scholarly journals Evaluating the performance of DNA metabarcoding for assessment of zooplankton communities in Western Lake Superior using multiple markers

2021 ◽  
Vol 5 ◽  
Author(s):  
Christy Meredith ◽  
Joel Hoffman ◽  
Anett Trebitz ◽  
Erik Pilgrim ◽  
Sarah Okum ◽  
...  
Keyword(s):  
Assessment Tool ◽  
Lake Superior ◽  
Rrna Genes ◽  
Crustacean Zooplankton ◽  
Morphological Identification ◽  
Mitochondrial Coi ◽  
Multiple Markers ◽  
Western Lake ◽  
Dna Metabarcoding ◽  
Zooplankton Communities

For DNA metabarcoding to attain its potential as a community assessment tool, we need to better understand its performance versus traditional morphological identification and work to address any remaining performance gaps in incorporating DNA metabarcoding into community assessments. Using fragments of the 18S nuclear and 16S mitochondrial rRNA genes and two fragments of the mitochondrial COI marker, we examined the use of DNA metabarcoding and traditional morphological identification for understanding the diversity and composition of crustacean zooplankton at 42 sites across western Lake Superior. We identified 51 zooplankton taxa (genus or species, depending on the finest resolution of the taxon across all identification methods), of which 17 were identified using only morphological traits, 13 using only DNA and 21 using both methods. The taxa found using only DNA metabarcoding included four species and one genus-level identification not previously known to occur in Lake Superior, the presence of which still needs to be confirmed. A substantial portion of taxa that were identified to genus or species by morphological identification, but not identified using DNA metabarcoding, had zero (“no record”) or < 2 (“underrepresented records”) reference barcodes in the BOLD or NCBI databases (63% for COI, 80% for 16S, 74% for 18S). The two COI marker fragments identified the most genus- and species-level taxa, whereas 18S was the only marker whose family-level percent sequence abundance patterns showed high correlation to composition patterns from morphological identification, based on a NMDS analysis of Bray-Curtis similarities. Multiple replicates were collected at a subset of sites and an occupancy analysis was performed, which indicated that rare taxa were more likely to be detected using DNA metabarcoding than traditional morphology. Our results support that DNA metabarcoding can augment morphological identification for estimating zooplankton diversity and composition of zooplankton over space and time, but may require use of multiple markers. Further addition of taxa to reference DNA databases will improve our ability to use DNA metabarcoding to identify zooplankton and other invertebrates in aquatic surveys.

Trends in Spring Crustacean Zooplankton Communities of Lake Superior:

2009 ◽  
pp. 401-438
Author(s):  
Owen T. Gorman ◽  
Lori M. Evrard ◽  
Michael H. Hoff ◽  
James H. Selgeby
Keyword(s):  
Lake Superior ◽  
Crustacean Zooplankton ◽  
Zooplankton Communities

Changes in the crustacean communities of Lakes Michigan, Huron, and Erie following the invasion of the predatory cladoceran Bythotrephes longimanus

2004 ◽  
Vol 61 (11) ◽  
pp. 2111-2125 ◽  
Author(s):  
Richard P Barbiero ◽  
Marc L Tuchman
Keyword(s):  
Zooplankton Community ◽  
Crustacean Zooplankton ◽  
Bythotrephes Longimanus ◽  
Zooplankton Community Structure ◽  
Cladoceran Species ◽  
Invertebrate Predators ◽  
Predatory Cladoceran ◽  
Leptodora Kindti ◽  
Escape Responses ◽  
Zooplankton Communities

The crustacean zooplankton communities in Lakes Michigan and Huron and the central and eastern basins of Lake Erie have shown substantial, persistent changes since the invasion of the predatory cladoceran Bythotrephes in the mid-1980s. A number of cladoceran species have declined dramatically since the invasion, including Eubosmina coregoni, Holopedium gibberum, Daphnia retrocurva, Daphnia pulicaria, and Leptodora kindti, and overall species richness has decreased as a result. Copepods have been relatively unaffected, with the notable exception of Meso cyclops edax, which has virtually disappeared from the lakes. These species shifts have for the most part been consistent and equally pronounced across all three lakes. Responses of crustacean species to the Bythotrephes invasion do not appear to be solely a consequence of size, and it is likely that other factors, e.g., morphology, vertical distribution, or escape responses, are important determinants of vulnerability to predation. Our results indicate that invertebrate predators in general, and invasive ones in particular, can have pronounced, lasting effects on zooplankton community structure.

Estimating Sediment and Nutrient Loads in Four Western Lake Superior Streams

2014 ◽  
Vol 50 (5) ◽  
pp. 1138-1154 ◽  
Author(s):  
Elaine M. Ruzycki ◽  
Richard P. Axler ◽  
George E. Host ◽  
Jerald R. Henneck ◽  
Norman R. Will
Keyword(s):  
Lake Superior ◽  
Nutrient Loads ◽  
Western Lake

The effect of a flood pulse on the water column of western Lake Superior, USA

2014 ◽  
Vol 40 (2) ◽  
pp. 455-462 ◽  
Author(s):  
Elizabeth C. Minor ◽  
Brandy Forsman ◽  
Stephanie J. Guildford
Keyword(s):  
Water Column ◽  
Lake Superior ◽  
Flood Pulse ◽  
Western Lake

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 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

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