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  • 1
    In: International Journal of Limnology, EDP Sciences, Vol. 59 ( 2023), p. 8-
    Abstract: DNA metabarcoding can be a promising alternative to microscopy for analysing phytoplankton, a key ecological indicator for freshwater ecosystems. The aim of this study was to evaluate the performance of different barcodes and associated primer pairs to assess microalgal diversity with DNA metabarcoding using a single barcode targeting all microalgae. We investigated barcodes in 16S and 23S rRNA genes, encoding for prokaryotic ribosomal sub-units, that are present in Cyanobacteria as well as in chloroplasts. In silico PCR tests were carried out on eight 16S and five 23S primer pairs using the Phytool reference library. Two and three pairs were selected for 16S and 23S, respectively, to perform an in vitro metabarcoding test based on a mock community made of DNA extracts of 10 microalgae strains. The 23S pairs enabled to detect all species, whereas 16S ones failed in the detection of some of them. One pair was selected for each genetic marker, based on its efficiency and specificity towards microalgae ( e.g. not heterotrophic bacteria). Another mock community covering a larger diversity (18 microalgae strains) was used to test the efficiency of the selected pairs and their ability to estimate relative abundances. The 23S pair performed better than the 16S one for detecting target species with also more accuracy to assess their relative abundances. We conclude that the 23S primer pair ECLA23S_F1/ECLA23S_R1 appears as a good candidate to decipher freshwater phytoplankton communities. As a next step, it will be necessary to confirm these results on a large diversity of natural communities.
    Type of Medium: Online Resource
    ISSN: 2823-1465
    Language: English
    Publisher: EDP Sciences
    Publication Date: 2023
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  • 2
    In: Metabarcoding and Metagenomics, Pensoft Publishers, Vol. 5 ( 2021-02-26)
    Abstract: DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.
    Type of Medium: Online Resource
    ISSN: 2534-9708
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2021
    detail.hit.zdb_id: 2913203-4
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  • 3
    In: Metabarcoding and Metagenomics, Pensoft Publishers, Vol. 5 ( 2021-12-15)
    Abstract: Methods for biomonitoring of freshwater phytoplankton are evolving rapidly with eDNA-based methods, offering great complementarity with microscopy. Metabarcoding approaches have been more commonly used over the last years, with a continuous increase in the amount of data generated. Depending on the researchers and the way they assigned barcodes to species (bioinformatic pipelines and molecular reference databases), the taxonomic assignment obtained for HTS DNA reads might vary. This is also true for traditional taxonomic studies by microscopy with regular adjustments of the classification and taxonomy. For those reasons (leading to non-homogeneous taxonomies), gap-analyses and comparisons between studies become even more challenging and the curation processes to find potential consensus names are time-consuming. Here, we present a web-based application (Phytool), developed with ShinyApp (Rstudio), that aims to make the harmonisation of taxonomy easier and in a more efficient way, using a complete and up-to-date taxonomy reference database for freshwater microalgae. Phytool allows users to homogenise and update freshwater phytoplankton taxonomical names from sequence files and data tables directly uploaded in the application. It also gathers barcodes from curated references in a user-friendly way in which it is possible to search for specific organisms. All the data provided are downloadable with the possibility to apply filters in order to select only the required taxa and fields (e.g. specific taxonomic ranks). The main goal is to make accessible to a broad range of users the connection between microscopy and molecular biology and taxonomy through different ready-to-use functions. This study estimates that only 25% of species of freshwater phytoplankton in Phytobs are associated with a barcode. We plead for an increased effort to enrich reference databases by coupling taxonomy and molecular methods. Phytool should make this crucial work more efficient. The application is available at https://caninuzzo.shinyapps.io/phytool_v1/
    Type of Medium: Online Resource
    ISSN: 2534-9708
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2021
    detail.hit.zdb_id: 2913203-4
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  • 4
    In: Science of The Total Environment, Elsevier BV, Vol. 914 ( 2024-03), p. 169774-
    Type of Medium: Online Resource
    ISSN: 0048-9697
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2024
