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  • expansion progress  (1)
  • fungalquantification  (1)
  • Wiley  (2)
  • 1
    Publication Date: 2024-01-22
    Description: Quantifying the abundances of fungi is key to understanding natural variation in mycorrhi-zal communities in relation to plant ecophysiology and environmental heterogeneity. High-throughput metabarcoding approaches have transformed our ability to characterize and com-pare complex mycorrhizal communities. However, it remains unclear how well metabarcodingread counts correlate with actual read abundances in the sample, potentially limiting their useas a proxy for species abundances. Here, we use droplet digital PCR (ddPCR) to evaluate the reliability of ITS2 metabarcodingdata for quantitative assessments of mycorrhizal communities in the orchid speciesNeottiaovatasampled at multiple sites. We performed specific ddPCR assays for eight families oforchid mycorrhizal fungi and compared the results with read counts obtained from metabar-coding. Our results demonstrate a significant correlation between DNA copy numbers measured byddPCR assays and metabarcoding read counts of major mycorrhizal partners ofN. ovata,highlighting the usefulness of metabarcoding for quantifying the abundance of orchid mycor-rhizal fungi. Yet, the levels of correlation between the two methods and the numbers of falsezero values varied across fungal families, which warrants cautious evaluation of the reliabilityof low-abundance families. This study underscores the potential of metabarcoding data for more quantitative analysesof mycorrhizal communities and presents practical workflows for metabarcoding and ddPCRto achieve a more comprehensive understanding of orchid mycorrhizal communities
    Keywords: droplet digital PCR ; fungalquantification ; metabarcoding ; mycorrhizalfungi ; orchid mycorrhiza
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 2
    Publication Date: 2024-03-14
    Description: Coral reef ecosystems in Indonesia are under threat due to changes in the environment driven by global climate change, along with local disturbances such as sedimentation and eutrophication. Consequently, comprehensive coral reef monitoring \nactivities have been initiated at numerous locations across Indonesia. In this study, the \nfindings from coral reef health surveys across 14 reef sites (within 40 hectares) in the \nBintan area (Riau Archipelago, Indonesia; 100\xe2\x80\x89km southeast of Singapore) revealed a \npotentially novel epizoic yellow sponge species (Phorbas sp.) that overgrows coral colonies. This species, tentatively classified as a new Phorbas sp. (order Poecilosclerida: \nfamily Hymedesmiidae), was identified through a combined approach employing classical taxonomic methods along with DNA barcoding using the cytochrome c oxidase \nI (COI) gene. At every site, three permanent 20-m transects were established to annually monitor live coral coverage and species composition between 2014 and 2017. \nThe survey indicated a notable change in the overall coral cover during this period. \nThe abundance of coral diseases was investigated in 2014 and 2017. Additionally, the \nprogress of Phorbas sp., was closely monitored (i.e., every second day for one week) \nat Bintan Island (site 11) during the dry season in August 2017. This approach aimed \nto approximate the relative impact of each incident on the coral\'s condition. The results indicated that the most comprehensive change occurred due to the overgrowth \nof Phorbas sp., which affected 12 scleractinian coral species across eight genera in \nalmost all sites except one. The abundance of this epizoic sponge infestation was \nhighest at Pulau Beralas Pasir (site 10), constituting 22.9% of all recorded life forms, \nand lowest at Pulau Pangkil-Besar (site 13), with only 0.7%. The expansion of the thin \nyellow sponge tissue was estimated to increase by up to 0.51\xe2\x80\x89\xc2\xb1\xe2\x80\x890.48\xe2\x80\x89cm2 \n per day on \nPorites coral.
    Keywords: coral disease ; coral health ; expansion progress ; novel sponge ; yellow band disease
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
    Location Call Number Limitation Availability
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