scholarly journals Effects of anthropogenic pressures on diatom communities using morphological and molecular approaches

2021 ◽  
Vol 4 ◽  
Author(s):  
Marco Teixeira ◽  
Salomé Almeida ◽  
Maria Feio ◽  
Andreia Mortágua ◽  
Manuela Sales
Keyword(s):  
Environmental Variables ◽  
High Throughput Sequencing ◽  
Dna Barcode ◽  
Ecological Indicator ◽  
Morphological Identification ◽  
Anthropogenic Pressure ◽  
Reference Library ◽  
Promising Alternative ◽  
The North ◽  
Diatom Communities

The relevance of molecular composition of diatom assemblages to detect river impairment caused by different intensive land uses (industrial, agricultural, and urbanization) was tested in this study with data from two rivers (Ferreira and Sousa rivers) and 21 sampling sites located in the north of Portugal. The Water Framework Directive (WFD) gives the legal basis for the use of this ecological indicator for water quality assessment (Vasselon et al. 2017 ). However, the morphological identification and count of diatoms using the light microscope requires a high level of expertise, is time-consuming and costly (Valentin et al. 2019). DNA metabarcoding combined with high-throughput sequencing techniques (HTS), offers a promising alternative to classic methodologies, reducing time and costs (Mortágua et al. 2019 ). Thus, here we compared the response of the two approaches in terms of ecological assessments (IPS Ecological Quality Ratios) to the different types of pressures felt in the 21 sites. Diatoms were sampled at 21 sites located in the North of Portugal in autumn of 2019 (Fig. 1). Samples were submitted in parallel to the molecular and morphological analyses. The eDNA was extracted, PCR amplified (312 bp rbcL DNA barcode), and finally sequenced (Illumina MiSeq). The Mothur software was used to obtain the Operational Taxonomic Units (OTUs), which were then taxonomically assigned to the species through the R-Syst::diatom version 7.1 (Rimet et al. 2018) reference library. EQR values indicated a good correlation between morphological and molecular methods (Fig. 2). PCA analysis (Fig. 3 ) revealed that in urban, agricultural, and industrial areas there is a greater concentration of nutrients (phosphorus and nitrogen), organic matter, and heavy metals due to the discharge of urban/industrial effluents, while in places considered natural (without any type of anthropogenic pressure) we find low levels of these pollutants and high concentrations of dissolved oxygen (DO). The BEST (BIO-ENV) analysis (Tables 1, 2) shows in the case of the morphological approach, the combination of 4 environmental variables (NO₃⁻, Li, K, and Cu) is highly correlated with the biological patterns, and in the molecular approach the combination of only 2 of the environmental variables (Li and K), explains the distribution of diatom communities composition and has a slightly higher correlation. The morphological methodology seems to demonstrate a better response to urban pressures, mainly to effluent discharges, while the molecular one demonstrates a more diffuse response with special emphasis on good correlation with variables such as zinc and nitrate, which may also be related to effluent discharges and use of fertilizers in agriculture. However, it is necessary to improve the reference library so that there is a better response of the molecular methodology to the existing pressures.

scholarly journals A reliable DNA barcode reference library for the identification of benthic invertebrates: essential for biomonitoring of the North Sea

2021 ◽  
Vol 4 ◽  
Author(s):  
Magdalini Christodoulou ◽  
Berry van der Hoorn ◽  
Laure Van den Bulcke ◽  
Sofie Derycke ◽  
Annelies De Backer ◽  
...  
Keyword(s):  
North Sea ◽  
High Throughput Sequencing ◽  
Dna Barcode ◽  
Morphological Identification ◽  
Indigenous Species ◽  
Reference Library ◽  
The North ◽  
Sampling Campaign ◽  
The North Sea ◽  
Cost Efficient

