1
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Girard EB, Didaskalou EA, Pratama AMA, Rattner C, Morard R, Renema W. Quantitative assessment of reef foraminifera community from metabarcoding data. Mol Ecol Resour 2024:e14000. [PMID: 39041197 DOI: 10.1111/1755-0998.14000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/20/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it is challenging to produce fast and accurate depiction of ecosystems due to methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative abundances of genes that may not correctly represent living communities from environmental DNA assessed with morphological methods. However, it has the potential to deliver fast descriptions of living communities provided that it is interpreted with validated species-specific calibrations and reference databases. Here, we developed a quantitative approach to retrieve from metabarcoding data the assemblages of living large benthic foraminifera (LBF), photosymbiotic calcifying protists, from Indonesian coral reefs that are under increasing anthropogenic pressure. To depict the diversity, we calculated taxon-specific correction factors to reduce biological biases by comparing surface area, biovolume and calcite volume, and the number of mitochondrial gene copies in seven common LBF species. To validate the approach, we compared calibrated datasets of morphological communities from mock samples with bulk reef sediment; both sample types were metabarcoded. The calibration of the data significantly improved the estimations of genus relative abundance, with a difference of ±5% on average, allowing for comparison of past morphological datasets with future molecular ones. Our results also highlight the application of our quantitative approach to support reef monitoring operations by capturing fine-scale processes, such as seasonal and pollution-driven dynamics, that require high-throughput sampling treatment.
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Affiliation(s)
- Elsa B Girard
- Naturalis Biodiversity Center, Leiden, The Netherlands
- IBED, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Andi M A Pratama
- Marine Science Department, Faculty of Marine Science and Fisheries, Hasanuddin University, Makassar, Indonesia
| | | | | | - Willem Renema
- Naturalis Biodiversity Center, Leiden, The Netherlands
- IBED, University of Amsterdam, Amsterdam, The Netherlands
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2
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Martens N, Russnak V, Woodhouse J, Grossart HP, Schaum CE. Metabarcoding reveals potentially mixotrophic flagellates and picophytoplankton as key groups of phytoplankton in the Elbe estuary. ENVIRONMENTAL RESEARCH 2024; 252:119126. [PMID: 38734293 DOI: 10.1016/j.envres.2024.119126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024]
Abstract
In estuaries, phytoplankton are faced with strong environmental forcing (e.g. high turbidity, salinity gradients). Taxa that appear under such conditions may play a critical role in maintaining food webs and biological carbon pumping, but knowledge about estuarine biota remains limited. This is also the case in the Elbe estuary where the lower 70 km of the water body are largely unexplored. In the present study, we investigated the phytoplankton composition in the Elbe estuary via metabarcoding. Our aim was to identify key taxa in the unmonitored reaches of this ecosystem and compare our results from the monitored area with available microscopy data. Phytoplankton communities followed distinct seasonal and spatial patterns. Community composition was similar across methods. Contributions of key classes and genera were correlated to each other (p < 0.05) when obtained from reads and biovolume (R2 = 0.59 and 0.33, respectively). Centric diatoms (e.g. Stephanodiscus) were the dominant group - comprising on average 55 % of the reads and 66-69 % of the biovolume. However, results from metabarcoding imply that microscopy underestimates the prevalence of picophytoplankton and flagellates with a potential for mixotrophy (e.g. cryptophytes). This might be due to their small size and sensitivity to fixation agents. We argue that mixotrophic flagellates are ecologically relevant in the mid to lower estuary, where, e.g., high turbidity render living conditions rather unfavorable, and skills such as phagotrophy provide fundamental advantages. Nevertheless, further findings - e.g. important taxa missing from the metabarcoding dataset - emphasize potential limitations of this method and quantitative biases can result from varying numbers of gene copies in different taxa. Further research should address these methodological issues but also shed light on the causal relationship of taxa with the environmental conditions, also with respect to active mixotrophic behavior.
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Affiliation(s)
- Nele Martens
- Institute of Marine Ecosystem and Fishery Science, Olbersweg 24, 22767, Hamburg, Germany.
| | - Vanessa Russnak
- Helmholtz-Zentrum hereon, Max-Planck-Straße 1, 21502, Geesthacht, Germany.
| | - Jason Woodhouse
- Institute of Cell and Systems Biology of Animals, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775, Stechlin, Germany; Institute of Biochemistry and Biology, Maulbeerallee 2, 14469, Potsdam, Germany.
| | - C-Elisa Schaum
- Institute of Marine Ecosystem and Fishery Science, Olbersweg 24, 22767, Hamburg, Germany; Center for Earth System Research and Sustainability, Bundesstraße 53-55, 20146, Hamburg, Germany.
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3
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Rund H, Wanzenböck J, Dobrovolny S, Kurmayer R. Relating target fish DNA concentration to community composition analysis in freshwater fish via metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172281. [PMID: 38588740 DOI: 10.1016/j.scitotenv.2024.172281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/04/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Metabarcoding has been widely accepted as a useful tool for biodiversity assessment based on eDNA. The method allows for the detection of entire groups of organisms in a single sample, making it particularly applicable in aquatic habitats. The high sensitivity of the molecular approaches is especially beneficial in detecting elusive and rare fish species, improving biodiversity assessments. Numerous biotic and abiotic factors that affect the persistence and availability of fish DNA in surface waters and therefore affecting species detectability, have been identified. However, little is known about the relationship between the total fish DNA concentration and the detectability of differential abundant species. In this study three controlled mock-community DNA samples (56 individual samples) were analyzed by (i) metabarcoding (MiSeq) of 12S rDNA (175 bp) and by (ii) total freshwater fish DNA quantification (via qPCR of 12S rDNA). We show that the fish DNA quantity affects the relative abundance of species-specific sequences and the detectability of rare species. In particular we found that samples with a concentration between 1000 pg/μL down to 10 pg/μL of total fish DNA revealed a stable relative frequency of DNA sequences obtained for a specific fish species, as well as a low variability between replicates. Additionally, we observed that even in complex mock-community DNA samples, a total fish DNA concentration of 23 pg/μL was sufficient to reliably detect all species in every replicate, including three rare species with proportions of ≤0.5 %. We also found that the DNA barcode similarity between species can affect detectability, if evenness is low. Our data suggest that the total DNA concentration of fish is an important factor to consider when analyzing and interpreting relative sequence abundance data. Therefore, the workflow proposed here will contribute to an ecologically and economically efficient application of metabarcoding in fish biodiversity assessment.
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Affiliation(s)
- Hans Rund
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria.
| | - Josef Wanzenböck
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria
| | - Stefanie Dobrovolny
- Department for Molecular Biology and Microbiology, Institute for Food Safety Vienna, Austrian Agency for Health and Food Safety, Spargelfeldstraße 191, 1220 Vienna, Austria
| | - Rainer Kurmayer
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria
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4
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Cahoon AB, Johnson KM, Brown SM, Manoylov KM, Nienow JA. The chloroplast and mitochondrial genomes of two Gomphonema parvulum (Bacillariophyta) environmental isolates from South Carolina (United States) and Virginia (United States). JOURNAL OF PHYCOLOGY 2024; 60:299-307. [PMID: 38433431 DOI: 10.1111/jpy.13415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/24/2023] [Accepted: 11/24/2023] [Indexed: 03/05/2024]
Abstract
Gomphonema parvulum is a cosmopolitan freshwater diatom that is used as an indicator in water quality biomonitoring. In this study, we report the culturing of two geographically separated isolates from southeastern North America, their morphology, and the sequencing and assembly of their mitochondrial and chloroplast genomes. Morphologically, both strains fit G. parvulum sensu lato, but the frustules from a protected habitat in South Carolina were smaller than those cited in the historic data of this species from the same location as well as a second culture from Virginia. Phylogenetic analyses using the rbcL gene placed both within a clade with G. parvulum. Genetic markers, including full chloroplast and mitochondrial genomes and the nuclear small subunit rRNA gene region were assembled from each isolate. The organellar genomes of the two strains varied slightly in size due to small differences in intergenic regions with chloroplast genomes of 121,035 bp and 121,482 bp and mitochondrial genomes of 34,639 bp and 34,654 bp. The intraspecific pairwise identities of the chloroplast and mitochondrial genomes of these two isolates were 97.9% and 95.4%, respectively. Multigene phylogenetic analysis demonstrated a close relationship between G. parvulum, Gomphoneis minuta, and Didymosphenia geminata.
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Affiliation(s)
- A Bruce Cahoon
- Department of Natural Sciences, The University of Virginia's College at Wise, Wise, Virginia, USA
| | - Katherine M Johnson
- Department of Biological and Environmental Sciences, Georgia College & State University, Milledgeville, Georgia, USA
| | - Sydney M Brown
- Department of Biological and Environmental Sciences, Georgia College & State University, Milledgeville, Georgia, USA
| | - Kalina M Manoylov
- Department of Biological and Environmental Sciences, Georgia College & State University, Milledgeville, Georgia, USA
| | - James A Nienow
- Department of Biology, Valdosta State University, Valdosta, Georgia, USA
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5
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Kelly MG, Mann DG, Taylor JD, Juggins S, Walsh K, Pitt JA, Read DS. Maximising environmental pressure-response relationship signals from diatom-based metabarcoding in rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169445. [PMID: 38159778 DOI: 10.1016/j.scitotenv.2023.169445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
DNA metabarcoding has been performed on a large number of river phytobenthos samples collected from the UK, using rbcL primers optimised for diatoms. Within this dataset the composition of non-diatom sequence reads was studied and the effect of including these in models for evaluating the nutrient gradient was assessed. Whilst many non-diatom taxonomic groups were detected, few contained the full diversity expected in riverine environments. This may be due to the performance of the current primers in characterising the wider phytobenthic community and influenced by the sampling method employed, as both were developed specifically for diatoms. Nevertheless, the study identified considerable diversity in some groups, e.g. Eustigmatophyceae and a wider distribution than previously thought for freshwater Phaeophyceae. These results offer a strong case for the benefits of metabarcoding for expanding knowledge of aquatic biodiversity in the UK and elsewhere. Many of the ASVs associated with non-diatoms showed significant pressure responses; however, models that included non-diatoms had similar predictive strength to those based on diatoms alone. Whilst limitations of the primers for assessing non-diatoms may play a role in explaining these results, the diatoms provide a strong signal along the nutrient gradient and other algae, therefore, add little unique information. We recommend that future developments should use ASVs to calculate metrics, with links to reference databases made as a final step to generate lists of taxa to support interpretation. Any further exploration of the potential of non-diatoms would benefit from access to a well-curated reference database, similar to diat.barcode. Such a database does not yet exist, and we caution against the indiscriminate use of NCBI GenBank as a taxonomic resource as many rbcL sequences deposited have not been curated.
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Affiliation(s)
- Martyn G Kelly
- Bowburn Consultancy, 11 Monteigne Drive, Bowburn, Durham DH6 5QB, UK; School of Geography, Nottingham University, Nottingham NG7 2RD, UK.
| | - David G Mann
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland, UK; Marine and Continental Waters, Institute for Food and Agricultural Research and Technology (IRTA), Crta de Poble Nou Km 5.5, E-43540 La Ràpita, Catalunya, Spain
| | - Joe D Taylor
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire OX10 8BB, UK
| | - Stephen Juggins
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Kerry Walsh
- Chief Scientist's Group, Environment Agency, Deanery Road, Bristol BS1 5AH, UK
| | - Jo-Anne Pitt
- Chief Scientist's Group, Environment Agency, Deanery Road, Bristol BS1 5AH, UK
| | - Daniel S Read
- UK Centre for Ecology & Hydrology (UKCEH), Wallingford, Oxfordshire OX10 8BB, UK
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6
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Fray D, McGovern CA, Casamatta DA, Biddanda BA, Hamsher SE. Metabarcoding reveals unique microbial mat communities and evidence of biogeographic influence in low-oxygen, high-sulfur sinkholes and springs. Ecol Evol 2024; 14:e11162. [PMID: 38529029 PMCID: PMC10961586 DOI: 10.1002/ece3.11162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/16/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
High-sulfur, low-oxygen environments formed by underwater sinkholes and springs create unique habitats populated by microbial mat communities. To explore the diversity and biogeography of these mats, samples were collected from three sites in Alpena, Michigan, one site in Monroe, Michigan, and one site in Palm Coast, Florida. Our study investigated previously undescribed eukaryotic diversity in these habitats and further explored their bacterial communities. Mat samples and water parameters were collected from sulfur spring sites during the spring, summer, and fall of 2022. Cyanobacteria and diatoms were cultured from mat subsamples to create a culture-based DNA reference library. Remaining mat samples were used for metabarcoding of the 16S and rbcL regions to explore bacterial and diatom diversity, respectively. Analyses of water chemistry, alpha diversity, and beta diversity articulated a range of high-sulfur, low-oxygen habitats, each with distinct microbial communities. Conductivity, pH, dissolved oxygen, temperature, sulfate, and chloride had significant influences on community composition but did not describe the differences between communities well. Chloride concentration had the strongest correlation with microbial community structure. Mantel tests revealed that biogeography contributed to differences between communities as well. Our results provide novel information on microbial mat composition and present evidence that both local conditions and biogeography influence these unique communities.
