Soil Protists Diversity, Distribution and Ecological Functioning

Soil protists occupy key nodes in soil food webs due to their high abundance, fast turnover and functional importance as bacterial grazers. However, methodological drawbacks obscure the knowledge of soil protists, so that many taxa remain unknown. The structure of natural protist communities and taxa-specific ecological functions are also largely unknown. This thesis aims to increase the knowledge on soil protists using a variety of approaches. In the first part, naked amoebae being presumably the most neglected protist morphogroup were cultivated from several distinct geographical locations across Europe and from high altitude sites in Tibet. During the course of this study, 16 new species and seven new genera were discovered, representing two eukaryotic supergroups (Amoebozoa and Excavata), three classes (Discosea, Variosea and Heterolobosea), and 12 genera (Cochliopodium, Stenamoeba, Acanthamoeba, Ischnamoeba n.g., Darbyshirella n.g., Heliamoeba n.g., Arboramoeba n.g., Angulamoeba n.g., Telaepolella, Schizoplasmodiopsis, Allovahlkampfia and Pagea n.g.). This vast number of taxonomic descriptions unveils the tremendous lack of knowledge especially on soil naked amoebae. The second part aims at deciphering the diversity and community structure of soil protists using four different techniques. First, a modified cultivation technique enabled the quantification of individual morphogroups, allowing determination often up to genus level. It was shown that soil moisture not only impacts the total abundance, but also affects the community composition of soil protists. Second, established cultures of morphologically indistinguishable Acanthamoeba spp. were sequenced, enabling differentiation to strain level. Highly diverse Acanthamoeba communities were detected that differed between geographically remote soils. Third, a high-throughput amplicon sequencing approach targeting the protist phylum Cercozoa illustrated that cercozoan communities strongly differed between geographically distant soils and that community composition depended on the type of land management. Finally, a metatranscriptomic approach unveiled the entire active protist community in different soil and litter samples, uncovering a previously unknown diversity. Each of these methods confirmed that soils harbour an enormous diversity of protists and all methods detected differences in soil protist communities depending on geographic origin or treatment. Therefore it is important to understand the respective advantages and disadvantages associated with each of those methods. Further, available skills, equipment and financial resources need to be considered before applying a method to study soil protists. The third part of this thesis aims to elucidate rarely considered ecological functions performed by soil protists. Generally, soil protists are considered as bacterivores, but diverse protists facultatively consumed fungi. The small amoeba Cryptodifflugia operculata revealed another feeding mode – trapping and consuming nematodes. Metatranscriptomic data revealed high relative abundances of both functional groups in all terrestrial soil samples indicating wider ecological functions carried out by soil protists as has been suggested before