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Methodological advances are essential for robust ecological research. Quantitative reconstructions of environmental conditions using testate amoebae rely on sound taxonomy. While the taxonomy of large species is relatively well resolved, this is not the case for most small taxa (typically

Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this, protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in soil studies. Recent methodological advances, particularly in molecular biology techniques, have made the study of soil protists more accessible, and have created a resurgence of interest in soil protistology. This ongoing revolution now enables comprehensive investigations of the structure and functioning of soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive review, we provide a synthesis of research gaps that should be prioritized in future studies of soil protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics that will establish soil protistology as a hub discipline connecting different fundamental and applied fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers in biology. (C) 2017 Elsevier Ltd. All rights reserved.

Molecular data have considerably contributed to building the taxonomy of protists. Recently, the systematics of Hyalospheniidae (Amoebozoa; Tubulinea; Arcellinida) has been widely revised, with implications extending to ecological, biogeographical and evolutionary investigations. Certain taxa, however, still have an uncertain phylogenetic position, including the common and conspicuous species Nebela militaris. A phylogenetic reconstruction of the Hyalospheniidae using partial sequences of the mitochondrial Cytochrome Oxidase Subunit 1 (COI) gene shows that N. militaris does not belong to genus Nebela, but should be placed in its own genus. The morphological singularities (strongly curved pseudostome and a marked notch in lateral view) and phylogenetic placement of our isolates motivated the creation of a new genus: Alabasta gen. nov. Based on their morphology, we include in this genus Nebela kivuense and Nebela longicollis. We discuss the position of genus Alabasta within Hyalospheniidae, and the species that could integrate this new genus based on their morphological characteristics.

In September 2014 we created a small raised bog of ca. 100m2 in the Botanical garden of Neuchâtel. The material (marl and peat) was collected from a degraded peatland in an industrial area of the region. The bog was planted with over 30 species of mosses and vascular plants collected from bogs in the Jura Mountains and from existing collections. This object corresponds to the three missions of the garden : 1) to inform the public as well as students about these unusual, fragile and threatened ecosystems, 2) to present characteristic peatland plants from the Jura Mountains (Sphagnum, Drosera, Eriophorum, Betula nana, etc.), and 3) to conduct research projects. During the winter 2014-15, the snow remained longer on the peatbog that on the adjacent path and meadow, thus providing evidence for a microclimatic effect of the bog. The excessively dry and hot summer 2015 allowed testing the resistance of the newly established bog vegetation. Most plants resisted well, including graminoids Eriophorum vaginatum, Trichophorum cespitosum or Carex sp., ericaceous (Vaccinium oxycoccos, myrtillus and vitis-idea) and mosses (especially Sphagnum). This living laboratory provides a unique opportunity to inform the public about the characteristics and functions of these ecosystems and the challenges of conserving and restoring them in a warmer world.

Sphagnum peatlands represent a globally significant pool and sink of carbon but these functions are threatened by ongoing climate change. Testate amoebae are useful bioindicators of hydrological changes, but little experimental work has been done on the impact of water table changes on communities. Using a mesocosm experimental setting that was previously used to assess the impact of drought disturbance on communities and ecosystem processes with three contrasted water table positions: wet (–4 cm), intermediate (–15 cm) and dry (–25 cm), we studied the capacity of testate amoeba communities to recover when the water table was kept at –10 cm for all plots. The overall experiment lasted three years. We assessed the taxonomic and functional trait responses of testate amoeba communities. The selected traits were hypothesised to be correlated to moisture content (response traits: shell size, aperture position) or trophic role (effect traits: mixotrophy, aperture size controlling prey range). During the disturbance phase, the mixotrophic species Hyalosphenia papilio dominated the wet and intermediate plots, while the community shifted to a dominance of “dry indicators” (Corythion dubium, Nebela tincta, Cryptodifflugia oviformis) and corresponding traits (loss of mixotrophy, and dominance of smaller taxa with ventral or ventral-central aperture) in dry plots. During the recovery phase we observed two contrasted trends in the previously wet and intermediate plots: communities remained similar where the Sphagnum carpet remained intact but species and traits indicators of drier conditions increased in plots where it had degraded. In the former dry plots, indicators and traits of wet conditions increased by the end of the experiment. This is one of the first experiment simulating a disturbance and subsequent recovery in ex-situ mesocosms of Sphagnum peatland focusing on the response of testate amoebae community structure as well as functional traits to water table manipulation. The results generally confirmed that testate amoebae respond within a few months to hydrological changes and thus represent useful bioindicators for assessing current and past hydrological changes in Sphagnum peatlands.