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Affiliation(s)
- Davis Fray
- Annis Water Resources InstituteGrand Valley State UniversityMuskegonMichiganUSA
| | | | - Dale A. Casamatta
- Department of BiologyUniversity of North FloridaJacksonvilleFloridaUSA
| | - Bopaiah A. Biddanda
- Annis Water Resources InstituteGrand Valley State UniversityMuskegonMichiganUSA
| | - Sarah E. Hamsher
- Annis Water Resources InstituteGrand Valley State UniversityMuskegonMichiganUSA
- Department of BiologyGrand Valley State UniversityAllendaleMichiganUSA
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7
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Owens LA, Friant S, Martorelli Di Genova B, Knoll LJ, Contreras M, Noya-Alarcon O, Dominguez-Bello MG, Goldberg TL. VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages. Nat Commun 2024; 15:402. [PMID: 38195557 PMCID: PMC10776621 DOI: 10.1038/s41467-023-44521-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Protocols for characterizing taxonomic assemblages by deep sequencing of short DNA barcode regions (metabarcoding) have revolutionized our understanding of microbial communities and are standardized for bacteria, archaea, and fungi. Unfortunately, comparable methods for host-associated eukaryotes have lagged due to technical challenges. Despite 54 published studies, issues remain with primer complementarity, off-target amplification, and lack of external validation. Here, we present VESPA (Vertebrate Eukaryotic endoSymbiont and Parasite Analysis) primers and optimized metabarcoding protocol for host-associated eukaryotic community analysis. Using in silico prediction, panel PCR, engineered mock community standards, and clinical samples, we demonstrate VESPA to be more effective at resolving host-associated eukaryotic assemblages than previously published methods and to minimize off-target amplification. When applied to human and non-human primate samples, VESPA enables reconstruction of host-associated eukaryotic endosymbiont communities more accurately and at finer taxonomic resolution than microscopy. VESPA has the potential to advance basic and translational science on vertebrate eukaryotic endosymbiont communities, similar to achievements made for bacterial, archaeal, and fungal microbiomes.
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Affiliation(s)
- Leah A Owens
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
| | - Sagan Friant
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Bruno Martorelli Di Genova
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, The University of Vermont, Burlington, VT, USA
| | - Laura J Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, Venezuela
| | - Oscar Noya-Alarcon
- Centro Amazónico de Investigación y Control de Enfermedades Tropicales-CAICET, Puerto Ayacucho, Amazonas, Venezuela
| | - Maria G Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University-New Brunswick, New Brunswick, NJ, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA
- Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA
- Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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8
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Marinchel N, Marchesini A, Nardi D, Girardi M, Casabianca S, Vernesi C, Penna A. Mock community experiments can inform on the reliability of eDNA metabarcoding data: a case study on marine phytoplankton. Sci Rep 2023; 13:20164. [PMID: 37978238 PMCID: PMC10656442 DOI: 10.1038/s41598-023-47462-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
Environmental DNA metabarcoding is increasingly implemented in biodiversity monitoring, including phytoplankton studies. Using 21 mock communities composed of seven unicellular diatom and dinoflagellate algae, assembled with different composition and abundance by controlling the number of cells, we tested the accuracy of an eDNA metabarcoding protocol in reconstructing patterns of alpha and beta diversity. This approach allowed us to directly evaluate both qualitative and quantitative metabarcoding estimates. Our results showed non-negligible rates (17-25%) of false negatives (i.e., failure to detect a taxon in a community where it was included), for three taxa. This led to a statistically significant underestimation of metabarcoding-derived alpha diversity (Wilcoxon p = 0.02), with the detected species richness being lower than expected (based on cell numbers) in 8/21 mock communities. Considering beta diversity, the correlation between metabarcoding-derived and expected community dissimilarities was significant but not strong (R2 = 0.41), indicating suboptimal accuracy of metabarcoding results. Average biovolume and rDNA gene copy number were estimated for the seven taxa, highlighting a potential, though not exhaustive, role of the latter in explaining the recorded biases. Our findings highlight the importance of mock communities for assessing the reliability of phytoplankton eDNA metabarcoding studies and identifying their limitations.
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Affiliation(s)
- Nadia Marinchel
- Department of Pure and Applied Sciences, University of Urbino, Urbino, Italy.
- Department of Biomolecular Sciences, University of Urbino, Urbino, Italy.
| | - Alexis Marchesini
- Research Institute on Terrestrial Ecosystems (IRET), National Research Council (CNR), Porano, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Davide Nardi
- DAFNAE, University of Padova, Legnaro, PD, Italy
| | - Matteo Girardi
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | - Silvia Casabianca
- Department of Biomolecular Sciences, University of Urbino, Urbino, Italy
- Fano Marine Center, Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
- CoNISMa, National Inter-University Consortium for Marine Sciences, Rome, Italy
| | - Cristiano Vernesi
- National Biodiversity Future Center, Palermo, Italy
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | - Antonella Penna
- Department of Biomolecular Sciences, University of Urbino, Urbino, Italy.
- Fano Marine Center, Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy.
- CoNISMa, National Inter-University Consortium for Marine Sciences, Rome, Italy.
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9
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Gregersen R, Pearman JK, Atalah J, Waters S, Vandergoes MJ, Howarth JD, Thomson-Laing G, Thompson L, Wood SA. A taxonomy-free diatom eDNA-based technique for assessing lake trophic level using lake sediments. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118885. [PMID: 37659373 DOI: 10.1016/j.jenvman.2023.118885] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/18/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Anthropogenic eutrophication is one of the most pressing issues facing lakes globally. Our ability to manage lake eutrophication is hampered by the limited spatial and temporal extents of monitoring records, stemming from the time-consuming and expensive nature of physiochemical and biological monitoring. Diatom-based biomonitoring presents an alternative to traditional eutrophication monitoring, yet it is restricted by the high degree of taxonomic expertise required. Environmental DNA metabarcoding, while providing a promising substitute for diatom community enumeration, is plagued by inadequate taxonomic coverage of reference databases and methodological bias, limiting its use for biomonitoring. Here we show that taxonomy-free diatom-biomonitoring, in which environmental DNA metabarcoding data is utilised but not assigned to specific taxonomic classes, presents an accurate, fast, and relatively automated alternative to taxonomically assigned eutrophication biomonitoring. Our taxonomy-free index accounted for 85% of trophic level variability across 89 lakes and had the lowest average prediction error of the three approaches tested. By not relying on taxonomic identification or metabarcoding reference databases, taxonomy-free biomonitoring maintains diatom diversity that is lost in taxonomic assignment using molecular approaches. Furthermore, by utilising lake sediments, the approach outlined here presents a time-integrated estimation of lake trophic level and thus does not require time-consuming seasonal sampling. Taxonomy-free biomonitoring addresses the limitations of traditional physicochemical eutrophication monitoring and taxonomic biomonitoring alternatives and can be used to extend the spatial and temporal extents of eutrophication monitoring.
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Affiliation(s)
- Rose Gregersen
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand.
| | - John K Pearman
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Javier Atalah
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Sean Waters
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | | | - Jamie D Howarth
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | | | - Lucy Thompson
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Susanna A Wood
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
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10
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Pozzi A, Nazzicari N, Capoferri R, Radovic S, Bongioni G. Assessment of residual plant DNA in bulk milk for Grana Padano PDO production by a metabarcoding approach. PLoS One 2023; 18:e0289108. [PMID: 37490502 PMCID: PMC10368264 DOI: 10.1371/journal.pone.0289108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 07/11/2023] [Indexed: 07/27/2023] Open
Abstract
The aim of this study was to evaluate the ability of DNA metabarcoding, by rbcl as barcode marker, to identify and classify the small traces of plant DNA isolated from raw milk used to produce Grana Padano (GP) cheese. GP is one of the most popular Italian PDO (Protected Designation of Origin) produced in Italy in accordance with the GP PDO specification rules that define which forage can be used for feeding cows. A total of 42 GP bulk tank milk samples were collected from 14 dairies located in the Grana Padano production area. For the taxonomic classification, a local database with the rbcL sequences available in NCBI on September 2020/March 2021 for the Italian flora was generated. A total of 8,399,591 reads were produced with an average of 204,868 per sample (range 37,002-408,724) resulting in 16, 31 and 28 dominant OTUs at family, genus and species level, respectively. The taxonomic analysis of plant species in milk samples identified 7 families, 14 genera and 14 species, the statistical analysis conducted using alpha and beta diversity approaches, did not highlight differences among the investigated samples. However, the milk samples are featured by a high plant variability and the lack of differences at multiple taxonomic levels could be due to the standardisation of the feed rationing, as requested by the GP rules. The results suggest that DNA metabarcoding is a valuable resource to explore plant DNA traces in a complex matrix such as milk.
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Affiliation(s)
- Anna Pozzi
- Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy
| | - Nelson Nazzicari
- CREA-Council for Agricultural Research and Analysis of Agricultural Economics, Research Centre for Animal Production and Aquaculture, Viale Piacenza, Lodi, Italy
| | - Rossana Capoferri
- Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy
| | | | - Graziella Bongioni
- Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy
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11
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Kalu EI, Reyes-Prieto A, Barbeau MA. Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy. ISME COMMUNICATIONS 2023; 3:21. [PMID: 36918616 PMCID: PMC10014957 DOI: 10.1038/s43705-023-00226-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
Protists (microbial eukaryotes) are a critically important but understudied group of microorganisms. They are ubiquitous, represent most of the genetic and functional diversity among eukaryotes, and play essential roles in nutrient and energy cycling. Yet, protists remain a black box in marine sedimentary ecosystems like the intertidal mudflats in the Bay of Fundy. The harsh conditions of the intertidal zone and high energy nature of tides in the Bay of Fundy provide an ideal system for gaining insights into the major food web players, diversity patterns and potential structuring influences of protist communities. Our 18S rDNA metabarcoding study quantified seasonal variations and vertical stratification of protist communities in Bay of Fundy mudflat sediments. Three 'SAR' lineages were consistently dominant (in terms of abundance, richness, and prevalence), drove overall community dynamics and formed the core microbiome in sediments. They are Cercozoa (specifically thecate, benthic gliding forms), Bacillariophyta (mainly cosmopolitan, typically planktonic diatoms), and Dinophyceae (dominated by a toxigenic, bloom-forming species). Consumers were the dominant trophic functional group and were comprised mostly of eukaryvorous and bacterivorous Cercozoa, and omnivorous Ciliophora, while phototrophs were dominated by Bacillariophyta. The codominance of Apicomplexa (invertebrate parasites) and Syndiniales (protist parasites) in parasite assemblages, coupled with broader diversity patterns, highlighted the combined marine and terrestrial influences on microbial communities inhabiting intertidal sediments. Our findings, the most comprehensive in a hypertidal benthic system, suggest that synergistic interactions of both local and regional processes (notably benthic-pelagic coupling) may drive heterogenous microbial distribution in high-energy coastal systems.
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Affiliation(s)
- Eke I Kalu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada.
| | | | - Myriam A Barbeau
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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12
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Turk Dermastia T, Vascotto I, Francé J, Stanković D, Mozetič P. Evaluation of the rbcL marker for metabarcoding of marine diatoms and inference of population structure of selected genera. Front Microbiol 2023; 14:1071379. [PMID: 36950161 PMCID: PMC10026700 DOI: 10.3389/fmicb.2023.1071379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Diatoms are one of the most important phytoplankton groups in the world's oceans. There are responsible for up to 40% of the photosynthetic activity in the Ocean, and they play an important role in the silicon and carbon cycles by decoupling carbon from atmospheric interactions through sinking and export. These processes are strongly influenced by the taxonomic composition of diatom assemblages. Traditionally, these have been assessed using microscopy, which in some cases is not reliable or reproducible. Next-generation sequencing enabled us to study diversity in a high-throughput manner and uncover new distribution patterns and diversity. However, phylogenetic markers used for this purpose, such as various 18S rDNA regions, are often insufficient because they cannot distinguish between some taxa. In this work, we demonstrate the performance of the chloroplast-encoded rbcL marker for metabarcoding marine diatoms compared to microscopy and 18S-V9 metabarcoding using a series of monthly samples from the Gulf of Trieste (GoT), northern Adriatic Sea. We demonstrate that rbcL is able to detect more taxa compared to 18S-V9 metabarcoding or microscopy, while the overall structure of the diatom assemblage was comparable to the other two methods with some variations, that were taxon dependent. In total, 6 new genera and 22 new diatom species for the study region were identified. We were able to spot misidentification of genera obtained with microscopy such as Pseudo-nitzschia galaxiae, which was mistaken for Cylindrotheca closterium, as well as genera that were completely overlooked, such as Minidiscus and several genera from the Cymatosiraceae family. Furthermore, on the example of two well-studied genera in the region, namely Chaetoceros and particularly Pseudo-nitzschia, we show how the rbcL method can be used to infer even deeper phylogenetic and ecologically significant differences at the species population level. Despite a very thorough community analysis obtained by rbcL the incompleteness of reference databases was still evident, and we shed light on possible improvements. Our work has further implications for studies dealing with taxa distribution and population structure, as well as carbon and silica flux models and networks.