Benthic macroinvertebrates are key components in environmental impact assessments. Nevertheless, their use as bioindicators can be constrained by the time- and cost-consuming processes needed for their morphological identification. The recent advances in high-throughput sequencing, particularly DNA metabarcoding can provide an alternative to morphology-based approaches. The main limitation for DNA-based tools to be implemented in biomonitoring projects is the considerable investment needed to build high-quality and curated taxonomic reference DNA sequence libraries for species identification. To begin addressing this shortage, Interreg NSR project GEANS aim in developing a curated DNA reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for the North Sea macrobenthos that will serve as the backbone of all the molecular protocols. For the collection of the macroinvertebrates, a targeted sampling campaign is underway across the North Sea Region, while existing collections are being scanned. Macrobenthic specimens are being processed following a series of standardised work flows covering sampling, morphological identifications, molecular lab processing and data handling. GEANS' reference library, currently holds DNA barcodes for 3443 specimens collected from various areas of the North Sea. In total 11 phyla, 28 classes, 80 orders, 280 families, 428 genera and 586 species (37 non-indigenous species) are represented within the library. Species-level identification is taxonomically verified for over 90 % of the species, while genus-level identifications are verified for almost 100 % of the genera. GEANS reference library covers so far over 30 % of North Sea species and its constantly enriched. All specimens are photographed and together with the accompanying sequences, collection and taxonomic data are archived in a dedicate BOLD project. Voucher specimens and DNA extracts are archived at three different institutes in Germany (Senckenberg am Meer), the Netherlands (Naturalis) and Belgium (ILVO). Once available, this DNA-library will be based on taxonomically well-curated specimens and it will support the implementation of fast, cost-efficient and reliable DNA-based identifications and subsequently environmental health assessments in the North Sea.

A reliable DNA barcode reference library for the identification of the North European shelf fish fauna

2014 ◽  
pp. n/a-n/a ◽  
Author(s):  
Thomas Knebelsberger ◽  
Monica Landi ◽  
Hermann Neumann ◽  
Matthias Kloppmann ◽  
Anne F. Sell ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Fish Fauna ◽  
Reference Library ◽  
The North ◽  
European Shelf

scholarly journals Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring

2018 ◽  
Author(s):  
Joeselle M. Serrana ◽  
Yo Miyake ◽  
Maribet Gamboa ◽  
Kozo Watanabe
Keyword(s):  
Community Composition ◽  
Environmental Variables ◽  
High Throughput Sequencing ◽  
Freshwater Ecosystems ◽  
Morphological Data ◽  
Morphological Identification ◽  
Biodiversity Assessment ◽  
Stream Macroinvertebrate ◽  
The Relationship ◽  
Diversity Metrics

AbstractConventional morphology-based identification is commonly used for routine assessment of freshwater ecosystems. However, cost and time efficient techniques such as high-throughput sequencing (HTS) based approaches may resolve the constraints encountered in conducting morphology-based surveys. Here, we characterized stream macroinvertebrate species diversity and community composition via metabarcoding and morphological analysis from environmental samples collected from the Shigenobu River Basin in Ehime Prefecture, Japan. We compared diversity metrics and assessed both approaches’ ability to evaluate the relationship between macroinvertebrate community and environmental variables. In total, we morphologically identified 45 taxa (3 families, six subfamilies, 31 genera, and five species) from 8,276 collected individuals from ten study sites. We detected 44 species by metabarcoding, with 35 species collapsed into 11 groups matching the morphologically identified taxa. A significant positive correlation between logged depth (number of HTS reads) and abundance of morphological taxa was observed, which implied that quantitative data can be used for subsequent analyses. Relatively higher estimates of alpha diversity were calculated from the metabarcoding data in comparison to morphology-based data. However, beta diversity estimates between metabarcoding and morphology data based on both incidence and abundance-based matrices were correlated proving that community differences between sampling sites were preserved in the molecular data. Also, both models were significant, but metabarcoding data (93%) explained a relatively higher percentage of variation in the relationship between community composition and the environmental variables than morphological data (91%). Overall, we present both the feasibility and limitations of HTS-driven estimations of taxonomic richness, community composition, and diversity metrics, and that metabarcoding was proven comparable and more sensitive against morphology-based analysis for stream macroinvertebrate biodiversity assessment and environmental monitoring.

scholarly journals Airborne Fungi in Show Caves from Southern Spain

2021 ◽  
Vol 11 (11) ◽  
pp. 5027
Author(s):  
Irene Dominguez-Moñino ◽  
Valme Jurado ◽  
Miguel Angel Rogerio-Candelera ◽  
Bernardo Hermosin ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
Entomopathogenic Fungi ◽  
Airborne Fungi ◽  
Southern Spain ◽  
Ecological Indicator ◽  
Outdoor Air ◽  
Northern Spain ◽  
Pochonia Chlamydosporia ◽  
The North ◽  
Show Caves ◽  
Characteristic Features

