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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. [ABSTRACT FROM AUTHOR]

High-throughput sequencing (HTS) of soil environmental DNA (eDNA) allows assessing the full diversity of soil micro-eukaryotes. The resulting operational taxonomic units (OTUs) can be assigned to potential taxonomic and functional identities using increasingly complete reference databases. HTS of soil eDNA is revealing a high diversity and abundance of potential eukaryovorous protists, thus challenging the paradigm of the predominantly bacterivorous function of soil phagotrophic protists (i.e. microbial loop). Using Illumina sequencing of soil eDNA and targeting the V9 region of the SSU rRNA gene, we investigated the taxonomic and functional diversities, distribution and co-occurrence patterns of soil micro-eukaryotes in three land-use categories: forests, meadows and croplands located in Switzerland. Each OTU was assigned to a broad functional category (phototrophs, phagotrophs, osmotrophs, or parasites). Total OTU richness was similar in the three land-use categories, but community composition differed significantly between forests and other land-uses. The proportion of fungal sequences (especially Basidiomycota) was highest, and phototroph (i.e. soil microalgae) sequences least abundant in forests. Seven OTUs representing phagotrophic protists, together accounting for >25% of all phagotroph sequences, were significantly correlated to the total number of phototroph sequences, thus suggesting algivory. At least three of these OTUs corresponded to known algal predators. These results suggest that beyond plants, soil microalgae represent a functionally significant but rarely considered input of carbon in soils that should be taken into account when modelling soil nutrient cycling. [ABSTRACT FROM AUTHOR]

In terrestrial ecosystems decomposing cadavers act as resource patches affecting nutrient cycling and soil communities, but the effects on soil communities are not well known. In this study we investigated nematode community response to decomposing pig cadavers ( Sus scrofa ) over a one-year period. As nematodes play key roles in soil food webs and are known to respond to disturbances and nutrient enrichment, we hypothesised that they would respond to decomposing cadavers and that this response would change over time. We compared the temporal patterns of nematode density and community structure under pig cadavers, either placed directly on the ground or hung 1 m aboveground (for effects of cadaveric fluids only), with two controls, i.e., bare soil and bags filled with soil placed on the ground (fake pigs – for microclimatic effects only). In the control and fake pig treatments nematode densities, community patterns and maturity indices did not change significantly. In contrast, density increased significantly underneath the ground and hanging pigs two weeks after the beginning of the experiment, and nematode family richness, Simpson diversity and maturity index were significantly reduced in the cadaver treatments. Most nematode families responded negatively to cadavers with the notable exceptions of Rhabditidae, Neodiplogasteridae and Diplogasteroididae. The latter two were found exclusively underneath the decomposing cadavers and are promising bioindicators of vertebrate cadaver decomposition. Even though diversity, density and communities were recovering after one year, the impact of cadavers was still significant for the maturity index. These contrasting patterns illustrate how decomposing cadavers contribute to increasing local biodiversity and suggest that soil nematodes could be used as a tool to document the presence of a decomposing cadaver, or to estimate the time elapsed since death (post-mortem interval). Patterns should, however, be compared in different settings and seasons before such a tool can be validated. [ABSTRACT FROM AUTHOR]

Although widely used in ecology, comparative analyses of diversity and niche properties are still lacking for microorganisms, especially focusing on niche variations. Quantifying the niches of microbial taxa is necessary to then forecast how taxa and the communities they compose might respond to environmental changes. In this study, we first identified important topoclimatic, edaphic, spatial and biotic drivers of the alpha and beta diversity of bacterial, archaeal, fungal and protist communities. Then, we calculated the niche breadth and position of each taxon along the important environmental gradients to determine how these vary within and among the taxonomic groups. We found that edaphic properties were the most important drivers of both, community diversity and composition, for all microbial groups. Protists and bacteria presented the largest niche breadths on average, followed by archaea, with fungi displaying the smallest. Niche breadth generally decreased towards environmental extremes, especially along edaphic gradients, suggesting increased specialization of microbial taxa in highly selective environments. Overall, we showed that microorganisms have well defined niches, as do macro-organisms, likely driving part of the observed spatial patterns of community variations. Assessing niche variation more widely in microbial ecology should open new perspectives, especially to tackle global change effects on microbes. • We studied bacterial, archaeal, fungal and protist communities in Alpine soils. • Edaphic properties, particularly pH, drive alpha and beta diversity of all groups. • Protists and Bacteria have, on average, larger environmental niche breadths. • On average, fungi proportionally harbor more generalist taxa while bacteria harbor more specialist taxa than any other group. • Small niche breadth towards environmental extremes suggests increased specialization. [ABSTRACT FROM AUTHOR]