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Affiliation(s)
- Timotej Turk Dermastia
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Ivano Vascotto
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Janja Francé
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - David Stanković
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
| | - Patricija Mozetič
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
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13
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Baricevic A, Chardon C, Kahlert M, Karjalainen SM, Pfannkuchen DM, Pfannkuchen M, Rimet F, Tankovic MS, Trobajo R, Vasselon V, Zimmermann J, Bouchez A. Recommendations for the preservation of environmental samples in diatom metabarcoding studies. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Implementation of DNA metabarcoding for diatoms for environmental monitoring is now moving from a research to an operational phase, requiring rigorous guidelines and standards. In particular, the first steps of the diatom metabarcoding process, which consist of sampling and storage, have been addressed in various ways in scientific and pilot studies and now need to be rationalised. The objective of this study was to compare three currently applied preservation protocols through different storage durations (ranging from one day to one year) for phytobenthos and phytoplankton samples intended for diatom DNA metabarcoding analysis. The experimental design used samples from four freshwater and two marine sites of diverse ecological characteristics. The impact of the sample preservation and storage duration was assessed through diatom metabarcoding endpoints: DNA quality and quantity, diversity and richness, diatom assemblage composition and ecological index values (for freshwater samples). The yield and quality of extracted DNA only decreased for freshwater phytobenthos samples preserved with ethanol. Diatom diversity was not affected and their taxonomic composition predominantly reflected the site origin. Only rare taxa (< 100 reads) differed among preservation methods and storage durations. For biomonitoring purposes, freshwater ecological index values were not affected by the preservation method and storage duration tested (including ethanol preservation), all treatments returning the same ecological status for a site. This study contributes to consolidating diatom metabarcoding. Thus, accompanied by operational standards, the method will be ready to be confidently deployed and prescribed in future regulatory monitoring.
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14
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Bíró T, Duleba M, Földi A, Kiss KT, Orgoványi P, Trábert Z, Vadkerti E, Wetzel CE, Ács É. Metabarcoding as an effective complement of microscopic studies in revealing the composition of the diatom community – a case study of an oxbow lake of Tisza River (Hungary) with the description of a new Mayamaea species. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.87497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Diatoms are valuable bioindicators and their traditional classification and identification are mainly based on the morphological characteristics of their frustules. However, in recent years, DNA-based methods have been proposed and are rapidly growing in the scientific literature as a complementary tool to assess the ecological status of freshwaters. Diatom-based ecological status assessment uses indices calculated from sensitivity and tolerance values as well as relative abundance of species. Correct assessment requires an accurate identification of species. In the present study, diatom assemblages of an oxbow lake were investigated using light and scanning electron microscopy as well as metabarcoding using rbcL marker, and the identification results were compared, intending to match barcode sequences of species that are currently missing in the diatom reference database. The investigated oxbow is an important wetland for bird conservation, although it is impacted by land use. Taxon lists based on morphology and metabarcoding considerably differed when bioinformatics analysis involved DADA2 pipeline with Diat.barcode database. Previously unknown sequence variants of four pennate species were found with additional BLAST search. Using phylogeny and p-distance calculations sequences could be matched to three small-celled naviculoid species that were found under a microscope. One of them was found to be a new species of the genus Mayamaea and was described as a new species, Mayamaea ectorii. Additionally, spatial distribution maps for several small-celled naviculoid species are provided for the Hungarian territory.
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Mondino A, Crovadore J, Lefort F, Ursenbacher S. Impact of invading species on biodiversity: Diet study of the green whip snake’s (Hierophis viridiflavus, L. 1789) in Switzerland. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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16
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Zhu D, Wu F, Li H, Wang T, Bao L, Ge J, Wang H. Diet preferences based on sequence read count: the role of species interaction in tissue bias correction. Mol Ecol Resour 2022; 23:159-173. [PMID: 35980601 DOI: 10.1111/1755-0998.13700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 07/26/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022]
Abstract
High-throughput sequencing and metabarcoding techniques provide a unique opportunity to study predator-prey relationships. However, in animal dietary preference studies, how to properly correct tissue bias within the sequence read count and the role of interactions between co-occurring species in metabarcoding mixtures remain largely unknown. In this study, we proposed two categories of tissue bias correction indices: sequence read count number per unit tissue (SCN) and its ratio form (SCN ratio). By constructing plant mock communities with different numbers of co-occurring species in metabarcoding mixtures and conducting feeding trails on captive sika deer (Cervus nippon), we demonstrated the features of the SCN and SCN ratio, evaluated their correction effects, and assessed the role of species interactions during tissue bias correction. Tissue differences between species are defined as the differential ability in generating sequence counts. Our study suggests that pure tissue differences among species without species interaction is not an optimal correction index for many biomes with limited tissue differences among species. Species interactions in mixtures may amplify tissue differences, which is beneficial for tissue bias correction. However, caution must be taken because varied species interaction among communities may increase the risk of worse correction. Correction effects based on the SCN and SCN ratio are comparable, while the SCN is less influenced by control species than the SCN ratio. According to our study, several suggestions were provided for future animal diet studies or other high-throughput sequencing studies containing tissue bias.
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Affiliation(s)
- Di Zhu
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station.,College of Life Sciences, Beijing Normal University, Beijing
| | - Feng Wu
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station.,College of Life Sciences, Beijing Normal University, Beijing
| | - Hailong Li
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,College of Agriculture and Life Sciences, Seoul National University, Seoul.,College of Geography and Ocean Science, YanBian University, Hunchun
| | - Tianming Wang
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station.,College of Life Sciences, Beijing Normal University, Beijing
| | - Lei Bao
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station.,College of Life Sciences, Beijing Normal University, Beijing
| | - Jianping Ge
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station.,College of Life Sciences, Beijing Normal University, Beijing
| | - Hongfang Wang
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station.,College of Life Sciences, Beijing Normal University, Beijing
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17
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Martin JL, Santi I, Pitta P, John U, Gypens N. Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Plankton metabarcoding is increasingly implemented in marine ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on microscopy (morphological). 18S rRNA gene is the most widely used marker for groups’ and species’ detection and classification within marine eukaryotic microorganisms. These datasets have commonly relied on the acquisition of organismal abundances directly from the number of DNA sequences (i.e. reads). Besides the inherent technical biases in metabarcoding, the largely varying 18S rRNA gene copy numbers (GCN) among marine protists (ranging from tens to thousands) is one of the most important biological biases for species quantification. In this work, we present a gene copy number correction factor (CF) for four marine planktonic groups: Bacillariophyta, Dinoflagellata, Ciliophora miscellaneous and flagellated cells. On the basis of the theoretical assumption that ‘1 read’ is equivalent to ‘1 GCN’, we used the GCN median values per plankton group to calculate the corrected cell number and biomass relative abundances. The species-specific absolute GCN per cell were obtained from various studies published in the literature. We contributed to the development of a species-specific 18S rRNA GCN database proposed by previous authors. To assess the efficiency of the correction factor we compared the metabarcoding, morphological and corrected relative abundances (in cell number and biomass) of 15 surface water samples collected in the Belgian Coastal Zone. Results showed that the application of the correction factor over metabarcoding results enables us to significantly improve the estimates of cell abundances for Dinoflagellata, Ciliophora and flagellated cells, but not for Bacillariophyta. This is likely to due to large biovolume plasticity in diatoms not corresponding to genome size and gene copy numbers. C-biomass relative abundance estimations directly from amplicon reads were only improved for Dinoflagellata and Ciliophora. The method is still facing biases related to the low number of species GCN assessed. Nevertheless, the increase of species in the GCN database may lead to the refinement of the proposed correction factor.
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18
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Pilgrim EM, Smucker NJ, Wu H, Martinson J, Nietch CT, Molina M, Darling JA, Johnson BR. Developing Indicators of Nutrient Pollution in Streams Using 16S rRNA Gene Metabarcoding of Periphyton-Associated Bacteria. WATER 2022; 14:1-24. [PMID: 36213613 PMCID: PMC9534034 DOI: 10.3390/w14152361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Indicators based on nutrient-biota relationships in streams can inform water quality restoration and protection programs. Bacterial assemblages could be particularly useful indicators of nutrient effects because they are species-rich, important contributors to ecosystem processes in streams, and responsive to rapidly changing conditions. Here, we sampled 25 streams weekly (12-14 times each) and used 16S rRNA gene metabarcoding of periphyton-associated bacteria to quantify the effects of total phosphorus (TP) and total nitrogen (TN). Threshold indicator taxa analysis identified assemblage-level changes and amplicon sequence variants (ASVs) that increased or decreased with increasing TP and TN concentrations (i.e., low P, high P, low N, and high N ASVs). Boosted regression trees confirmed that relative abundances of gene sequence reads for these four indicator groups were associated with nutrient concentrations. Gradient forest analysis complemented these results by using multiple predictors and random forest models for each ASV to identify portions of TP and TN gradients at which the greatest changes in assemblage structure occurred. Synthesized statistical results showed bacterial assemblage structure began changing at 24 μg TP/L with the greatest changes occurring from 110 to 195 μg/L. Changes in the bacterial assemblages associated with TN gradually occurred from 275 to 855 μg/L. Taxonomic and phylogenetic analyses showed that low nutrient ASVs were commonly Firmicutes, Verrucomicrobiota, Flavobacteriales, and Caulobacterales, Pseudomonadales, and Rhodobacterales of Proteobacteria, whereas other groups, such as Chitinophagales of Bacteroidota, and Burkholderiales, Rhizobiales, Sphingomonadales, and Steroidobacterales of Proteobacteria comprised the high nutrient ASVs. Overall, the responses of bacterial ASV indicators in this study highlight the utility of metabarcoding periphyton-associated bacteria for quantifying biotic responses to nutrient inputs in streams.
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Affiliation(s)
- Erik M. Pilgrim
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Nathan J. Smucker
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Huiyun Wu
- School of Public Health & Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - John Martinson
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Christopher T. Nietch
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Marirosa Molina
- United States Environmental Protection Agency, Office of Research and Development, Research Triangle Park, NC 27711, USA
| | - John A. Darling
- United States Environmental Protection Agency, Office of Research and Development, Research Triangle Park, NC 27711, USA
| | - Brent R. Johnson
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
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Blancher P, Lefrançois E, Rimet F, Vasselon V, Argillier C, Arle J, Beja P, Boets P, Boughaba J, Chauvin C, Deacon M, Duncan W, Ejdung G, Erba S, Ferrari B, Fischer H, Hänfling B, Haldin M, Hering D, Hette-Tronquart N, Hiley A, Järvinen M, Jeannot B, Kahlert M, Kelly M, Kleinteich J, Koyuncuoğlu S, Krenek S, Langhein-Winther S, Leese F, Mann D, Marcel R, Marcheggiani S, Meissner K, Mergen P, Monnier O, Narendja F, Neu D, Onofre Pinto V, Pawlowska A, Pawlowski J, Petersen M, Poikane S, Pont D, Renevier MS, Sandoy S, Svensson J, Trobajo R, Tünde Zagyva A, Tziortzis I, van der Hoorn B, Vasquez MI, Walsh K, Weigand A, Bouchez A. A strategy for successful integration of DNA-based methods in aquatic monitoring. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent advances in molecular biomonitoring open new horizons for aquatic ecosystem assessment. Rapid and cost-effective methods based on organismal DNA or environmental DNA (eDNA) now offer the opportunity to produce inventories of indicator taxa that can subsequently be used to assess biodiversity and ecological quality. However, the integration of these new DNA-based methods into current monitoring practices is not straightforward, and will require coordinated actions in the coming years at national and international levels.
