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Protists are abundant, diverse and perform essential functions in soils. Protistan community structure and its change across time or space are traditionally studied at the species level but the relative importance of the processes shaping these patterns depends on the taxon phylogenetic resolution. Using 18S rDNA amplicon data of the Cercozoa, a group of dominant soil protists, from an agricultural field in western Germany, we observed a turnover of relatively closely related taxa (from sequence variants to genus‐level clades) across soil depth; while across soil habitats (rhizosphere, bulk soil, drilosphere), we observed turnover of relatively distantly related taxa, confirming Paracercomonadidae as a rhizosphere‐associated clade. We extended our approach to show that closely related Cercozoa encounter divergent arbuscular mycorrhizal (AM) fungi across soil depth and that distantly related Cercozoa encounter closely related AM fungi across soil compartments. This study suggests that soil Cercozoa community assembly at the field scale is driven by niche‐based processes shaped by evolutionary legacy of adaptation to conditions primarily related to the soil compartment, followed by the soil layer, giving a deeper understanding on the selection pressures that shaped their evolution. [ABSTRACT FROM AUTHOR]

Functional traits are increasingly used in ecology to link the structure of microbial communities to ecosystem processes. We investigated two important protistan lineages, Cercozoa and Endomyxa (Rhizaria) in soil using Illumina sequencing and analyzed their diversity and functional traits along with their responses to environmental factors in grassland and forest across Germany. From 600 soil samples, we obtained 2,101 Operational Taxonomic Units representing ∼18 million Illumina reads (region V4, 18S rRNA gene). All major taxonomic and functional groups were present, dominated by small bacterivorous flagellates (Glissomonadida). Endomyxan plant parasites were absent from forests. In grassland, Cercozoa and Endomyxa were promoted by more intensive land use management. Grassland and forest strikingly differed in community composition. Relative abundances of bacterivores and eukaryvores were inversely influenced by environmental factors. These patterns provide new insights into the functional organization of soil biota and indications for a more sustainable land-use management. [ABSTRACT FROM AUTHOR]

Artodiscus saltans, first described by Penard (1890), has a unique morphology. Without genetic data it could not yet been reliably placed into a wider taxonomical context. We present morphological data for A. saltans from different aquatic habitats of four European countries. We subjected three cells of one strain from Germany to molecular analyses and, interestingly, obtained six different rDNA sequences. Phylogenetic analyses of these SSU rDNA sequences revealed that A. saltans branches close to the amoebozoan Multicilia marina (Variosea, Amoebozoa). [ABSTRACT FROM AUTHOR]

Soil protists are increasingly appreciated as essential components of soil foodwebs; however, there is a dearth of information on the factors structuring their communities. Here we investigate the importance of different biotic and abiotic factors as key drivers of spatial and seasonal distribution of protistan communities. We conducted an intensive survey of a 10 m2 grassland plot in Germany, focusing on a major group of protists, the Cercozoa. From 177 soil samples, collected from April to November, we obtained 694 Operational Taxonomy Units representing >6 million Illumina reads. All major cercozoan taxonomic and functional groups were present, dominated by the small flagellates of the Glissomonadida. We found evidence of environmental selection structuring the cercozoan communities both spatially and seasonally. Spatial analyses indicated that communities were correlated within a range of 3.5 m. Seasonal variations in the abundance of bacterivores and bacteria, followed by that of omnivores suggested a dynamic prey-predator succession. The most influential edaphic properties were moisture and clay content, which differentially affected each functional group. Our study is based on an intense sampling of protists at a small scale, thus providing a detailed description of the biodiversity of different taxa/functional groups and the ecological processes involved in shaping their distribution. [ABSTRACT FROM AUTHOR]

16 S rRNA genes and transcripts of Acidobacteria were investigated in 57 grassland and forest soils of three different geographic regions. Acidobacteria contributed 9-31% of bacterial 16 S rRNA genes whereas the relative abundances of the respective transcripts were 4-16%. The specific cellular 16 S rRNA content (determined as molar ratio of rRNA : rRNA genes) ranged between 3 and 80, indicating a low in situ growth rate. Correlations with flagellate numbers, vascular plant diversity and soil respiration suggest that biotic interactions are important determinants of Acidobacteria 16 S rRNA transcript abundances in soils. While the phylogenetic composition of Acidobacteria differed significantly between grassland and forest soils, high throughput denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism fingerprinting detected 16 S rRNA transcripts of most phylotypes in situ. Partial least squares regression suggested that chemical soil conditions such as pH, total nitrogen, C : N ratio, ammonia concentrations and total phosphorus affect the composition of this active fraction of Acidobacteria. Transcript abundance for individual Acidobacteria phylotypes was found to correlate with particular physicochemical ( pH, temperature, nitrogen or phosphorus) and, most notably, biological parameters (respiration rates, abundances of ciliates or amoebae, vascular plant diversity), providing culture-independent evidence for a distinct niche specialization of different Acidobacteria even from the same subdivision. [ABSTRACT FROM AUTHOR]

