The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.

/pdf/metatranscriptomic-census-of-active-protists-in-soils-10gkavy980.pdf

Metatranscriptomic census of active protists in soils.

This review highlights the presence and ecological roles of fungi in lakes, and aims to stim- ulate research in aquatic mycology. In the study of lentic systems, this field is an almost completely neglected topic and, if considered at all, has often been restricted to specific groups of fungi, such as yeasts, filamentous fungi (e.g. aquatic hyphomycetes), or phycomycetes (an obsolete taxonomic category that included various fungal and fungal-like organisms). We document that aquatic fungi are common in various lentic habitats. They play potentially crucial roles in nutrient and carbon cycling and interact with other organisms, thereby influencing food web dynamics. The development and application of molecular methods have greatly increased the potential for unraveling the biodiversity and ecological roles of fungi in lake ecosystems. We searched the literature for reports on all fungi occurring in lake ecosystems. The present study summarizes information on the highly diverse mycoflora in lake micro- habitats and highlights the main processes they influence. We also point out ecological niches of fungi in lakes that have been examined only superficially or ignored completely. We demonstrate that we now have the methodology to perform systematic studies to finally fill in some of the large gaps in this field.

/pdf/fungi-in-lake-ecosystems-240rbqqw7o.pdf

Fungi in lake ecosystems

Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data.

Fungi are a highly complex group of organisms of the kingdom Eumycota (i.e. the true-fungi) and other fungus-like organisms traditionally studied by mycologists, such as slime molds (Myxomycota) and oomycota (Straminopiles or Heterokonts). They constitute a significant proportion of the as yet undiscovered biota that is crucial in ecological processes and human well-being, through at least three main trophic modes: saprophytism, parasitism, or symbiosis. In addition to direct benefit (sources of antibiotics) or adverse effects (agents of disease), fungi can impact many environmental processes, particularly those associated with the decomposition of organic matter. They are present in almost all regions and climates, even under extreme conditions. However, studies have focussed mostly on economically interesting species, and knowledge of their diversity and functions is mainly restricted to soil, rhizosphere, mangrove, and lotic ecosystems. In this study, we review the diversity and potential functions of microscopic fungi in aquatic ecosystems, with focus on the pelagic environments where they often are regarded as allochthonous material, of low ecological significance for food-web processes. Recent environmental 18S rDNA surveys of microbial eukaryotes have (1) unveiled a large reservoir of unexpected fungal diversity in pelagic systems, (2) emphasized their ecological potentials for ecosystem functioning, and (3) opened new perspectives in the context of food-web dynamics. In spite of persisting methodological difficulties, we conclude that a better documentation of the diversity and quantitative and functional importance of fungi will improve our understanding of pelagic processes and biogeochemical cycling.

Diversity and functions of microscopic fungi: a missing component in pelagic food webs

Benthic macroinvertebrate community structure in Lake Taihu, China: Effects of trophic status, wind-induced disturbance and habitat complexity

We investigated the genetic diversity of eukaryotic microorganisms (0.8–20 μm) by sequencing cloned 18S rRNA genes in six genetic libraries constructed from six locations in Lake Taihu, a large shallow subtropical lake in China. Genetic libraries of eukaryotic ribosomal RNA were screened by restriction fragment length polymorphism (RFLP) analysis, and one clone representative of each RFLP pattern was partially sequenced. A total of 528 clones were clustered into 165 RFLP patterns and finally into 131 operational taxonomic unit (OTUs). Phylogenetic analysis revealed that each library included many unique OTUs, as well as members of distantly related phylogenetic groups. A majority of the clones were from alveolates, stramenopiles, cercozoa, cryptophytes, chlorophytes, and fungi, with members of choanoflagellida, euglenida, centroheliozoa, ancyromonadidae, ichthyosporea, and kathablepharid representing a minor fraction of the library. Six OTUs (15 clones) were not related to any known eukaryotic group. Canonical correspondence analysis suggested that the differences in eukaryotic microorganism community composition of in the six regions were partially related to trophic status, sediment resuspension, and top-down regulation by metazooplankton.

Genetic Diversity of Eukaryotic Microorganisms in Lake Taihu, a Large Shallow Subtropical Lake in China

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Genetic Diversity of Eukaryotic Microorganisms in Lake Taihu, a Large Shallow Subtropical Lake in China