To plan and stimulate such an integration, the European network DNAqua-Net (COST Action CA15219) brought together international experts from academia, as well as key environmental biomonitoring stakeholders from different European countries. Together, this transdisciplinary consortium developed a roadmap for implementing DNA-based methods with a focus on inland waters assessed by the EU Water Framework Directive (2000/60/EC). This was done through a series of online workshops held in April 2020, which included fifty participants, followed by extensive synthesis work.
The roadmap is organised around six objectives: 1) to highlight the effectiveness and benefits of DNA-based methods, 2) develop an adaptive approach for the implementation of new methods, 3) provide guidelines and standards for best practice, 4) engage stakeholders and ensure effective knowledge transfer, 5) support the environmental biomonitoring sector to achieve the required changes, 6) steer the process and harmonise efforts at the European level.
This paper provides an overview of the forum discussions and the common European views that have emerged from them, while reflecting the diversity of situations in different countries. It highlights important actions required for a successful implementation of DNA-based biomonitoring of aquatic ecosystems by 2030.
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20
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Kulaš A, Gligora Udovič M, Tapolczai K, Žutinić P, Orlić S, Levkov Z. Diatom eDNA metabarcoding and morphological methods for bioassessment of karstic river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154536. [PMID: 35304150 DOI: 10.1016/j.scitotenv.2022.154536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/20/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Karst ecosystems play a unique role as exceptional natural habitats in sustaining biodiversity. This study focuses on diatoms, a diverse group of microeukaryotes in the periphytic community of a karstic river. In a multi-microhabitat study along the Krka River (Croatia), our goal was to obtain a detailed overview of diatom diversity and community structure using morphological and molecular approaches, and to assess the applicability of eDNA metabarcoding as a reliable tool for biomonitoring assessment. The results revealed a relatively low agreement in the diatom community composition between the two approaches, but also provided complementary information, with no differences in beta diversity detected between microhabitats. The SIMPER analysis underlined the importance of the molecular approach in identifying diatom community composition, due to errors in distinguishing between deposited diatom cells that occurred in the morphological analysis. In contrast, the morphological approach indicated a clear diatom community separation along the river with a strong location effect. Despite certain differences, both approaches provided a feasible assessment of the ecological status according to the relationship to environmental pressures, classifying the Krka River as High (morphological approach) or Good (molecular approach) throughout the most of its course. Moreover, diatom diversity based on both approaches provides a reliable dataset applicable in routine monitoring assessment and offers a deeper understanding of the presented ecological status. The incompleteness of a reference database presents one major drawback of the molecular approach, which needs further updating in order to improve routine diatom metabarcoding.
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Affiliation(s)
- Antonija Kulaš
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, HR-10000 Zagreb, Croatia.
| | - Marija Gligora Udovič
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Kálmán Tapolczai
- Premium Postdoctoral Research Program, Hungarian Academy of Sciences, Budapest, Hungary; Research Group of Limnology, Center for Natural Science, University of Pannonia, Egyetem u. 10, H-8200 Veszprém, Hungary; Balaton Limnological Research Institute, Eötvös Loránd Research Network (ELKH), Klebelsberg Kuno u. 3, Tihany, Hungary
| | - Petar Žutinić
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Sandi Orlić
- Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; Center of Excellence for Science and Technology Integrating Mediterranean Region (STIM), HR-10000 Zagreb, Croatia
| | - Zlatko Levkov
- Institute of Biology, Faculty of Natural Science, Ss Cyril and Methodius University, Skopje, Macedonia
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21
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Steinke D, deWaard SL, Sones JE, Ivanova NV, Prosser SWJ, Perez K, Braukmann TWA, Milton M, Zakharov EV, deWaard JR, Ratnasingham S, Hebert PDN. Message in a Bottle-Metabarcoding enables biodiversity comparisons across ecoregions. Gigascience 2022; 11:6575387. [PMID: 35482490 PMCID: PMC9049109 DOI: 10.1093/gigascience/giac040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/24/2022] [Accepted: 03/29/2022] [Indexed: 12/31/2022] Open
Abstract
Background Traditional biomonitoring approaches have delivered a basic understanding of biodiversity, but they cannot support the large-scale assessments required to manage and protect entire ecosystems. This study used DNA metabarcoding to assess spatial and temporal variation in species richness and diversity in arthropod communities from 52 protected areas spanning 3 Canadian ecoregions. Results This study revealed the presence of 26,263 arthropod species in the 3 ecoregions and indicated that at least another 3,000–5,000 await detection. Results further demonstrate that communities are more similar within than between ecoregions, even after controlling for geographical distance. Overall α-diversity declined from east to west, reflecting a gradient in habitat disturbance. Shifts in species composition were high at every site, with turnover greater than nestedness, suggesting the presence of many transient species. Conclusions Differences in species composition among their arthropod communities confirm that ecoregions are a useful synoptic for biogeographic patterns and for structuring conservation efforts. The present results also demonstrate that metabarcoding enables large-scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric used in prior efforts to track change in arthropod communities.
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Affiliation(s)
- D Steinke
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - S L deWaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - J E Sones
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - N V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - S W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - K Perez
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - T W A Braukmann
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - M Milton
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - E V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - J R deWaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - S Ratnasingham
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - P D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
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22
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Pérez-Burillo J, Valoti G, Witkowski A, Prado P, Mann DG, Trobajo R. Assessment of marine benthic diatom communities: insights from a combined morphological-metabarcoding approach in Mediterranean shallow coastal waters. MARINE POLLUTION BULLETIN 2022; 174:113183. [PMID: 35090287 DOI: 10.1016/j.marpolbul.2021.113183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 06/14/2023]
Abstract
We investigated the advantages and disadvantages of light microscope (LM)-based identifications and DNA metabarcoding, based on a 312-bp rbcL marker, for examining benthic diatom communities from Mediterranean shallow coastal environments. For this, we used biofilm samples collected from different substrata in the Ebro delta bays. We show that 1) Ebro delta bays harbour high-diversity diatom communities [LM identified 249 taxa] and 2) DNA metabarcoding effectively reflects this diversity at genus- but not species level, because of the incompleteness of the DNA reference library. Nevertheless, DNA metabarcoding offers new opportunities for detecting small, delicate and rare diatom species missed by LM and diatoms that lack silica frustules. The primers used, though designed for diatoms, successfully amplified rarely reported members of other stramenopile groups. Combining LM and DNA approaches offers stronger support for ecological studies of benthic microalgal communities in shallow coastal environments than using either approach on its own.
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Affiliation(s)
- Javier Pérez-Burillo
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Ràpita, Tarragona, Spain; Departament de Geografia, Universitat Rovira i Virgili, C/ Joanot Martorell 15, E43500 Vila-seca, Tarragona, Spain
| | - Greta Valoti
- Università Politecnica delle Marche, Piazza Roma, 22, IT60131 Ancona, Italy
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland
| | - Patricia Prado
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Ràpita, Tarragona, Spain
| | - David G Mann
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Ràpita, Tarragona, Spain; Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland, UK
| | - Rosa Trobajo
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Ràpita, Tarragona, Spain.
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23
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Sanyal A, Larsson J, van Wirdum F, Andrén T, Moros M, Lönn M, Andrén E. Not dead yet: Diatom resting spores can survive in nature for several millennia. AMERICAN JOURNAL OF BOTANY 2022; 109:67-82. [PMID: 34648178 DOI: 10.1002/ajb2.1780] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Understanding the adaptive capacities of species over long timescales lies in examining the revived recent and millennia-old resting spores buried in sediments. We show for the first time the revival, viability, and germination rate of resting spores of the diatom Chaetoceros deposited in sub-seafloor sediments from three ages (recent: 0 to 80 years; ancient: ~1250 (Medieval Climate Anomaly) and ~6600 (Holocene Thermal Maximum) calendar year before present. METHODS Recent and ancient Chaetoceros spores were revived to examine their viability and germination rate. Light and scanning electron microscopy and Sanger sequencing was done to identify the species. RESULTS We show that ~6600 cal. year BP old Chaetoceros resting spores are still viable and that the vegetative reproduction in recent and ancient resting spores varies. The time taken to germinate is three hours to 2 to 3 days in both recent and ancient spores, but the germination rate of the spores decreased with increasing age. The germination rate of the recent spores was ~41% while that of the ancient spores were ~31% and ~12% for the ~1250 and ~6600 cal. year BP old resting spores, respectively. Based on the morphology of the germinated vegetative cells we identified the species as Chaetoceros muelleri var. subsalsum. Sanger sequences of nuclear and chloroplast markers identified the species as Chaetoceros muelleri. CONCLUSIONS We identify a unique model system, Chaetoceros muelleri var. subsalsum and show that recent and ancient resting spores of the species buried in sediments in the Baltic Sea can be revived and used for long-term evolutionary studies.
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Affiliation(s)
- Anushree Sanyal
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, SE-14189 Huddinge, Stockholm, Sweden
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
| | - Josefine Larsson
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, SE-14189 Huddinge, Stockholm, Sweden
| | - Falkje van Wirdum
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, SE-14189 Huddinge, Stockholm, Sweden
| | - Thomas Andrén
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, SE-14189 Huddinge, Stockholm, Sweden
| | - Matthias Moros
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestraße 15, DE-18119 Rostock, Germany
| | - Mikael Lönn
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, SE-14189 Huddinge, Stockholm, Sweden
| | - Elinor Andrén
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, SE-14189 Huddinge, Stockholm, Sweden
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24
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Martins FMS, Feio MJ, Porto M, Filipe AF, Bonin A, Serra SRQ, Alves PC, Taberlet P, Beja P. Assessing changes in stream macroinvertebrate communities across ecological gradients using morphological versus DNA metabarcoding approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149030. [PMID: 34311381 DOI: 10.1016/j.scitotenv.2021.149030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Freshwater macroinvertebrates provide valuable indicators for biomonitoring ecosystem change in relation to natural and anthropogenic drivers. DNA metabarcoding is an efficient approach for estimating such indicators, but its results may differ from morphotaxonomic approaches traditionally used in biomonitoring. Here we test the hypothesis that despite differences in the number and identity of taxa recorded, both approaches may retrieve comparable patterns of community change, and detect similar ecological gradients influencing such changes. We compared results obtained with morphological identification at family level of macroinvertebrates collected at 80 streams under a Water Framework Directive biomonitoring program in Portugal, with results obtained with metabarcoding from the ethanol preserving the bulk samples, using either single (COI-M19BR2, 16S-Inse01, 18S-Euka02) or multiple markers. Metabarcoding recorded less families and different communities compared to morphotaxonomy, but community sensitivities to disturbance estimated with the IASPT index were more similar across approaches. Spatial variation in local community metrics and the factors influencing such variation were significantly correlated between morphotaxonomy and metabarcoding. After reducing random noise in the dissimilarity matrices, the spatial variation in community composition was also significantly correlated across methods. A dominant gradient of community change was consistently retrieved, and all methods identified a largely similar set of anthropogenic stressors strongly influencing such gradient. Overall, results confirm our initial hypothesis, suggesting that morphotaxonomy and metabarcoding can estimate consistent spatial patterns of community variation and their main drivers. These results are encouraging for macroinvertebrate biomonitoring using metabarcoding approaches, suggesting that they can be intercalibrated with morphotaxonomic approaches to recover equivalent spatial and temporal gradients of ecological change.
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Affiliation(s)
- Filipa M S Martins
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal.
| | - Maria J Feio
- Universidade de Coimbra, MARE, Centro de Ciências do Mar e do Ambiente, Departamento de Ciência da Vida, Coimbra, Portugal
| | - Miguel Porto
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Ana F Filipe
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Aurélie Bonin
- Université Grenoble Alpes, CNRS, Laboratoire d'Ecologie Alpine (LECA), Grenoble, France
| | - Sónia R Q Serra
- Universidade de Coimbra, MARE, Centro de Ciências do Mar e do Ambiente, Departamento de Ciência da Vida, Coimbra, Portugal
| | - Paulo C Alves
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal
| | - Pierre Taberlet
- Université Grenoble Alpes, CNRS, Laboratoire d'Ecologie Alpine (LECA), Grenoble, France; UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Pedro Beja
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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25
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Konschak M, Zubrod JP, Duque Acosta TS, Bouchez A, Kroll A, Feckler A, Röder N, Baudy P, Schulz R, Bundschuh M. Herbicide-Induced Shifts in the Periphyton Community Composition Indirectly Affect Feeding Activity and Physiology of the Gastropod Grazer Physella acuta. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14699-14709. [PMID: 34677949 DOI: 10.1021/acs.est.1c01819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Herbicides are well known for unintended effects on freshwater periphyton communities. Large knowledge gaps, however, exist regarding indirect herbicide impacts on primary consumers through changes in the quality of periphyton as a food source (i.e., diet-related effects). To address this gap, the grazer Physella acuta (Gastropoda) was fed for 21 days with periphyton that grew for 15 days in the presence or absence of the herbicide diuron (8 μg/L) to quantify changes in the feeding rate, growth rate, and energy storage (neutral lipid fatty acids; NLFAs) of P. acuta. Periphyton biomass, cell viability, community structure, and FAs served as proxies for food quality that support a mechanistic interpretation of the grazers' responses. Diuron changed the algae periphyton community and fatty acid profiles, indicating alterations in the food quality, which could explain differences in the snails' feeding rate compared to the control. While the snails' growth rate was, despite an effect size of 55%, not statistically significantly changed, NLFA profiles of P. acuta were altered. These results indicate that herbicides can change the food quality of periphyton by shifts in the algae composition, which may affect the physiology of grazers.