An ever-increasing diversity of potentially toxic chemical compounds are being developed and released into the environment as a result of human activities (e.g. agriculture, drugs, and cosmetics). Among these, pesticides have been shown to affect non-targeted wildlife since the 1960s. A range of ecotoxicological tests are used to assess the toxicity of pesticides on various model organisms. However most model organisms are metazoans, while the majority of Eukaryotes are unicellular microorganisms known as protists. Protists are ubiquitous organisms of key functional roles in all ecosystems but are so far little studied with respect to pesticide impact. To fill this gap, we developed a new ecotoxicological test based on Euglypha rotunda, a common soil amoeba, grown in culture flask with Escherichia coli as sole food source. We tested this assay with the herbicide S-metolachlor, which is known to affect cell division in seedling shoots and roots of weeds. Reproducible growth conditions were obtained for E. rotunda. The growth of E. coli was not affected by the herbicide. The growth of E. rotunda was affected by the herbicide in a non-linear way, growth being significantly reduced at ca. 15 μg/L, but not at 150 μg/ L. Our results show the potential for using soil protists in ecotoxicology and adds to the growing body of evidence for non-linear impacts of pesticides on non-target organisms. With the acquisition of additional data, the protocol should be suitable for standard ecotoxicological tests.

We describe here a new species of sphagnicolous testate amoeba found abundantly in the forested part of the Le Cachot peatland (Jura Mountains, Neuchâtel, Switzerland) based on microscopical observations (LM, SEM). The new species, called Nebela gimlii was placed in a phylogenetic tree based on mitochondrial cytochrome oxidase sequences (COI), and branched robustly within the N. collaris complex next to the morphologically similar N. guttata and N. tincta. It is however genetically clearly distinct from these two species, and differs morphologically from them by its smaller size and stouter shape of the shell. This new species completes the phylogeny of the Nebela collaris species complex, with now eight species described, mostly from peatlands and acidic forest litter, and further demonstrates the existence of an unknown diversity within testate amoebae. Improving the taxonomy of testate amoebae in peatlands and clarifying the ecology of newly discovered species should make these organisms even more valuable as bioindicator and for palaeoecological reconstruction.

The community composition of any group of organisms should theoretically be determined by a combination of assembly processes including resource partitioning, competition, environmental filtering, and phylogenetic legacy. Environmental DNA studies have revealed a huge diversity of protists in all environments, raising questions about the ecological significance of such diversity and the degree to which they obey to the same rules as macroscopic organisms. The fast‐growing cultivable protist species on which hypotheses are usually experimentally tested represent only a minority of the protist diversity. Addressing these questions for the lesser known majority can only be inferred through observational studies. We conducted an environmental DNA survey of the genus Nebela, a group of closely related testate (shelled) amoeba species, in different habitats within Sphagnum‐dominated peatlands. Identification based on the mitochondrial cytochrome c oxidase 1 gene, allowed species‐level resolution as well as phylogenetic reconstruction. Community composition varied strongly across habitats and associated environmental gradients. Species showed little overlap in their realized niche, suggesting resource partitioning, and a strong influence of environmental filtering driving community composition. Furthermore, phylogenetic clustering was observed in the most nitrogen‐poor samples, supporting phylogenetic inheritance of adaptations in the group of N. guttata. This study showed that the studied free‐living unicellular eukaryotes follow to community assembly rules similar to those known to determine plant and animal communities; the same may be true for much of the huge functional and taxonomic diversity of protists.