of characters in early life stages, the morphological identification of ichthyoplankton is often impractical and many studies identify only fish larvae. Additionally, its accuracy shows great variation between taxonomists and laboratories according to their experience and specialty. DNA barcoding emerged as an alternative to provide assertive identification of fish eggs and larvae, but it becomes too expensive and laborious when the study demands the processing of huge amounts of organisms. DNA metabarcoding can overcome these limitations as a rapid, cost-effective, broad and accurate taxonomy tool, allowing the identification of multiple individuals simultaneously. Here, we present the identification of a sample containing 68 fish eggs and another containing 293 fish larvae from a single site in the São Francisco River Basin, Eastern Brazil, through DNA metabarcoding. We used a low-cost saline DNA extraction followed by PCR amplification with three primer sets targeting the 12S rRNA gene: MiFish (~170bp), Teleo_1 (~60bp), and NeoFish (~190bp). The latter was recently developed by our research group specifically for the identification of Neotropical fishes. All the amplified samples were sequenced in a single multiplexed Illumina MiniSeq run. We performed the filtering steps and assigned Amplicon Sequence Variants (ASVs) using a DADA2/Phyloseq based pipeline and a custom 12S reference sequence database including 101 species and 70 genera from the Jequitinhonha and São Francisco basins. The species Cyphocharax gilbert, Leporinus taeniatus, Megaleporinus elongatus, Prochilodus argenteus, P. costatus and Psalidodon fasciatus were detected by all three primer sets in the larva pool, while Pterygoplichthys etentaculatus was detected solely by NeoFish (Fig. 1). Within the egg pool, all three markers detected the species Characidium zebra, Curimatella lepidura, M. elongatus, Pimelodus fur and P. costatus, but Brycon orthotaenia was detected only by NeoFish, P. maculatus only by Teleo, and P. pohli by MiFish and Teleo (Fig. 1). The consistency in species detection among all three markers underpins the credibility of this method to accurately describe the sample composition. Considering that most of species were exclusive to the larvae or egg pool, our experiment highlights the importance of including the identification of fish eggs in reproduction studies, as it can provide additional information about which species are spawning in an area. Furthermore, the application of DNA metabarcoding to the study of ichthyoplankton can help decision makers create more informed guidelines for conservation of economically and ecologically important fish species.

The genus Cystoseira s.l. (Ochrophyta, Fucales, Sargassaceae) in the Black Sea: morphological variability and molecular taxonomy of Gongolaria barbata and endemic Ericaria crinita f. bosphorica comb. nov.

Phytotaxa ◽  
2021 ◽  
Vol 480 (1) ◽  
pp. 1-21
Author(s):  
SOFIA S. SADOGURSKA ◽  
JOÃO NEIVA ◽  
ANNALISA FALACE ◽  
ESTER A. SERRÃO ◽  
ÁLVARO ISRAEL
Keyword(s):  
Mediterranean Sea ◽  
Black Sea ◽  
Molecular Taxonomy ◽  
Morphological Variability ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Morphological Data ◽  
The Black Sea ◽  
Morphological Identification ◽  
Additional Tool

Brown algae of the genus Cystoseira sensu lato form the most diverse and productive marine ecosystems throughout the Mediterranean Sea and have equal roles also in the Black Sea where they have been decreasing in the recent years. The taxonomy of Cystoseira s.l. taxa from the Black Sea is still not well understood, and questions arise when related taxa have to be delimited. In addition to morphological descriptions, this study provides for the first time molecular data of the Black Sea Cystoseira s.l. distinct morphologies as an additional tool to clarify their identities and phylogenetic affinities. The analysis of two mitochondrial markers (cytochrome oxidase subunit 1—COI, and 23S-tRNAVal intergenic spacer—mt-spacer) showed that Cystoseira s.l. specimens from the Black Sea belong to two recently resurrected genera, namely Gongolaria and Ericaria. Molecular data confirm the morphological identification of G. barbata, which is characterized by high morphological plasticity in the Black Sea. The morphological data presented in this study support the transition of G. barbata to the genus Gongolaria, which was previously proposed based solely on genetic data. For the Black Sea endemic taxon C. bosphorica, sequence divergence suggests conspecificity with Mediterranean Sea species E. crinita and E. barbatula. However, considering original morphological characteristics of the taxon, its geographical isolation, and endemism, the new combination Ericaria crinita f. bosphorica comb. nov. is proposed.

scholarly journals Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 461 ◽  
Author(s):  
Carina Carneiro de Melo Moura ◽  
Fabian Brambach ◽  
Kevin Jair Hernandez Bado ◽  
Konstantin V. Krutovsky ◽  
Holger Kreft ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Evolutionary Rate ◽  
Molecular Data ◽  
Morphological Identification ◽  
Chloroplast Gene ◽  
Taxonomic Level ◽  
Morphological Taxonomy ◽  
Traditional Taxonomy ◽  
Lowland Forests ◽  
Interspecific Genetic Distance

DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level.

Sign in / Sign up

Export Citation Format

Share Document