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Affiliation(s)
- Marco Konschak
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau, Germany
| | - Jochen P Zubrod
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau, Germany
- Eußerthal Ecosystem Research Station, University of Koblenz-Landau, Birkenthalstraße 13, D-76857 Eußerthal, Germany
| | - Tomás S Duque Acosta
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau, Germany
| | - Agnès Bouchez
- UMR CARRTEL, INRAE, USMB, 75bis Avenue de Corzent, F-742003 Thonon-les-Bains, France
| | - Alexandra Kroll
- Swiss Centre for Applied Ecotoxicology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Alexander Feckler
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau, Germany
- Eußerthal Ecosystem Research Station, University of Koblenz-Landau, Birkenthalstraße 13, D-76857 Eußerthal, Germany
| | - Nina Röder
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau, Germany
| | - Patrick Baudy
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau, Germany
| | - Ralf Schulz
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau, Germany
- Eußerthal Ecosystem Research Station, University of Koblenz-Landau, Birkenthalstraße 13, D-76857 Eußerthal, Germany
| | - Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau, Germany
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Lennart Hjelms väg 9, SE-75007 Uppsala, Sweden
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Bachiller E, Giménez J, Albo‐Puigserver M, Pennino MG, Marí‐Mena N, Esteban A, Lloret‐Lloret E, Bellido JM, Coll M. Trophic niche overlap between round sardinella ( Sardinella aurita) and sympatric pelagic fish species in the Western Mediterranean. Ecol Evol 2021; 11:16126-16142. [PMID: 34824816 PMCID: PMC8601905 DOI: 10.1002/ece3.8293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 01/27/2023] Open
Abstract
The northward expansion of round sardinella (Sardinella aurita) in the Mediterranean Sea, together with declines and fluctuations in biomass and landings of European sardine (Sardina pilchardus) and anchovy (Engraulis encrasicolus) observed in recent decades, may suggest potential inter-specific competition in the pelagic domain. The coexistence of sympatric zooplanktivorous fish species might therefore be exposed in part to trophic niche overlap and competition for food. Combining visual diet characterization under the microscope with DNA metabarcoding from stomach contents of fish collected in spring results show that predation on relatively large krill is equally important for sardinella than for the other two niche overlapping species. Furthermore, an important overlap is found in their isotopic niche, especially with anchovy, using nitrogen (δ15N) and carbon (δ13C) stable isotopes in muscle tissue. In fact, the three fish species are able to feed effectively in the whole prey size spectrum available during the sampled season, from the smallest diatoms and copepods to the larger prey (i.e., decapods and euphausiids), including fish larvae. Moreover, effective predation upon other large prey like siphonophores, which is observed only when multi-proxy analyses in stomach contents are applied, might also be relevant in the diet of sardinella. The overlapping diet composition in spring, together with the effective use of food resource by sardinella, can be of special interest in potential future scenarios with warmer water temperature leading to lower zooplankton and/or higher jellyfish availability, where sardinella may take advantage over other species due to its feeding plasticity.
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Affiliation(s)
- Eneko Bachiller
- Marine Renewable Resources DepartmentInstitute of Marine Science (ICM‐CSIC)BarcelonaSpain
| | - Joan Giménez
- Marine Renewable Resources DepartmentInstitute of Marine Science (ICM‐CSIC)BarcelonaSpain
- MaREI CentreEnvironmental Research InstituteUniversity College CorkCorkIreland
- School of Biological, Earth, and Environmental SciencesUniversity College CorkCorkIreland
| | - Marta Albo‐Puigserver
- Marine Renewable Resources DepartmentInstitute of Marine Science (ICM‐CSIC)BarcelonaSpain
- Centro de Ciências do MarUniversidade do Algarve (CCMAR‐UAlg)FaroPortugal
| | | | | | - Antonio Esteban
- Centro Oceanográfico de MurciaInstituto Español de OceanografíaSan Pedro del PinatarSpain
| | - Elena Lloret‐Lloret
- Marine Renewable Resources DepartmentInstitute of Marine Science (ICM‐CSIC)BarcelonaSpain
| | - José María Bellido
- Centro Oceanográfico de MurciaInstituto Español de OceanografíaSan Pedro del PinatarSpain
| | - Marta Coll
- Marine Renewable Resources DepartmentInstitute of Marine Science (ICM‐CSIC)BarcelonaSpain
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Nistal-García A, García-García P, García-Girón J, Borrego-Ramos M, Blanco S, Bécares E. DNA metabarcoding and morphological methods show complementary patterns in the metacommunity organization of lentic epiphytic diatoms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147410. [PMID: 33971606 DOI: 10.1016/j.scitotenv.2021.147410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
Diatoms are important organisms in freshwater ecosystems due to their position as primary producers and therefore, analyzing their assemblages provides relevant information on ecosystem functioning. Diatoms have historically been identified based on morphological traits, which is time-consuming and requires well-trained specialists. Nevertheless, DNA barcoding offers an alternative approach to overcome some limitations of the morphological method. Here, we assess if both approaches are comparable methods to study patterns and mechanisms (including environmental filtering and dispersal limitation) of epiphytic diatom metacommunities using a comprehensive dataset from 22 Mediterranean ponds at different taxonomic resolutions. We used a fragment of rbcL barcode gene combined with High-Throughput Sequencing to infer diatom community composition. The overall degree of correspondence between both approaches was assessed by Procrustean rotation analysis and Procrustean randomization tests, whereas the role of local environmental variables and geographical distances was studied using a comprehensive combination of BIOENV, Mantel tests and distance-based redundancy analysis. Our results showed a relatively poor correspondence in the compositional variation of diatom metacommunity between both approaches. We speculate that the incompleteness of the reference database and the bioinformatics processing are the biases most likely affecting the molecular approach, whereas the limited counting effort and the presence of cryptic species are presumably the major biases related with the morphological method. On the other hand, variation in diatom community composition detected with both approaches was strongly related to the environmental template, which may be related with the narrow community-environment relationships in diatoms. Nevertheless, we found no significant relationship between compositional variation and geographical distances. Overall, our work shows the complementary nature of both approaches and highlights the importance of DNA metabarcoding to address empirical research questions of community ecology in freshwaters, especially once the reference databases include most genotypes of occurring taxa and bioinformatics biases are overcome.
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Affiliation(s)
| | - Pedro García-García
- Genetic Unit, University of León, Campus de Vegazana S/N, 24071 León, Spain.
| | - Jorge García-Girón
- Ecology Unit, University of León, Campus de Vegazana S/N, 24071 León, Spain.
| | - María Borrego-Ramos
- Institute of Environment, Natural Resources and Biodiversity, La Serna, 58, 24007 León, Spain.
| | - Saúl Blanco
- Ecology Unit, University of León, Campus de Vegazana S/N, 24071 León, Spain; Institute of Environment, Natural Resources and Biodiversity, La Serna, 58, 24007 León, Spain.
| | - Eloy Bécares
- Ecology Unit, University of León, Campus de Vegazana S/N, 24071 León, Spain; Institute of Environment, Natural Resources and Biodiversity, La Serna, 58, 24007 León, Spain.
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28
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Pissaridou P, Cantonati M, Bouchez A, Tziortzis I, Dörflinger G, Vasquez MI. How can integrated morphotaxonomy- and metabarcoding-based diatom assemblage analyses best contribute to the ecological assessment of streams? METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.68438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Environmental conditions, such as nutrient concentrations, salinity, elevation etc., shape diatom assemblages of periphytic biofilms. These assemblages respond rapidly to environmental changes, a fact which makes diatoms valuable bioindicators. Hence, freshwater biomonitoring programmes currently use diatom indices (e.g. EU Water Framework Directive - WFD). To date, microscopy-based assessments require high taxonomic expertise for diatom identification at the species level. High-throughput technologies now provide cost-effective identification approaches that are promising, complementary or alternative tools for bioassessment. The suitability of the metabarcoding method is evaluated for the first time in the Cyprus streams WFD monitoring network, an eastern Mediterranean country with many endemic species and results are compared to the results acquired from the morphotaxonomic analysis. Morphotaxonomic identification was conducted microscopically, using the most updated taxonomic concepts, literature and online resources. At the same time, DNA metabarcoding involved the use of the rbcL 312 bp barcode, high-throughput sequencing and bioinformatic analysis. The ecological status was calculated using the IPS Index. Results show a positive correlation between morpho-taxonomic and molecular IPS scores. Discrepancies between the two methodologies are related to the limitations of both techniques. This study confirmed that Fistulifera saprophila can have a crucial role in key differences observed, as it negatively influences IPS scores and microscopy methods frequently overlook it. Importantly, gaps in the DNA barcoding reference databases lead to a positive overestimation in IPS scores. Overall, we conclude that DNA metabarcoding offsets the morphotaxonomic methodology for the ecological quality assessment of freshwaters.
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Ajani PA, Verma A, Kim JH, Woodcock S, Nishimura T, Farrell H, Zammit A, Brett S, Murray SA. Using qPCR and high-resolution sensor data to model a multi-species Pseudo-nitzschia (Bacillariophyceae) bloom in southeastern Australia. HARMFUL ALGAE 2021; 108:102095. [PMID: 34588117 DOI: 10.1016/j.hal.2021.102095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Harmful algal blooms, including those caused by the toxic diatom Pseudo-nitzschia, can have significant impacts on human health, ecosystem functioning and ultimately food security. In the current study we characterized a bloom of species of Pseudo-nitzschia that occurred in a south-eastern Australian oyster-growing estuary in 2019. Using light microscopy, combined with molecular (ITS/5.8S and LSU D1-D3 rDNA regions) and toxicological evidence, we observed the bloom to consist of multiple species of Pseudo-nitzschia including P. cf. cuspidata, P. hasleana, P. fraudulenta and P. multiseries, with P. cf. cuspidata being the only species that produced domoic acid (3.1 pg DA per cell). As several species of Pseudo-nitzschia co-occurred, only one of which produced DA, we developed a rapid, sensitive and efficient quantitative real-time polymerase chain reaction (qPCR) assay to detect only species belonging to the P. pseudodelicatissima complex Clade I, to which P. cf. cuspidata belongs, and this indicated that P. cuspidata or closely related strains may have dominated the Pseudo-nitzschia community at this time. Finally, using high resolution water temperature and salinity sensor data, we modeled the relationship between light microscopy determined abundance of P. delicatissima group and environmental variables (temperature, salinity, rainfall) at two sites within the estuary. A total of eight General Linear Models (GLMs) explaining between 9 and 54% of the deviance suggested that the temperature (increasing) and/or salinity (decreasing) data were generally more predictive of high cell concentrations than the rainfall data at both sites, and that overall, cell concentrations were more predictive at the more oceanic site than the more upstream site, using this method. We conclude that the combination of rapid molecular methods such as qPCR and real-time sensor data modeling, can provide a more rapid and effective early warning of harmful algal blooms of species of Pseudo-nitzschia, resulting in more beneficial regulatory and management outcomes.
