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It is often discussed whether the biogeography of free-living protists is better explained by the ‘everything is everywhere’(EiE) hypothesis, which postulates that only ecology drives their distribution, or by the alternative hypothesis of ‘moderate endemicity’ in which geographic barriers can limit their dispersal. To formally test this, it would be necessary not only to find organisms restricted to a geographical area but also to check for their presence in any other place with a similar ecology. We propose the use of environmental niche models to generate and test null EiE distributions. Here we have analysed the distribution of 18S rDNA variants (ribotypes) of the myxomycete Badhamia melanospora (belonging to the protozoan phylum Amoebozoa) using 125 specimens from 91 localities. Two geographically structured groups of ribotypes congruent with slight morphological differences in the spores can be distinguished. One group comprises all populations from Argentina and Chile, and the other is formed by populations from North America together with human-introduced populations from other parts of the world. Environmental climatic niche models constructed separately for the two groups have significant differences, but show several overlapping areas. However, only specimens from one group were found in an intensively surveyed area in South America where both niche models overlap. It can be concluded that everything is not everywhere for B. melanospora. This taxon constitutes a complex formed by at least two cryptic species that probably diverged allopatrically in North and South America.

Interactions occur between two or more organisms affecting each other. Interactions are decisive for the ecology of the organisms. Without direct experimental evidence the analysis of interactions is difficult. Correlation analyses that are based on co-occurrences are often used to approximate interaction. Here, we present a new mathematical model to estimate the interaction strengths between taxa, based on changes in their relative abundances across environmental gradients.

This study reveals the diversity and distribution of two major ubiquitous groups of soil amoebae, the genus Acanthamoeba and the Myxomycetes (plasmodial slime-moulds) that are rarely, if ever, recovered in environmental sampling studies. We analyzed 150 grassland soil samples from three Biodiversity Exploratories study regions in Germany. We developed specific primers targeting the V2 variable region in the first part of the small subunit of the ribosomal RNA gene for high-throughput pyrotag sequencing. From ca. 1 million reads, applying very stringent filtering and clustering parameters to avoid overestimation of the diversity, we obtained 273 acanthamoebal and 338 myxomycete operational taxonomic units (OTUs, 96% similarity threshold). This number is consistent with the genetic diversity known in the two investigated lineages, but unequalled to date by any environmental sampling study. Only very few OTUs were identical to already known sequences. Strikingly different OTUs assemblages were found between the three German regions (PerMANOVA p.value = 0.001) and even between sites of the same region (multiple-site Simpson-based similarity indices <0.4), showing steep biogeographical gradients.

Collection details including locality, date, and (as far as possible) habitat characteristics must also be provided, accompanied in parasitic and symbiotic taxa by an accurately identified host voucher or its DNA/tissue sample wherever this is available. [...]the extracted DNA must be deposited in a recognized DNA bank or museum collection and cited with a unique identifier to allow checks and further genetic analyses. [...]the large majority of protists are currently uncultivable by known means or not available in culture collections, and genetic data only exist for a very small fraction of described species. [...]it is imperative to establish standard barcoding protocols for future protist barcoding projects that will substantially increase the number of collected, described, but uncultivable protists.

ABSTRACT Plants modulate the soil microbiota by root exudation assembling a complex rhizosphere microbiome with organisms spanning different trophic levels. Here, we assessed the diversity of bacterial, fungal and cercozoan communities in landraces and modern varieties of wheat. The dominant taxa within each group were the bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria; the fungi phyla Ascomycota, Chytridiomycota and Basidiomycota; and the Cercozoa classes Sarcomonadea, Thecofilosea and Imbricatea. We showed that microbial networks of the wheat landraces formed a more intricate network topology than that of modern wheat cultivars, suggesting that breeding selection resulted in a reduced ability to recruit specific microbes in the rhizosphere. The high connectedness of certain cercozoan taxa to bacteria and fungi indicated trophic network hierarchies where certain predators gain predominance over others. Positive correlations between protists and bacteria in landraces were preserved as a subset in cultivars as was the case for the Sarcomonadea class with Actinobacteria. The correlations between the microbiome structure and plant genotype observed in our results suggest the importance of top-down control by organisms of higher trophic levels as a key factor for understanding the drivers of microbiome community assembly in the rhizosphere. Protists as a key factor in rhizosphere microbiome assembly was demonstrated in landraces and modern cultivars of wheat.

Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a ‘slow-fast’ axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that ‘slow’ and ‘fast’ strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification. Although co-occurring species may differ widely in their response traits, coordinated functional trait shifts may emerge at the community level in response to environmental factors. Here, the authors use data from 150 grassland sites to identify a coordinated slow-fast strategy response to land-use intensification across above- and belowground taxa.