The aerobiology of caves in Southern Spain possesses special characteristics, different from caves located in Northern Spain. Previous studies demonstrated the influence of outdoor air on caves in the north and the existence of two different patterns, depending on the season. In summer there is an abundance of Ascomycota, whereas in winter Basidiomycota predominates, which are related to the periods of stagnation and ventilation, respectively. In caves in Southern Spain the presence of airborne Basidiomycota is scarce and Ascomycota represents the main group of fungi widely distributed across the caves in all seasons. The most characteristic features were the abundant presence of entomopathogenic fungi (Beauveria bassiana, Parengyodontium album, Pochonia chlamydosporia, Leptobacillium symbioticum, Leptobacillium leptobactrum) and Cladosporium cladosporioides in Cueva del Tesoro, Cueva de Ardales and Gruta de las Maravillas. However, the presence of yeasts of the genera Cutaneotrichosporon, Trichosporon, Cryptococcus, Naganishia, Cystobasidium, Microstroma and Phragmotaenium was exclusive to Gruta de las Maravillas. Fungal hazard in the three show caves were determined using an ecological indicator based on the concentration of spores in cave air.

Investigation on Eutrophication Level for Gucheng Lake by the Model of Butterfly Catastrophe

2013 ◽  
Vol 726-731 ◽  
pp. 2051-2056
Author(s):  
Hua Wang ◽  
Yi Yi Zhou ◽  
Feng Qiang Ji
Keyword(s):  
Fuzzy Membership ◽  
Ecological Indicator ◽  
Pollution Load ◽  
The South ◽  
Flood Season ◽  
The North ◽  
Gucheng Lake ◽  
Dry Seasons ◽  
Membership Value ◽  
Water Eutrophication

Based on the field measured results in the typical periods of flood season and dry season of Gucheng Lake, the present eutrophication levels of the lake were investigated by the Model of Butterfly Catastrophe, in which series of the environmental factors were considered including the ecological indicator of chlorophylla, the nutrient indicator of total nitrogen and total phosphorus, and the physical index of water transparency. The results showed that: the water eutrophication levels of Gucheng Lake were mal-distributed in space and time; the lake eutrophication tendency in flood seasons were more obvious than that in dry seasons; the eutrophication levels in the south part of the lake were relatively lower than that in the north and the average comprehensive mutation of fuzzy membership value in the south was about 0.3006 in the dry seasons. Due to the increased pollution load and the hydrodynamic conditions, the eutrophication degree in the estuary areas were higher and the fuzzy membership value was close to 0.235, achieving the medium eutrophication level.

scholarly journals Taming the Wild West of Molecular Tools Application in Aquatic Research and Biomonitoring

2019 ◽  
Vol 3 ◽  
Author(s):  
Alexander Weigand ◽  
Agnès Bouchez ◽  
Pieter Boets ◽  
Kat Bruce ◽  
Fedor Ciampor ◽  
...  
Keyword(s):  
Working Group ◽  
High Throughput Sequencing ◽  
Group Structure ◽  
Time Budget ◽  
Good Practice ◽  
Dna Barcode ◽  
Environmental Parameters ◽  
Full Potential ◽  
Molecular Tools ◽  
Wild West

Modern high-throughput sequencing technologies are becoming a game changer in many fields of aquatic research and biomonitoring. To unfold their full potential, however, the independent development of approaches has to be streamlined. This discussion must be fuelled by stakeholders and practitioners and, scientific results collaboratively filtered to identify the most promising avenues. Furthermore, aspects such as time, budget, skills and the application context have to be considered, finally communicating good practice strategies to target audiences. Since 2016, the EU COST Action DNAqua-Net is taming the wild west of molecular tools application in aquatic research and biomonitoring. After nucleating available knowledge by the formation of a highly international and transdisciplinary network of scientists, stakeholders, practitioners and enterprises, fields of high methodological diversity were identified. Relevant aspects are currently ground truthed, thereby reducing the plethora of pipelines, parameters and protocols to a subset of good practices or standardisations. To effectively bridge the science-application interface, the very same network is exploited for the dissemination of results (Leese et al. 2018). The internal working group structure of DNAqua-Net is used to provide an overview of existing methodological fields of diversity in DNA-based aquatic biomonitoring: WG1 -DNA Barcode References: Different marker systems are targeted for the same organism group. Even in case the same molecular marker is investigated, different primer pairs are frequently applied for DNA metabarcoding. Both aspects challenge the further development of high-quality and complete DNA barcode reference libraries (Weigand et al. 2019). WG2 -Biotic Indices & Metrics: Index systems are developed from molecular data in various ways: from the estimation of species' biomass (as a proxy for abundance) from sequence reads, to the correlation of presence/absence data of molecular operational taxonomic units (MOTUs) with environmental parameters (Pawlowski et al. 2018). WG3 -Field & Lab Protocols: Using environmental DNA (eDNA) metabarcoding as an example, diverse sampling techniques based on varying water volumes, different filter systems and collection devices as well as a multitude of laboratory protocols for PCR, replication and sequencing are considered. WG4 -Data Analysis & Storage: During the process of MOTU identification, varying threshold values and conceptually different pipelines are used, potentially impacting the final list of MOTUs or species retrieved. Furthermore, routine storage concepts for big biodiversity data are only in development and some sample types (e.g. eDNA) have no sophisticated metadata descriptions. WG5 -Implementation Strategy & Legal Issues: The working group picks up collaboratively filtered good practice strategies and generates room for discussions at the science-policy interface (Hering et al. 2018). The CEN working group WG28 "DNA methods" has been initiated and the development of standardisations is fostered.

