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

Frontiers in Microbiology

卷:12

Indranil Mukherjee¹  Michaela M. Salcher¹  Karel Šimek¹  Kasia Piwosz²  Vesna Grujčić⁴ 

[1] Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia;

[2] Centre ALGATECH, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia;

[3] Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland;

[4] Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden;

关键词: aquatic microbial food webs;    CARD-FISH;    grazing by protists;    protists;    unicellular eukaryotes;    bacterivorous;   

DOI  :  10.3389/fmicb.2021.640066

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown