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CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology

The result's identifiers

  • Result code in IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F21%3A00542712" target="_blank" >RIV/60077344:_____/21:00542712 - isvavai.cz</a>

  • Alternative codes found

    RIV/61388971:_____/21:00542712

  • Result on the web

    <a href="https://www.frontiersin.org/articles/10.3389/fmicb.2021.640066/full" target="_blank" >https://www.frontiersin.org/articles/10.3389/fmicb.2021.640066/full</a>

  • DOI - Digital Object Identifier

    <a href="http://dx.doi.org/10.3389/fmicb.2021.640066" target="_blank" >10.3389/fmicb.2021.640066</a>

Alternative languages

  • Result language

    angličtina

  • Original language name

    CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology

  • Original language description

    Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so to microbial eukaryotes. Application of this technique revealed that Paraphysomonas or Spumella-like chrysophytes, considered to be among the most prominent members of protistan communities in pelagic environments, are omnipresent but actually less abundant than expected, in contrast to little known groups such as heterotrophic cryptophyte lineages (e.g., CRY1), cercozoans, katablepharids, or the MAST lineages. Combination of CARD-FISH with tracer techniques and application of double CARD-FISH allow visualization of food vacuole contents of specific flagellate groups, thus considerably challenging our current, simplistic view that they are predominantly bacterivores. Experimental manipulations with natural communities revealed that larger flagellates are actually omnivores ingesting both prokaryotes and other protists. These new findings justify our proposition of an updated model of microbial food webs in pelagic environments, reflecting more authentically the complex trophic interactions and specific roles of flagellated protists, with inclusion of at least two additional trophic levels in the nanoplankton size fraction. Moreover, we provide a detailed CARD-FISH protocol for protists, exemplified on mixo- and heterotrophic nanoplanktonic flagellates, together with tips on probe design, a troubleshooting guide addressing most frequent obstacles, and an exhaustive list of published probes targeting protists.

  • Czech name

  • Czech description

Classification

  • Type

    J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database

  • CEP classification

  • OECD FORD branch

    10606 - Microbiology

Result continuities

  • Project

    Result was created during the realization of more than one project. More information in the Projects tab.

  • Continuities

    P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Others

  • Publication year

    2021

  • Confidentiality

    S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Data specific for result type

  • Name of the periodical

    Frontiers in Microbiology

  • ISSN

    1664-302X

  • e-ISSN

    1664-302X

  • Volume of the periodical

    12

  • Issue of the periodical within the volume

    MAR 4 2021

  • Country of publishing house

    CH - SWITZERLAND

  • Number of pages

    24

  • Pages from-to

    640066

  • UT code for WoS article

    000629999400001

  • EID of the result in the Scopus database

    2-s2.0-85102799654