    detail.hit.zdb_id: 121506-1
    SSG: 12
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  • 5
    In: JAMA Network Open, American Medical Association (AMA), Vol. 6, No. 8 ( 2023-08-23), p. e2330495-
    Abstract: Few population-based studies in the US collected individual-level data from families during the COVID-19 pandemic. Objective To examine differences in COVID-19 pandemic–related experiences in a large sociodemographically diverse sample of children and caregivers. Design, Setting, and Participants The Environmental influences on Child Health Outcomes (ECHO) multi-cohort consortium is an ongoing study that brings together 64 individual cohorts with participants (24 757 children and 31 700 caregivers in this study) in all 50 US states and Puerto Rico. Participants who completed the ECHO COVID-19 survey between April 2020 and March 2022 were included in this cross-sectional analysis. Data were analyzed from July 2021 to September 2022. Main Outcomes and Measures Exposures of interest were caregiver education level, child life stage (infant, preschool, middle childhood, and adolescent), and urban or rural (population & amp;lt;50 000) residence. Dependent variables included COVID-19 infection status and testing; disruptions to school, child care, and health care; financial hardships; and remote work. Outcomes were examined separately in logistic regression models mutually adjusted for exposures of interest and race, ethnicity, US Census division, sex, and survey administration date. Results Analyses included 14 646 children (mean [SD] age, 7.1 [4.4] years; 7120 [49%] female) and 13 644 caregivers (mean [SD] age, 37.6 [7.2] years; 13 381 [98%] female). Caregivers were racially (3% Asian; 16% Black; 12% multiple race; 63% White) and ethnically (19% Hispanic) diverse and comparable with the US population. Less than high school education (vs master’s degree or more) was associated with more challenges accessing COVID-19 tests (adjusted odds ratio [aOR], 1.88; 95% CI, 1.06-1.58), lower odds of working remotely (aOR, 0.04; 95% CI, 0.03-0.07), and more food access concerns (aOR, 4.14; 95% CI, 3.20-5.36). Compared with other age groups, young children (age 1 to 5 years) were least likely to receive support from schools during school closures, and their caregivers were most likely to have challenges arranging childcare and concerns about work impacts. Rural caregivers were less likely to rank health concerns (aOR, 0.77; 95% CI, 0.69-0.86) and social distancing (aOR, 0.82; 95% CI, 0.73-0.91) as top stressors compared with urban caregivers. Conclusions Findings in this cohort study of US families highlighted pandemic-related burdens faced by families with lower socioeconomic status and young children. Populations more vulnerable to public health crises should be prioritized in recovery efforts and future planning.
    Type of Medium: Online Resource
    ISSN: 2574-3805
    Language: English
    Publisher: American Medical Association (AMA)
    Publication Date: 2023
    detail.hit.zdb_id: 2931249-8
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  • 6
    In: Molecular Ecology, Wiley, Vol. 32, No. 1 ( 2023-01), p. 124-137
    Abstract: Environmental filtering is often found to dominate assembly rules in diatoms. These microalgae are diverse, especially at subspecies level, and tend to exhibit a niche phylogenetic conservatism. Therefore, other rules, such as competition or mass effects, should be detectable when environmental gradients and dispersal barriers are limited. We used metabarcoding to analyse benthic littoral diatom communities in 153 sites in a large lake (Geneva) exhibiting weak geographical barriers and weak environmental gradients outside river estuaries. We assessed assembly rules using variance partitioning, phylogenetic and source tracking analyses. No phylogenetic over‐dispersion of communities, indicative of exclusive competition, was detected. Instead, we found these communities to be phylogenetically over‐clustered, indicating environmental filtering, which was even stronger near river estuaries where environmental gradients are stronger. Finally, using a Bayesian method (SourceTracker), we found that rivers flowing into the lake bring communities that settle, especially in sites close to estuaries. Rivers with the highest discharges are primarily responsible for immigration, explaining 27% of lake composition. Therefore, despite favourable conditions to observe other rules, our results support that diatom communities are prominently assembled by environmental filtering and immigration processes, in particular from rivers. However, this does not exclude that other assembly rules may be at play at a finer spatial, temporal and/or phylogenetic scale.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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