scholarly journals A DNA barcode reference library of the French Polynesian shore fishes

2019 ◽  
Author(s):  
Erwan Delrieu-Trottin ◽  
Jeffrey T. Williams ◽  
Diane Pitassy ◽  
Amy Driskell ◽  
Nicolas Hubert ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Biological Diversity ◽  
Dna Barcode ◽  
Reef Fishes ◽  
French Polynesia ◽  
Morphological Characters ◽  
Reference Library ◽  
Society Islands ◽  
Extensive Collection ◽  
I Gene

AbstractThe emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km2area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.

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 An insight into biosecurity plant-disease diagnostics at MPI

2019 ◽  
Vol 72 ◽  
pp. 281
Author(s):  
Robert K. Taylor ◽  
Merje Toome-Heller ◽  
Wellcome W.H. Ho ◽  
Brett J.R. Alexander
Keyword(s):  
New Zealand ◽  
High Throughput Sequencing ◽  
Test Methods ◽  
Molecular Techniques ◽  
Morphological Identification ◽  
Sample Type ◽  
Emerging Pathogens ◽  
Post Entry ◽  
Biochemical Testing ◽  
Diagnostic Work

The Mycology and Bacteriology team of the Ministry for Primary Industries’ Plant Health and Environment Laboratory is responsible for the identification and verification of all suspected exotic, new, and emerging pathogens affecting plants and the environment in New Zealand. We work in an applied diagnostic environment where results can have significant implications for biosecurity. Sample submissions often result in detection of new to New Zealand fungi and bacteria on plants for which information on fungal and bacterial associations is generally sparse. The complexity of testing required is quite varied with samples being submitted from post entry quarantine (looking for a known pathogen using specific tests), border or surveillance (unknown pathogens requiring multiple tests), or a biosecurity response (scaling up to test large numbers, identification resolution required to strain level). Applied test methods depend largely on the sample type and consist of morphological identification, biochemical testing, pathogenicity testing, serological and molecular techniques, including high throughput sequencing. A profile of our diagnostic work and the most commonly detected taxa and host associations are presented.

scholarly journals debar, a sequence-by-sequence denoiser for COI-5P DNA barcode data

2021 ◽  
Author(s):  
Cameron M. Nugent ◽  
Tyler A. Elliott ◽  
Sujeevan Ratnasingham ◽  
Paul D. N. Hebert ◽  
Sarah J. Adamowicz
Keyword(s):  
High Throughput Sequencing ◽  
Dna Barcode ◽  
R Package ◽  
Error Rates ◽  
Real World Data ◽  
Species Discovery ◽  
Consensus Sequences ◽  
In Silico Studies ◽  
Coi Sequences

AbstractDNA barcoding and metabarcoding are now widely used to advance species discovery and biodiversity assessments. High-throughput sequencing (HTS) has expanded the volume and scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates of biodiversity. Denoising —the separation of biological signal from instrument (technical) noise—of barcode and metabarcode data currently employs abundance-based methods which do not capitalize on the highly conserved structure of the cytochrome c oxidase subunit I (COI) region employed as the animal barcode. This manuscript introduces debar, an R package that utilizes a profile hidden Markov model to denoise indel errors in COI sequences introduced by instrument error. In silico studies demonstrated that debar recognized 95% of artificially introduced indels in COI sequences. When applied to real-world data, debar reduced indel errors in circular consensus sequences obtained with the Sequel platform by 75%, and those generated on the Ion Torrent S5 by 94%. The false correction rate was less than 0.1%, indicating that debar is receptive to the majority of true COI variation in the animal kingdom. In conclusion, the debar package improves DNA barcode and metabarcode workflows by aiding the generation of more accurate sequences aiding the characterization of species diversity.

Sign in / Sign up

Export Citation Format

Share Document