Protists are the most important predators of soil microbes like bacteria and fungi and are highly diverse in terrestrial ecosystems. However, the structure of protistan communities throughout the soil profile is still poorly explored. Here, we used Illumina sequencing to track differences in the relative abundance and diversity of Cercozoa, a major group of protists, at two depths; 10–30 cm (topsoil) and 60–75 cm (subsoil) in an agricultural field in Germany. At the two depths, we also distinguished among three soil compartments: rhizosphere, drilosphere (earthworm burrows) and bulk soil. With increasing depth, we found an overall decline in richness, but we were able to detect subsoil specific phylotypes and contrasting relative abundance patterns between topsoil and subsoil for different clades. We also found that the compartment effect disappeared in the subsoil when compared to the topsoil. More studies are now needed to describe and isolate these possibly subsoil specific phylotypes and better understand their ecology and function. [ABSTRACT FROM AUTHOR]

• Soil freeze-thaw (FT) significantly decreased soil microbial biomass C. • Microbial biomass C losses after FT were particularly high in C-rich soils. • FT decreased the microbial C:N ratio within the first hours after thawing. • Stoichiometric shifts are associated with increased microbial metabolic expenditure. • The soil organic C content strongly shaped biochemical responses to FT. Freeze-thaw (FT) events exert a great physiological stress on soil microorganisms and hence impact biogeochemical processes in soils. As numerous environmental factors affect microbial and chemical responses to FT, a better understanding of the leverage factors that regulate the responses to FT events is required. To date, FT-induced shifts and transformations in microbial and resource stoichiometry have received particularly little attention. We exposed fifteen Luvisol soils with different time after restoration and corresponding differences in soil organic C contents from a postmining agricultural chronosequence to a single FT event and analysed changes in soil chemistry and microbial stoichiometry one hour and eighteen hours after thawing. FT considerably altered soil biochemical attributes within the first hours of thawing. Microbial biomass C declined substantially after FT, and its relative losses were positively correlated with enhanced dissolved organic C contents. Thus, microbial cell lysis likely led to the significant increase of dissolved organic C. Moreover, microbial biomass C losses were disproportionally higher in C-rich soils, suggesting that soil microorganisms in high-C soils might be particularly prone to FT stress. Microbial biomass N marginally decreased one hour after thawing, yet returned to initial levels eighteen hours after thawing. The alternating responses of microbial biomass C and N caused a strong stoichiometric reduction of the microbial C:N ratio. The resulting microbial oversaturation with N relative to C is likely the first step in the chain of processes that generally lead to the high N losses commonly recorded in agricultural soils in the aftermath of FT events. Metabolic activity of the soil microbial community increased with the relative decline of the microbial biomass C:N ratio eighteen hours after thawing, suggesting increased levels of microbial metabolic expenditure due to stoichiometric shifts. The strength of the FT-driven biochemical responses was strongly dependent on soil organic C content, indicating that high-C soils might be especially vulnerable to initial C and N losses due to shifts in microbial stoichiometry. [ABSTRACT FROM AUTHOR]

Abstract: Research on soil microbiota is one of the frontiers in biodiversity research. Bacterivores, such as protozoans, contribute significantly to mineralization processes and key ecosystem functions in soil. Protozoan grazing on rhizobacteria stimulates microbial mineralization processes and thereby indirectly nutrient cycling. Understanding the diversity of protozoans and their fundamental functions is essential for knowledge of nutrient cycling. However, reliable data on protozoan numbers and taxonomic composition in soil are scarce. We compared the occurrence of morphotypes of small cultivable protozoans of eight different grassland and forest sites in Germany. The investigated sites differed both in landscape type and intensity of land use. Additionally, we modified a liquid aliquot method to determine protozoan abundances and community structure on the morphotype level in soil. Protozoan abundances at the investigated sites ranged between 1.7 and 12.7×104 ind.g−1 dry weight. The dominant groups were various amoebae (49.9±12.4%) and cercozoans (32.4±13.2%), followed by stramenopiles (7.7±4.2%), euglenozoans (7.5±7.6%), apusomonads (1.5±1.5%) and ciliates (0.5±0.7%). Heterotrophic flagellates and naked amoebae showed similar contributions to total protozoan abundances at all sites. Protozoan abundances were slightly higher and more variable in grassland sites compared to forest sites. Both habitat types showed a surprisingly similar community structure on a rough taxonomic level, but a more diverse pattern at a higher taxonomic resolution. [Copyright &y& Elsevier]

A major drawback in testate amoeba research is a general lack of scientific studies combining molecular approaches and classical laboratory experiments. We isolated five yet uncultured testate amoebae of the genus Phryganella Penard, 1902 from three different rivers and one pond in Germany. Based on established cultures we show their morphology, which we studied by light and electron microscopy, and present their unique feeding mode on abundant and common pennate diatoms like Nitzschia spp. and Synedra spp., whose frustules are bent and frequently, but not always, broken during the feeding process. We further obtained the first SSU rDNA sequences of strains of the family Phryganellidae, all of which contain introns. We used the sequences to confirm the taxonomic placement of the Phryganellidae in the Arcellinida (Amoebozoa), branching as a sister group to the Cryptodifflugiidae., (© 2018 International Society of Protistologists.)