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Affiliation(s)
- Penelope A Ajani
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia; Food Agility CRC Ltd, 81 Broadway, Ulitmo, NSW 2007, Australia.
| | - Arjun Verma
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia; Food Agility CRC Ltd, 81 Broadway, Ulitmo, NSW 2007, Australia
| | - Jin Ho Kim
- Department of Earth and Marine Science, College of Ocean Sciences, Jeju National University, Jeju 63243, Korea
| | - Stephen Woodcock
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | | | - Hazel Farrell
- NSW Food Authority, NSW Department of Primary Industries, PO Box 232, Taree 2430, Australia
| | - Anthony Zammit
- NSW Food Authority, NSW Department of Primary Industries, PO Box 232, Taree 2430, Australia
| | - Steve Brett
- Microalgal Services, 308 Tucker Rd, Ormond 3204, Australia
| | - Shauna A Murray
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia; Food Agility CRC Ltd, 81 Broadway, Ulitmo, NSW 2007, Australia
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30
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Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
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Identification and semi-quantification of Atlantic salmon in processed and mixed seafood products using Droplet Digital PCR (ddPCR). Food Chem Toxicol 2021; 154:112329. [PMID: 34116106 DOI: 10.1016/j.fct.2021.112329] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/12/2021] [Accepted: 06/05/2021] [Indexed: 11/24/2022]
Abstract
Fishery products are often subject to substitution fraud, which is hard to trace due to a lack of morphologic traits when processed, gutted, or decapitated. Traditional molecular methods (DNA barcoding) fail to identify products containing multiple species and cannot estimate original weight percentages. As a proof of concept, an Atlantic salmon (Salmo salar) specific ddPCR assay was designed to authenticate mixed food products. The method proved to be specific and able to accurately quantify S. salar when using DNA extracts, even in the presence of DNA from closely related salmon species. The ddPCR estimates correlated well with the percentage of S. salar in artificially assembled tissue mixtures. The effect of common salmon processing techniques (freezing, smoking, poaching with a "Bellevue" recipe and marinating with a 'Gravad lax' recipe) on the ddPCR output was investigated and freezing and marinating appeared to lower the copies detected by the ddPCR. Finally, the assay was applied to 46 retail products containing Atlantic or Pacific salmon, and no indications of substitution fraud were detected. The method allows for a semi-quantitative evaluation of the S. salar content in processed food products and can rapidly screen Atlantic salmon products and flag potentially tampered samples for further investigation.
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Pissaridou P, Vasselon V, Christou A, Chonova T, Papatheodoulou A, Drakou K, Tziortzis I, Dörflinger G, Rimet F, Bouchez A, Vasquez MI. Cyprus' diatom diversity and the association of environmental and anthropogenic influences for ecological assessment of rivers using DNA metabarcoding. CHEMOSPHERE 2021; 272:129814. [PMID: 33582508 DOI: 10.1016/j.chemosphere.2021.129814] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/12/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Human activities are the leading cause of environmental impairments. Appropriate biomonitoring of ecosystems is needed to assess these activities effectively. In freshwater ecosystems, periphytic and epilithic biofilms have diatom assemblages. These assemblages respond rapidly to environmental changes, making diatoms valuable bioindicators. For this reason, freshwater biomonitoring programs are currently using diatoms (e.g., Water Framework Directive). In the past ten years, DNA metabarcoding coupled with next-generation sequencing and bioinformatics represents a complementary approach for diatom biomonitoring. In this study, this approach is used for the first time in Cyprus by considering the association of environmental and anthropogenic pressures to diatom assemblages. Statistical analysis was then applied to identify the environmental (i.e., river types, geo-morphological) and anthropogenic (i.e., physicochemical, human land-use pressures) variables' role in the observed diatom diversity. Results indicate differences in diatom assemblages between intermittent and perennial rivers. Achnanthidium minutissimum was more abundant in intermittent rivers; whereas Amphora pediculus and Planothidium caputium in perennial ones. Additionally, we could demonstrate the correlation between nutrients (e.g., nitrogen, phosphorus), stations' local characteristics (e.g., elevation), and land use activities on the observed differences in diatom diversity. Finally, we conclude that multi-stressors and anthropogenic pressures together as multiple stressors have a significant statistical relationship to the observed diatom diversity and play a pivotal role in determining Cyprus' rivers' ecological status.
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Affiliation(s)
- Panayiota Pissaridou
- Department of Chemical Engineering, Cyprus University of Technology, Archiepiskopou Kyprianou 30, Limassol, 3036, Cyprus
| | | | - Andreas Christou
- Department of Chemical Engineering, Cyprus University of Technology, Archiepiskopou Kyprianou 30, Limassol, 3036, Cyprus
| | | | - Athina Papatheodoulou
- Department of Chemical Engineering, Cyprus University of Technology, Archiepiskopou Kyprianou 30, Limassol, 3036, Cyprus; I.A.CO. Environmental & Water Consultants Ltd, 3 Stavrou Ave. Office 202, Strovolos, 2035, Cyprus
| | - Katerina Drakou
- Department of Chemical Engineering, Cyprus University of Technology, Archiepiskopou Kyprianou 30, Limassol, 3036, Cyprus
| | - Iakovos Tziortzis
- Water Development Department, Kennedy Avenue 100-110, 1047, Pallouriotissa, Cyprus
| | - Gerald Dörflinger
- Water Development Department, Kennedy Avenue 100-110, 1047, Pallouriotissa, Cyprus
| | | | - Agnes Bouchez
- INRAE, UMR CARRTEL, Thonon-les-bains, F-74200, France
| | - Marlen I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, Archiepiskopou Kyprianou 30, Limassol, 3036, Cyprus.
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Kelly MG, Jones T, Walsh K. Potential for cross-contamination of diatom DNA samples when using toothbrushes. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.66503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The use of toothbrushes and similar devices for sampling diatoms from hard surfaces is a well-established approach. Toothbrushes are routinely cleaned and reused when sampling for analysis by light microscopy. This paper looks at the scale of contamination encountered when this technique is used to sample diatoms for metabarcoding analyses, as well as at the scale of contamination to be expected if stream, rather than distilled water, is used to wash diatoms from stones. Although some contamination attributable to toothbrushes was detected, read numbers were low and had no effect on index calculation or ecological status estimates. However, if the primary focus of a study is to thoroughly document diversity in a sample, then even this small level of contamination may be unacceptable and more stringent measures may be required.
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Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches. WATER 2021. [DOI: 10.3390/w13101351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Benthic diatoms have traditionally been used as bioindicators of aquatic ecosystems. Because diatom-based monitoring of water quality is required by European legislation, molecular-based methods had emerged as useful alternatives to classical methods based on morphological identification using light microscopy. The aim of this study was to test the reliability of DNA metabarcoding combined with High-Throughput Sequencing (HTS) techniques in the bioassessment of the trophic status of 22 Mediterranean shallow ponds in NW Spain. For each pond, the Trophic Diatom Index (TDI) was calculated from inventories obtained by identification using light microscopy (LM) followed by high-throughput sequencing (HTS) at the molecular level. Ponds were subsequently classified into five water quality classes. The results showed a good correspondence between both methods, especially after applying a correction factor that depended on the biovolume of the cells. This correspondence led to the assignment to the same quality class in 59% of the ponds. The determination and quantification of valves or DNA sequences was one of the main pitfalls, which mainly included those related to the variability in the relative abundances of some species. Accordingly, ponds with similar relative abundances for the dominant species were assigned to the same quality class. Moreover, other difficulties leading the discrepancies were the misidentification of some species due to the presence of semi-cryptic taxa, the incompleteness of the reference database and the bioinformatic protocol. Thus, the validation of DNA-based methods for the identification of freshwater diatoms represents an important goal, as an alternative to using traditional methods in Mediterranean shallow ponds.
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Sagova-Mareckova M, Boenigk J, Bouchez A, Cermakova K, Chonova T, Cordier T, Eisendle U, Elersek T, Fazi S, Fleituch T, Frühe L, Gajdosova M, Graupner N, Haegerbaeumer A, Kelly AM, Kopecky J, Leese F, Nõges P, Orlic S, Panksep K, Pawlowski J, Petrusek A, Piggott JJ, Rusch JC, Salis R, Schenk J, Simek K, Stovicek A, Strand DA, Vasquez MI, Vrålstad T, Zlatkovic S, Zupancic M, Stoeck T. Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring. WATER RESEARCH 2021; 191:116767. [PMID: 33418487 DOI: 10.1016/j.watres.2020.116767] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/14/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.
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Affiliation(s)
- M Sagova-Mareckova
- Dept. of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6, 16500, Czechia.
| | - J Boenigk
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - A Bouchez
- UMR CARRTEL, INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - K Cermakova
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, 15, av. Sécheron, 1202 Geneva, Switzerland
| | - T Chonova
- UMR CARRTEL, INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland
| | - U Eisendle
- University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - T Elersek
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Via Salaria km 29,300 - C.P. 10, 00015 Monterotondo St., Rome, Italy
| | - T Fleituch
- Institute of Nature Conservation, Polish Academy of Sciences, ul. Adama Mickiewicza 33, 31-120 Krakow, Poland
| | - L Frühe
- Ecology Group, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - M Gajdosova
- Dept. of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czechia
| | - N Graupner
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - A Haegerbaeumer
- Dept. of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - A-M Kelly
- School of Natural Sciences, Trinity College Dublin, University of Dublin, College Green, Dublin 2, D02 PN40, Ireland
| | - J Kopecky
- Epidemiology and Ecology of Microoganisms, Crop Research Institute, Drnovská 507, 16106 Prague 6, Czechia
| | - F Leese
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany; Aquatic Ecosystem Resarch, University of Duisburg-Essen, Universitaetsstrasse 5 D-45141 Essen, Germany
| | - P Nõges
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - S Orlic
- Institute Ruđer Bošković, Bijenička 54, 10000 Zagreb, Croatia; Center of Excellence for Science and Technology Integrating Mediterranean, Bijenička 54,10 000 Zagreb, Croatia
| | - K Panksep
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - J Pawlowski
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, 15, av. Sécheron, 1202 Geneva, Switzerland; Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - A Petrusek
- Dept. of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czechia
| | - J J Piggott
- School of Natural Sciences, Trinity College Dublin, University of Dublin, College Green, Dublin 2, D02 PN40, Ireland
| | - J C Rusch
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway; Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - R Salis
- Department of Biology, Faculty of Science, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| | - J Schenk
- Dept. of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - K Simek
- Institute of Hydrobiology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czechia
| | - A Stovicek
- Dept. of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6, 16500, Czechia
| | - D A Strand
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway
| | - M I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, 30 Arch. Kyprianos Str., 3036 Limassol, Cyprus
| | - T Vrålstad
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway
| | - S Zlatkovic
- Ministry of Environmental Protection, Omladinskih brigada 1, 11070 Belgrade, Serbia; Agency "Akvatorija", 11. krajiške divizije 49, 11090 Belgrade, Serbia
| | - M Zupancic
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - T Stoeck
- Ecology Group, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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37
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Benthic Diatoms in River Biomonitoring—Present and Future Perspectives within the Water Framework Directive. WATER 2021. [DOI: 10.3390/w13040478] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The European Water Framework Directive 2000/60/EC (WFD) has been implemented over the past 20 years, using physicochemical, biological and hydromorphological elements to assess the ecological status of surface waters. Benthic diatoms (i.e., phytobenthos) are one of the most common biological quality elements (BQEs) used in surface water monitoring and are particularly successful in detecting eutrophication, organic pollution and acidification. Herein, we reviewed their implementation in river biomonitoring for the purposes of the WFD, highlighting their advantages and disadvantages over other BQEs, and we discuss recent advances that could be applied in future biomonitoring. Until now, phytobenthos have been intercalibrated by the vast majority (26 out of 28) of EU Member States (MS) in 54% of the total water bodies assessed and was the most commonly used BQE after benthic invertebrates (85% of water bodies), followed by fish (53%), macrophytes (27%) and phytoplankton (4%). To meet the WFD demands, numerous taxonomy-based quality indices have been developed among MS, presenting, however, uncertainties possibly related to species biogeography. Recent development of different types of quality indices (trait-based, DNA sequencing and predictive modeling) could provide more accurate results in biomonitoring, but should be validated and intercalibrated among MS before their wide application in water quality assessments.
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38
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Smucker NJ, Pilgrim EM, Nietch CT, Darling JA, Johnson BR. DNA metabarcoding effectively quantifies diatom responses to nutrients in streams. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02205. [PMID: 32602216 PMCID: PMC7731896 DOI: 10.1002/eap.2205] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 04/02/2020] [Accepted: 05/04/2020] [Indexed: 05/18/2023]
Abstract
Nutrient pollution from human activities remains a common problem facing stream ecosystems. Identifying ecological responses to phosphorus and nitrogen can inform decisions affecting the protection and management of streams and their watersheds. Diatoms are particularly useful because they are a highly diverse group of unicellular algae found in nearly all aquatic environments and are sensitive responders to increased nutrient concentrations. Here, we used DNA metabarcoding of stream diatoms as an approach to quantifying effects of total phosphorus (TP) and total nitrogen (TN). Threshold indicator taxa analysis (TITAN) identified operational taxonomic units (OTUs) that increased or decreased along TP and TN gradients along with nutrient concentrations at which assemblages had substantial changes in the occurrences and relative abundances of OTUs. Boosted regression trees showed that relative abundances of gene sequence reads for OTUs identified by TITAN as low P, high P, low N, or high N diatoms had strong relationships with nutrient concentrations, which provided support for potentially using these groups of diatoms as metrics in monitoring programs. Gradient forest analysis provided complementary information by characterizing multi-taxa assemblage change using multiple predictors and results from random forest models for each OTU. Collectively, these analyses showed that notable changes in diatom assemblage structure and OTUs began around 20 µg TP/L, low P diatoms decreased substantially and community change points occurred from 75 to 150 µg/L, and high P diatoms became increasingly dominant from 150 to 300 µg/L. Diatoms also responded to TN with large decreases in low N diatoms occurring from 280 to 525 µg TN/L and a transition to dominance by high N diatoms from 525-850 µg/L. These diatom responses to TP and TN could be used to inform protection efforts (i.e., anti-degradation) and management goals (i.e., nutrient reduction) in streams and watersheds. Our results add to the growing support for using diatom metabarcoding in monitoring programs.