Abstract: Peatlands represent massive global C pools and sinks. Carbon accumulation depends on the ratio between net primary production and decomposition, both of which can change under projected increases of atmospheric CO2 and N deposition. The decomposition of litter is influenced by 1) the quality of the litter, and 2) the microenvironmental conditions in which the litter decomposes. This study aims at experimentally testing the effects of these two drivers in the context of global change. We studied the in situ litter decomposition from three common peatland species (Eriophorum vaginatum, Polytrichum strictum and Sphagnum fallax) collected after one year of litter production under pre-treatment conditions (elevated CO2: 560 ppm or enhanced N: 3 g m−2 y−1 NH4NO3) and decomposed the following year under treatment conditions (same as pre-treatment). By considering the cross-effects between pre-treatments and treatments, we distinguished between the effects on mass loss of 1) the pre-treatment-induced litter quality and 2) the treatment conditions under which the litters were decomposing. The combination between CO2 pre-treatment and CO2 treatment reduced Polytrichum decomposition by −24% and this can be explained by litter quality-driven decomposition changes brought by the pre-treatment. CO2 pre-treatment reduced Eriophorum litter quality, although this was not sufficient to predict decomposition. The N addition pre-treatment reduced the decomposition of Eriophorum, due to enhanced lignin and soluble phenols concentrations in the initial litter, and reduced litter-driven losses of starch and enhanced litter-driven losses of soluble phenols. While decomposition indices based on initial litter quality provide a broad explanation of quantitative and qualitative decomposition, they can only be taken as first approximations. Indeed, the microbial ATP activity, the litter N loss and resulting litter quality, were strongly altered irrespective of the compounds'' initial concentration and by means of processes that occurred independently of the initial litter-qualitative changes. The experimental design was valuable to assess litter- and ecosystem-driven decomposition pathways simultaneously or independently. The ability to separate these two drivers makes it possible to attest the presence of litter-qualitative changes even without any litter biochemical determinations, and shows the screening potential of this approach for future experiments dealing with multiple plant species. [Copyright &y& Elsevier]

Beta diversity is a key component of biodiversity with implications ranging from species dynamics to ecosystem functioning. However, β-diversity and its drivers have received little attention, especially for micro-eukaryotes which play key roles in soil functioning. We studied the diversity of soil micro-eukaryotes in a Swiss lowland floodplain using high-throughput Illumina sequencing of soil DNA. We determined the temporal vs. spatial patterns of soil micro-eukaryotic α- and β-diversity in six contrasted habitats sampled over one year. We identified the drivers of these patterns among soil conditions and functions and identified indicator taxa of habitats in each season. We found higher spatial than temporal variability and a strong space-time interaction in soil micro-eukaryotic diversity patterns as well as in their edaphic drivers, which contrasts with previous observation of bacterial diversity patterns. Our results show that, although soil micro-eukaryotic diversity indeed varies seasonally, it is correlated most strongly with edaphic variables and vegetation but the strength of correlations with individual drivers varied seasonally. Microbial diversity patterns and their drivers can thus differ quite substantially among seasons and taxa. Despite the dominance of spatial patterns, the temporal component of microbial diversity should not be ignored to accurately estimate the diversity and the complexity of soil microbial community assembly processes. Given the importance of soil microbial diversity for ecosystem functioning such knowledge is relevant for land management. Image 1 • We studied floodplain soil micro-eukaryotic diversity by Illumina sequencing of e-DNA. • Alpha and beta diversity varied more spatially among habitats than seasonally. • The edaphic drivers of α and β diversities changed among habitats and seasons. • These patterns reflect seasonal flood dynamics and soil biogeochemical cycles. • Thus, microbial ecology of dynamic systems should best be studied over time and space. [ABSTRACT FROM AUTHOR]

A high diversity of Apicomplexa was recently found in tropical soils presumably reflecting the diversity of their invertebrate hosts, but such patterns have not been explored in colder regions. We analysed the diversity of Apicomplexa and their potential metazoan hosts in litter and mosses collected in 11 different alpine habitats using an eDNA metabarcoding approach. The abundance and diversity of Apicomplexa phylotypes and of their potential invertebrate hosts were positively correlated. This confirms that eDNA metabarcoding is a useful tool to explore the unknown biodiversity of free-living eukaryotes, as well as potential host-parasite interactions. Future studies should aim at describing this diversity using a combination of morphological and molecular approaches. • We found a high diversity of Apicomplexa sequences in alpine moss and litter eDNA. • Read numbers of Apicomplexa and their Metazoa hosts are positively correlated. • EDNA metabarcoding allows a fast comparison of Apicomplexa and Metazoa diversity. [ABSTRACT FROM AUTHOR]