Soil protists: a fertile frontier in soil biology research

Abstract

Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.

Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

“…Although the curating pipeline discarded the majority of CCS reads, many of which might still be of high quality, the 650 OTUs that passed all filtering steps comprised a large and broad diversity of eukaryotes. Almost all major microbial lineages were sampled, from known abundant taxa in soils such as Ciliophora, Cercozoa, Apicomplexa and fungi, to rarer lineages in soil such as the mainly aquatic Bacillariophyceae (diatoms) and Chlorophyta (green algae) (Bahram et al, ; Foissner, ; Geisen, Cornelia, Jörg, & Michael, ; Geisen et al, , ; Mahé et al, ). A few main protist groups lacked new OTUs altogether, including Cryptista, Retaria, Rhodophyceae and Glaucophyta, but these are almost exclusively aquatic and thus less likely to be recovered among soil sequences even if present in the environment at very low abundance (Geisen et al, ; Lallias et al, ; de Vargas et al, ).…”

“…Although the curating pipeline discarded the majority of CCS reads, many of which might still be of high quality, the 650 OTUs that passed all filtering steps comprised a large and broad diversity of eukaryotes. Almost all major microbial lineages were sampled, from known abundant taxa in soils such as Ciliophora, Cercozoa, Apicomplexa and fungi, to rarer lineages in soil such as the mainly aquatic Bacillariophyceae (diatoms) and Chlorophyta (green algae) (Bahram et al, 2018;Foissner, 1987;Geisen, Cornelia, Jörg, & Michael, 2014;Geisen et al, 2018Geisen et al, , 2015Mahé et al, 2017).…”

Competition and predation as possible causes of bacterial rarity

“…Moreover, in soil, predation pressure on bacteria is likely to be stronger because of the huge taxonomic and functional diversity of protist predators and nematodes (Geisen et al, 2018). While overall predation by protists reduced abundances of the taxa that were dominant in the control, the effect was most pronounced for taxa in the Rare/Fast category.…”

“…Protists are among the key predators of bacteria (Geisen et al, 2018). Bacterial resistance mechanisms against predation by protists include morphological defences, such as the formation of filaments or cell aggregates, and chemical defences, such as toxin production (Jürgens and Matz, 2002).…”

“…However, in both cases at high nutrient levels consumption by herbivores or predators ultimately was the factor that shaped community composition. In the bacterial world, competition and predation can also be modified by nutrient availability (Bohannan and Lenski, 2000b;Hahn and Höfle, 2001;Geisen et al, 2018). Protection of tissues of slow-growing plant species is essential as the cost of their tissue loss is relatively high (Herms and Mattson 1992).…”