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Affiliation(s)
- Nathan J. Smucker
- Office of Research and DevelopmentUnited States Environmental Protection AgencyCincinnatiOhio45268USA
| | - Erik M. Pilgrim
- Office of Research and DevelopmentUnited States Environmental Protection AgencyCincinnatiOhio45268USA
| | - Christopher T. Nietch
- Office of Research and DevelopmentUnited States Environmental Protection AgencyCincinnatiOhio45268USA
| | - John A. Darling
- Office of Research and DevelopmentUnited States Environmental Protection AgencyResearch Triangle ParkNorth Carolina27711USA
| | - Brent R. Johnson
- Office of Research and DevelopmentUnited States Environmental Protection AgencyCincinnatiOhio45268USA
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39
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Bailet B, Apothéloz-Perret-Gentil L, Baričević A, Chonova T, Franc A, Frigerio JM, Kelly M, Mora D, Pfannkuchen M, Proft S, Ramon M, Vasselon V, Zimmermann J, Kahlert M. Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140948. [PMID: 32736102 DOI: 10.1016/j.scitotenv.2020.140948] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/09/2020] [Accepted: 07/11/2020] [Indexed: 06/11/2023]
Abstract
Ecological assessment of lakes and rivers using benthic diatom assemblages currently requires considerable taxonomic expertise to identify species using light microscopy. This traditional approach is also time-consuming. Diatom metabarcoding is a promising alternative and there is increasing interest in using this approach for routine assessment. However, until now, analysis protocols for diatom metabarcoding have been developed and optimised by research groups working in isolation. The diversity of existing bioinformatics methods highlights the need for an assessment of the performance and comparability of results of different methods. The aim of this study was to test the correspondence of outputs from six bioinformatics pipelines currently in use for diatom metabarcoding in different European countries. Raw sequence data from 29 biofilm samples were treated by each of the bioinformatics pipelines, five of them using the same curated reference database. The outputs of the pipelines were compared in terms of sequence unit assemblages, taxonomic assignment, biotic index score and ecological assessment outcomes. The three last components were also compared to outputs from traditional light microscopy, which is currently accepted for ecological assessment of phytobenthos, as required by the Water Framework Directive. We also tested the performance of the pipelines on the two DNA markers (rbcL and 18S-V4) that are currently used by the working groups participating in this study. The sequence unit assemblages produced by different pipelines showed significant differences in terms of assigned and unassigned read numbers and sequence unit numbers. When comparing the taxonomic assignments at genus and species level, correspondence of the taxonomic assemblages between pipelines was weak. Most discrepancies were linked to differential detection or quantification of taxa, despite the use of the same reference database. Subsequent calculation of biotic index scores also showed significant differences between approaches, which were reflected in the final ecological assessment. Use of the rbcL marker always resulted in better correlation among molecular datasets and also in results closer to these generated using traditional microscopy. This study shows that decisions made in pipeline design have implications for the dataset's structure and the taxonomic assemblage, which in turn may affect biotic index calculation and ecological assessment. There is a need to define best-practice bioinformatics parameters in order to ensure the best representation of diatom assemblages. Only the use of similar parameters will ensure the compatibility of data from different working groups. The future of diatom metabarcoding for ecological assessment may also lie in the development of new metrics using, for example, presence/absence instead of relative abundance data.
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Affiliation(s)
- Bonnie Bailet
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE - 750 07 Uppsala, Sweden.
| | | | - Ana Baričević
- Center for Marine Research, Ruđer Bosˇković Institute, Rovinj, Croatia.
| | - Teofana Chonova
- Research Department for Limnology, Mondsee, Faculty of Biology, University of Innsbruck, Mondsee, Austria; CARRTEL, French National Institute for Agricultural Research (INRA), University of Savoie Mont Blanc, 75 bis avenue de Corzent, 74200 Thonon-les-Bains, France.
| | - Alain Franc
- BioGeCo, French National Institute for Agricultural Research (INRA), 69 route d'Arcachon, 33610 Cesta, France.
| | - Jean-Marc Frigerio
- BioGeCo, French National Institute for Agricultural Research (INRA), 69 route d'Arcachon, 33610 Cesta, France.
| | - Martyn Kelly
- Bowburn Consultancy, 11 Monteigne Drive, Bowburn, Durham DH6 5QB, UK; School of Geography, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Demetrio Mora
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany.
| | | | - Sebastian Proft
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany
| | | | - Valentin Vasselon
- AFB, Pôle R&D "ECLA", INRA, UMR CARRTEL, 75bis av. de Corzent - CS 50511, FR-74200 Thonon-les-Bains, France
| | - Jonas Zimmermann
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany.
| | - Maria Kahlert
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE - 750 07 Uppsala, Sweden.
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Apothéloz-Perret-Gentil L, Bouchez A, Cordier T, Cordonier A, Guéguen J, Rimet F, Vasselon V, Pawlowski J. Monitoring the ecological status of rivers with diatom eDNA metabarcoding: A comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index. Mol Ecol 2020; 30:2959-2968. [PMID: 32979002 PMCID: PMC8358953 DOI: 10.1111/mec.15646] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/24/2020] [Accepted: 09/02/2020] [Indexed: 01/04/2023]
Abstract
Recently, several studies demonstrated the usefulness of diatom eDNA metabarcoding as an alternative to assess the ecological quality of rivers and streams. However, the choice of the taxonomic marker as well as the methodology for data analysis differ between these studies, hampering the comparison of their results and effectiveness. The aim of this study was to compare two taxonomic markers commonly used in diatom metabarcoding and three distinct analytical approaches to infer a molecular diatom index. We used the values of classical morphological diatom index as a benchmark for this comparison. We amplified and sequenced both a fragment of the rbcL gene and the V4 region of the 18S rRNA gene for 112 epilithic samples from Swiss and French rivers. We inferred index values using three analytical approaches: by computing it directly from taxonomically assigned sequences, by calibrating de novo the ecovalues of all metabarcodes, and by using a supervised machine learning algorithm to train predictive models. In general, the values of index obtained using the two "taxonomy-free" approaches, encompassing molecular assignment and machine learning, were closer correlated to the values of the morphological index than the values based on taxonomically assigned sequences. The correlations of the three analytical approaches were higher in the case of rbcL compared to the 18S marker, highlighting the importance of the reference database which is more complete for the rbcL marker. Our study confirms the effectiveness of diatom metabarcoding as an operational tool for rivers ecological quality assessment and shows that the analytical approaches by-passing the taxonomic assignments are particularly efficient when reference databases are incomplete.
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Affiliation(s)
- Laure Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene ecodiagnostics, Geneva, Switzerland
| | - Agnès Bouchez
- UMR CARRTEL, INRAE, Université Savoie Mont-Blanc, Thonon, France
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene ecodiagnostics, Geneva, Switzerland
| | - Arielle Cordonier
- Department of Territorial Management, Water Ecology Service, Geneva, Switzerland
| | - Julie Guéguen
- UMR CARRTEL, INRAE, Université Savoie Mont-Blanc, Thonon, France
| | - Frederic Rimet
- UMR CARRTEL, INRAE, Université Savoie Mont-Blanc, Thonon, France
| | - Valentin Vasselon
- Pôle R&D "ECLA", Thonon-les-Bains, France.,OFB, Site INRA UMR CARRTEL, Thonon-les-Bains, France
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene ecodiagnostics, Geneva, Switzerland.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
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Novis PM, Sales RE, Gordon K, Manning N, Duleba M, Ács É, Dressler M, Schallenberg M. Lindavia intermedia (Bacillariophyceae) and Nuisance lake Snow in New Zealand: Chitin Content and Quantitative PCR Methods to Estimate Cell Concentrations and Expression of Chitin Synthase 1. JOURNAL OF PHYCOLOGY 2020; 56:1232-1244. [PMID: 32396981 DOI: 10.1111/jpy.13014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Lake snow, caused by the freshwater centric diatom Lindavia intermedia, has become problematic in several large, oligotrophic New Zealand lakes over the past decade. Macroaggregates produced by L. intermedia foul fishing lines, intake screens, and water filters, and have a negative impact on recreational values. It was confirmed that the fibers constituting lake snow are composed of chitin, two chitin synthase genes (chs1 and 2) from L. intermedia were characterized, new qPCR-based tools to quantify the abundance of the species and measure expression of chs2 relative to the reference gene act1 (the product of which has cytoskeletal functions) were developed. The strong heterogeneity and mucilaginous nature of lake snow samples create particular difficulties for calibrations of gene or transcript copy numbers with cell densities and obtaining high yields of mRNA. However, data collected from four lakes during November 2018 and February and May 2019 show that abundance of L. intermedia is always high when lake snow is also abundant, but that a full range of L. intermedia abundance can occur when lake snow is absent, suggesting that chitin production is not obligate in L. intermedia. This result is consistent with the available data for chs2 expression, which suggest higher transcription when lake snow is abundant. Lake snow production by L. intermedia therefore requires an as yet undetermined stimulus independent of cell abundance.
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Affiliation(s)
- Phil M Novis
- Allan Herbarium, Manaaki Whenua - Landcare Research, P.O. Box 69040, Lincoln, 7640, New Zealand
| | - Ruth E Sales
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Keith Gordon
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Nathan Manning
- Otago Regional Council, 14 Rogers St, Cromwell, 9310, New Zealand
| | - Mónika Duleba
- MTA Centre for Ecological Research, Danube Research Institute, 1113, Budapest, Hungary
| | - Éva Ács
- MTA Centre for Ecological Research, Danube Research Institute, 1113, Budapest, Hungary
| | - Mirko Dressler
- Department of Allgemeine u. Spezielle Botanik, Universität Rostock, Wismarsche Str. 44/45, 18051, Rostock, Germany
| | - Marc Schallenberg
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
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Seymour M, Edwards FK, Cosby BJ, Kelly MG, de Bruyn M, Carvalho GR, Creer S. Executing multi-taxa eDNA ecological assessment via traditional metrics and interactive networks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:138801. [PMID: 32498163 DOI: 10.1016/j.scitotenv.2020.138801] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/31/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Current approaches to ecological assessment are limited by the traditional morpho-taxonomic methods presently employed and the inability to meet increasing demands for rapid assessments. Advancements in high throughput sequencing now enable rapid high-resolution ecological assessment using environmental DNA (eDNA). Here we test the ability of using eDNA-based ecological assessment methods against traditional assessment of two key indicator groups (diatoms and macroinvertebrates) and show how eDNA across multiple gene regions (COI, rbcL, 12S and 18S) can be used to infer interactive networks that link to ecological assessment criteria. We compared results between taxonomic and eDNA based assessments and found significant positive associations between macroinvertebrate (p < 0.001 R2 = 0.645) and diatom (p = 0.015, R2 = 0.222) assessment metrics. We further assessed the ability of eDNA based assessment to identify environmentally sensitive genera and found an order of magnitude greater potential for 18S, versus COI or rbcL, to determine environmental filtering of ecologically assessed communities. Lastly, we compared the ability of traditional metrics against co-occurrence network properties of our combined 18S, COI and rbcL indicator genera to infer habitat quality measures currently used by managers. We found that transitivity (network connectivity), linkage density and cohesion were significantly associated with habitat modification scores (HMS), whereas network properties were inconsistent with linking to the habitat quality score (HQS) metric. The incorporation of multi-marker eDNA network assessment opens up a means for finer scale ecological assessment, currently limited using traditional methods. While utilization of eDNA-based assessment is recommended, direct comparisons with traditional approaches are difficult as the methods are intrinsically different and should be treated as such with regards to future research. Overall, our findings show that eDNA can be used for effective ecological assessment while offering a wider range of scope and application compared to traditional assessment methods.