Forest litter harbors complex networks of microorganisms whose major components are bacteria, fungi and protists. Protists, being highly selective consumers of bacteria and fungi could influence decomposition processes by shifting competitive microbial interactions. We investigated the eukaryotic diversity from 18 samples of one-year beech (Fagus sylvatica) leaf litter by RNA-based high-throughput sequencing of the small-subunit ribosomal RNA gene. By applying a metatranscriptomics approach, we avoided biases inherent to PCR-based methods, and could therefore focus on elusive protistan groups. We obtained 14 589 eukaryotic assembled sequences (contigs) representing 2223 unique taxa. Fungi dominated the eukaryotic assemblage, followed by an equal proportion of protists and plants. Among protists, the phylum Amoebozoa clearly dominated, representing more than twice the proportion of Alveolata (mostly ciliates) and Rhizaria (mostly Cercozoa), which are often retrieved as the dominant protistan groups in soils, revealing potential primer biases. By assigning functional traits to protists, we could assess that the proportion of free-living and heterotrophs was much higher than that of parasites and autotrophs, opening the way to a better understanding of the role played by the protistan communities and how biodiversity interacts with decomposition processes.

The phylogenetic position of the slime-mould genus Lamproderma (Myxomycetes, Amoebozoa) challenges traditional taxonomy: although it displays the typical characters of the order Stemonitales, it appears to be sister to Physarales. This study provides a small subunit (18S or SSU) ribosomal RNA gene-based phylogeny of Lamproderma and its allies, with new sequences from 49 specimens in 12 genera. We found that the order Stemonitales and Lamproderma were both ancestral to Physarales and that Lamproderma constitutes several clades intermingled with species of Diacheopsis, Colloderma and Elaeomyxa. We suggest that these genera may have evolved from Lamproderma by multiple losses of fruiting body stalks and that many taxonomic revisions are needed. We found such high genetic diversity within three Lamproderma species that they probably consist of clusters of sibling species. We discuss the contrasts between genetic and morphological divergence and implications for the morphospecies concept, highlighting the phylogenetically most reliable morphological characters and pointing to others that have been overestimated. In addition, we showed that the first part (~600 bases) of the SSU rDNA gene is a valuable tool for phylogeny in Myxomycetes, since it displayed sufficient variability to distinguish closely related taxa and never failed to cluster together specimens considered of the same species.

Myxomycetes, or plasmodial slime-moulds, are one of the largest groups in phylum Amoebozoa. Nonetheless, only ∼10% are in the database for the small subunit (SSU) ribosomal RNA gene, the most widely used gene for phylogenetics and barcoding. Most sequences belong to dark-spored Myxomycetes (order Fuscisporida); the 318 species of superorder Lucisporidia (bright-spored) are represented by only eleven genuine sequences. To compensate for this, we provide 66 new sequences, 37 SSU rRNA and 29 elongation factor 1-alpha (EF-1α), for 82% of the genera of Lucisporidia. Phylogenetic analyses of single- and two-gene alignments produce congruent topologies and reveal both morphological characters that have been overemphasised and those that have been overlooked in past classifications. Both classical orders, Liceida and Trichiida, and several families and genera are para/polyphyletic; some previously unrecognised clades emerge. We discuss possible evolutionary pathways. Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding. We report a new group I intron insertion site for Myxomycetes in one Licea.

Plasmodial slime molds (Myxogastria or Myxomycetes) are common and widespread unicellular organisms that are commonly assumed to have a sexual life cycle culminating with the formation of often macroscopic fruiting bodies that efficiently disseminate spores. However, laboratory studies based on mating compatibility revealed the coexistence of asexual as well as sexual strains. To test this hypothesis in natural populations, we investigated the genetic variability of two species of the genus Lamproderma. Detailed ecological relevés were carried out in 2007 and 2009 in several deep ravines in the Elbsandsteingebirge (Saxony, south-eastern Germany). Morphological characters of 93 specimens of Lamproderma were recorded and genetic analyses, based on the small subunit ribosomal gene, the internal transcribed spacer 1 and partial elongation factor 1α sequences were carried out for 52 specimens. Genetic analyses showed the existence of two major clades, each composed of several discrete lineages. Most of these lineages were composed of several identical sequences (SSU, ITS 1 and EF-1α) which is explained best by an asexual mode of reproduction. Detrended Correspondence Analysis of morphological characters revealed two morphospecies that corresponded to the two major clades, except for one genotype (Lc6), thus challenging the morphospecies concept. Genetic patterns were not related to the geographical distribution: specimens belonging to the same genotype were found in distinct ravines, suggesting effective long-distance dispersal via spores, except for the Lc6 genotype which was found only in one ravine. Implications for the morphological and biological species concept are discussed.