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Affiliation(s)
- Mathew Seymour
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
| | | | - Bernard J Cosby
- NERC Centre for Ecology & Hydrology, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Martyn G Kelly
- Bowburn Consultancy, 11 Monteigne Drive, Bowburn, Durham DH6 5QB, UK
| | - Mark de Bruyn
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
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Pérez-Burillo J, Trobajo R, Vasselon V, Rimet F, Bouchez A, Mann DG. Evaluation and sensitivity analysis of diatom DNA metabarcoding for WFD bioassessment of Mediterranean rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138445. [PMID: 32334210 DOI: 10.1016/j.scitotenv.2020.138445] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
Our study of 164 diatom samples from Catalonia (NE Spain) is the first to evaluate the applicability of DNA metabarcoding, based on high throughput sequencing (HTS) using a 312-bp rbcL marker, for biomonitoring Mediterranean rivers. For this, we compared the values of a biotic index (IPS) and the ecological status classes derived from them, between light microscope-based (LM) and HTS methods. Very good correspondence between methods gives encouraging results concerning the applicability of DNA metabarcoding for Catalan rivers for the EU Water Framework Directive (WFD). However, in 10 sites, the ecological status class was downgraded from "Good"/"High" obtained by LM to "Moderate"/"Poor"/"Bad" by HTS; these "critical" sites are especially important, because the WFD requires remedial action by water managers for any river with Moderate or lower status. We investigated the contribution of each species to the IPS using a "leave-one-out" sensitivity analysis, paying special attention to critical sites. Discrepancies in IPS between LM and HTS were mainly due to the misidentification and overlooking in LM of a few species, which were better recovered by HTS. This bias was particularly important in the case of Fistulifera saprophila, whose clear underrepresentation in LM was important for explaining 8 out of the 10 critical sites and probably reflected destruction of weakly-silicified frustules during sample preparation. Differences between species in the rbcL copy number per cell affected the relative abundance obtained by HTS for Achnanthidium minutissimum, Nitzschia inconspicua and Ulnaria ulna, which were also identified by the sensitivity analysis as important for the WFD. Only minor IPS discrepancies were attributed to the incompleteness of the reference library, as most of the abundant and influential species (to the IPS) were well represented there. Finally, we propose that leave-one-out analysis is a good method for identifying priority species for isolation and barcoding.
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Affiliation(s)
- Javier Pérez-Burillo
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Rápita, Catalonia, Spain; Departament de Geografia, Universitat Rovira i Virgili, C/Joanot Martorell 15, E43500 Vila-seca, Catalonia, Spain.
| | - Rosa Trobajo
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Rápita, Catalonia, Spain
| | - Valentin Vasselon
- Pôle R&D "ECLA", France; AFB, Site INRA UMR CARRTEL, Thonon-les-Bains, France
| | - Frédéric Rimet
- INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - Agnès Bouchez
- INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - David G Mann
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Rápita, Catalonia, Spain; Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland, UK
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44
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Santoferrara L, Burki F, Filker S, Logares R, Dunthorn M, McManus GB. Perspectives from Ten Years of Protist Studies by High-Throughput Metabarcoding. J Eukaryot Microbiol 2020; 67:612-622. [PMID: 32498124 DOI: 10.1111/jeu.12813] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/29/2020] [Accepted: 05/29/2020] [Indexed: 01/07/2023]
Abstract
During the last decade, high-throughput metabarcoding became routine for analyzing protistan diversity and distributions in nature. Amid a multitude of exciting findings, scientists have also identified and addressed technical and biological limitations, although problems still exist for inference of meaningful taxonomic and ecological knowledge based on short DNA sequences. Given the extensive use of this approach, it is critical to settle our understanding on its strengths and weaknesses and to synthesize up-to-date methodological and conceptual trends. This article summarizes key scientific and technical findings, and identifies current and future directions in protist research that uses metabarcoding.
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Affiliation(s)
- Luciana Santoferrara
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.,Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sabine Filker
- Department of Molecular Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Micah Dunthorn
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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45
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Feio MJ, Serra SRQ, Mortágua A, Bouchez A, Rimet F, Vasselon V, Almeida SFP. A taxonomy-free approach based on machine learning to assess the quality of rivers with diatoms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 722:137900. [PMID: 32199386 DOI: 10.1016/j.scitotenv.2020.137900] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 06/10/2023]
Abstract
Diatoms are a compulsory biological quality element in the ecological assessment of rivers according to the Water Framework Directive. The application of current official indices requires the identification of individuals to species or lower rank under a microscope based on the valve morphology. This is a highly time-consuming task, often susceptible of disagreements among analysts. In alternative, the use of DNA metabarcoding combined with High-Throughput Sequencing (HTS) has been proposed. The sequences obtained from environmental DNA are clustered into Operational Taxonomic Units (OTUs), which can be assigned to a taxon using reference databases, and from there calculate biotic indices. However, there is still a high percentage of unassigned OTUs to species due to the incompleteness of reference libraries. Alternatively, we tested a new taxonomy-free approach based on diatom community samples to assess rivers. A combination of three machine learning techniques is used to build models that predict diatom OTUs expected in test sites, under reference conditions, from environmental data. The Observed/Expected OTUs ratio indicates the deviation from reference condition and is converted into a quality class. This approach was never used with diatoms neither with OTUs data. To evaluate its efficiency, we built a model based on OTUs lists (HYDGEN) and another based on taxa lists from morphological identification (HYDMORPH), and also calculated a biotic index (IPS). The models were trained and tested with data from 81 sites (44 reference sites) from central Portugal. Both models were considered accurate (linear regression for Observed and Expected richness: R2 ≈ 0.7, interception ≈ 0.8) and sensitive to global anthropogenic disturbance (Rs2 > 0.30 p < 0.006 for global disturbance). Yet, the HYDGEN model based on molecular data was sensitive to more types of pressures (such as, changes in land use and habitat quality), which gives promising insights to its use for bioassessment of rivers.
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Affiliation(s)
- Maria João Feio
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Portugal.
| | - Sónia R Q Serra
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Portugal
| | - Andreia Mortágua
- Department of Biology and Geobiotec - Geobiosciences, Geotechnologies and Geoengineering Research Centre, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Agnès Bouchez
- UMR CARRTEL, INRAE, Université Savoie Mont-Blanc, F-74200 Thonon, France
| | - Frédéric Rimet
- UMR CARRTEL, INRAE, Université Savoie Mont-Blanc, F-74200 Thonon, France
| | - Valentin Vasselon
- Pôle R&D "ECLA", France; AFB, Site INRA UMR CARRTEL, Thonon-les-Bains, France
| | - Salomé F P Almeida
- Department of Biology and Geobiotec - Geobiosciences, Geotechnologies and Geoengineering Research Centre, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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46
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Buchner D, Beermann AJ, Laini A, Rolauffs P, Vitecek S, Hering D, Leese F. Analysis of 13,312 benthic invertebrate samples from German streams reveals minor deviations in ecological status class between abundance and presence/absence data. PLoS One 2019; 14:e0226547. [PMID: 31869356 PMCID: PMC6927632 DOI: 10.1371/journal.pone.0226547] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/28/2019] [Indexed: 11/18/2022] Open
Abstract
Benthic invertebrates are the most commonly used organisms used to assess ecological status as required by the EU Water Framework Directive (WFD). For WFD-compliant assessments, benthic invertebrate communities are sampled, identified and counted. Taxa × abundance matrices are used to calculate indices and the resulting scores are compared to reference values to determine the ecological status class. DNA-based tools, such as DNA metabarcoding, provide a new and precise method for species identification but cannot deliver robust abundance data. To evaluate the applicability of DNA-based tools to ecological status assessment, we evaluated whether the results derived from presence/absence data are comparable to those derived from abundance data. We analysed benthic invertebrate community data obtained from 13,312 WFD assessments of German streams. Broken down to 30 official stream types, we compared assessment results based on abundance and presence/absence data for the assessment modules “organic pollution” (i.e., the saprobic index) and “general degradation” (a multimetric index) as well as their underlying metrics. In 76.6% of cases, the ecological status class did not change after transforming abundance data to presence/absence data. In 12% of cases, the status class was reduced by one (e.g., from good to moderate), and in 11.2% of cases, the class increased by one. In only 0.2% of cases, the status shifted by two classes. Systematic stream type-specific deviations were found and differences between abundance and presence/absence data were most prominent for stream types where abundance information contributed directly to one or several metrics of the general degradation module. For a single stream type, these deviations led to a systematic shift in status from ‘good’ to ‘moderate’ (n = 201; with only n = 3 increasing). The systematic decrease in scores was observed, even when considering simulated confidence intervals for abundance data. Our analysis suggests that presence/absence data can yield similar assessment results to those for abundance-based data, despite type-specific deviations. For most metrics, it should be possible to intercalibrate the two data types without substantial efforts. Thus, benthic invertebrate taxon lists generated by standardised DNA-based methods should be further considered as a complementary approach.
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Affiliation(s)
- Dominik Buchner
- University of Duisburg-Essen, Aquatic Ecosystem Research, Essen, Germany
| | - Arne J. Beermann
- University of Duisburg-Essen, Aquatic Ecosystem Research, Essen, Germany
- Centre for Water and Environmental Research (ZWU), Essen, Germany
| | - Alex Laini
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parma, Italy
| | - Peter Rolauffs
- University of Duisburg-Essen, Aquatic Ecology, Essen, Germany
| | - Simon Vitecek
- WasserCluster Lunz, Lunz am See, Austria
- University of Natural Resources Vienna, Wien, Austria
| | - Daniel Hering
- Centre for Water and Environmental Research (ZWU), Essen, Germany
- University of Duisburg-Essen, Aquatic Ecology, Essen, Germany
| | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Essen, Germany
- Centre for Water and Environmental Research (ZWU), Essen, Germany
- * E-mail:
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47
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Kelly M. Adapting the (fast-moving) world of molecular ecology to the (slow-moving) world of environmental regulation: lessons from the UK diatom metabarcoding exercise. METABARCODING AND METAGENOMICS 2019. [DOI: 10.3897/mbmg.3.39041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Development of effective metabarcoding-based tools for ecological assessment requires more than just detailed knowledge of ecology and molecular genetics. There is also a need to understand the context within which they will be used, and for the organisation that uses it to understand the techniques involved and, more especially, how the data that are produced differs from that generated by traditional ecological methods. Lessons learnt during the development of a metabarcoding tool for phytobenthos in the UK are set out in this paper. This attempted to develop a molecular “mirror” of the existing light microscopy-based approach to ecological assessment. Although this conservative approach does not exploit the full potential of metabarcoding data, it does mean that benchmarks exist against which performance and data can be judged. However, the pace of developments within molecular ecology means that regulators will need to find ways of incorporating new scientific insights whilst, at the same time, ensuring a stable regulatory regime. Installation of a metabarcoding technique within a regulatory organisation, in other words, is more than a transaction in which one approach is switched for another. A deeper transformation of the organisation is required.
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Valentin V, Frédéric R, Isabelle D, Olivier M, Yorick R, Agnès B. Assessing pollution of aquatic environments with diatoms’ DNA metabarcoding: experience and developments from France water framework directive networks. METABARCODING AND METAGENOMICS 2019. [DOI: 10.3897/mbmg.3.39646] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
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.
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49
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Tapolczai K, Keck F, Bouchez A, Rimet F, Kahlert M, Vasselon V. Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00409] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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50
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Diat.barcode, an open-access curated barcode library for diatoms. Sci Rep 2019; 9:15116. [PMID: 31641158 PMCID: PMC6805954 DOI: 10.1038/s41598-019-51500-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 09/25/2019] [Indexed: 11/08/2022] Open
Abstract
Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge diversity, which makes them excellent ecological indicators of aquatic ecosystems. Usually, diatoms are identified using characteristics of their exoskeleton morphology. DNA-barcoding is an alternative to this and the use of High-Throughput-Sequencing enables the rapid analysis of many environmental samples at a lower cost than analyses under microscope. However, to identify environmental sequences correctly, an expertly curated reference library is needed. Several curated libraries for protists exists; none, however are dedicated to diatoms. Diat.barcode is an open-access library dedicated to diatoms which has been maintained since 2012. Data come from two sources (1) the NCBI nucleotide database and (2) unpublished sequencing data of culture collections. Since 2017, several experts have collaborated to curate this library for rbcL, a chloroplast marker suitable for species-level identification of diatoms. For the latest version of the database (version 7), 605 of the 3482 taxonomical names originally assigned by the authors of the rbcL sequences were modified after curation. The database is accessible at https://www6.inra.fr/carrtel-collection_eng/Barcoding-database.
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