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Toshiaki Kudo - One of the best experts on this subject based on the ideXlab platform.
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Multiple alignments of symbiotic protist cellulase and catalytic domains of the members of the glycoside hydrolase family 7.
2013Co-Authors: Nemuri Todaka, Moriya Ohkuma, Toshiaki Kudo, Tetsushi Inoue, Kanako Saita, Christine A Nalepa, Michael Lenz, Shigeharu MoriyaAbstract:Rs, Reticulitermes speratus symbiotic protists; Hs, Hodotermopsis sjostedti symbiotic protists; Nk, Neotermes koshunensis symbiotic protists; Md, Mastotermes darwiniensis symbiotic protists; Cp, Cryptocercus punctulatus symbiotic protists; Numbered clones (for example SM2038A27) are clone names of cellulase genes identified in this study from the symbiotic protists of termites; CBH, cellobiohydrolase; EG, endoglucanase; TrCel7A, a cellobiohydrolase component, Trichoderma reesei Cel7A [Uni Prot. P00725]; PgCBH-homo, Pseudotrichonympha grassii PgCBH-homo1 [Q95YH1]; TrCel7B, an endo-β-1,4-glucanase (EG) component, T. reesei Cel7B [P07981]; FoCel7B, an EG component, Fusarium oxysporum Cel7B [P46237]; HiCel7B, an EG component, Humicola insolens Cel7B [P56680]. The alignments were performed using CLUSTAL_W and subsequent manual refinement based on the three-dimensional structures of reference sequences. Arabic numerals denote the number of residues from each N terminal end. Solid and open circles under the column indicate the sites of putative proton donors and general acids/bases, respectively. Shaded columns represent conserved positions within the sequences. White letters with black shading denote cysteine residues composing the disulfide bond of T. reesei Cel7A. The asterisks represent the putative Protistan GHF7 CBH homologue cysteine residue sites corresponding to the cysteine residue sites of T. reesei Cel7A. The underlined sequences in TrCel7A indicate the loop-forming regions covering the catalytic tunnel [22], [23].
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phylogenetic analysis of cellulolytic enzyme genes from representative lineages of termites and a related cockroach
PLOS ONE, 2010Co-Authors: Nemuri Todaka, Moriya Ohkuma, Toshiaki Kudo, Tetsushi Inoue, Kanako Saita, Christine A Nalepa, Michael Lenz, Shigeharu MoriyaAbstract:The relationship between xylophagous termites and the protists resident in their hindguts is a textbook example of symbiosis. The essential steps of lignocellulose degradation handled by these protists allow the host termites to thrive on a wood diet. There has never been a comprehensive analysis of lignocellulose degradation by protists, however, as it has proven difficult to establish these symbionts in pure culture. The trends in lignocellulose degradation during the evolution of the host lineage are also largely unknown. To clarify these points without any cultivation technique, we performed meta-expressed sequence tag (EST) analysis of cDNA libraries originating from symbiotic Protistan communities in four termite species and a wood-feeding cockroach. Our results reveal the establishment of a degradation system with multiple enzymes at the ancestral stage of termite-Protistan symbiosis, especially GHF5 and 7. According to our phylogenetic analyses, the enzymes comprising the Protistan lignocellulose degradation system are coded not only by genes innate to the protists, but also genes acquired by the protists via lateral transfer from bacteria. This gives us a fresh perspective from which to understand the evolutionary dynamics of symbiosis.
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identification and characterization of ectosymbionts of distinct lineages in bacteroidales attached to flagellated protists in the gut of termites and a wood feeding cockroach
Environmental Microbiology, 2006Co-Authors: Satoko Noda, Yuichi Hongoh, Toshiaki Kudo, Tetsushi Inoue, Christine A Nalepa, Miho Kawai, Charunee Vongkaluang, Moriya OhkumaAbstract:Bacterial attachments to nearly the entire surface of flagellated protists in the guts of termites and the wood-feeding cockroach Cryptocercus are often observed. Based on the polymerase chain reaction-amplified 16S rRNA gene sequences, we investigated the phylogenetic relationships of the rod-shaped, attached bacteria (ectosymbionts) of several protist species from five host taxa and confirmed their identity by fluorescence in situ hybridizations. These ectosymbionts are affiliated with the order Bacteroidales but formed three distinct lineages, each of which may represent novel bacterial genera. One lineage consisted of the closely related ectosymbionts of two species of the protist genus Devescovina (Cristamonadida). The second lineage comprised three phylotypes identified from the protist Streblomastix sp. (Oxymonadida). The third lineage included ectosymbionts of the three protist genera Hoplonympha, Barbulanympha and Urinympha in the family Hoplonymphidae (Trichonymphida). The ultrastructural observations indicated that these rod-shaped ectosymbionts share morphological similarities of their cell walls and their point of attachment with the protist but differ in shape. Elongated forms of the ectosymbionts appeared in all the three lineages. The protist cells Streblomastix sp. and Hoplonympha sp. display deep furrows and vane-like structures, but these impressive structures are probably evolutionarily convergent because both the host protists and their ectosymbionts are distantly related.
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two different size distributions of engulfment related vesicles among symbiotic protists of the lower termite reticulitermes speratus
Microbes and Environments, 2004Co-Authors: Isao Kiuchi, Shigeharu Moriya, Toshiaki KudoAbstract:We analyzed symbiotic Protistan engulfment systems using the method of fluorescent imaging. Symbiotic protists can be divided into two Protistan groups, Type S (protists that contain uniformly small and spherical vesicles) and Type L (protists that contain vesicles that vary in both size and form). This classification corresponds not to the taxonomic classification, but to the micro-habitats of the protists. Our results suggested that these protists might have adapted to different resources in the hindgut environment of lower termites.
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Phylogenetic position and in situ identification of ectosymbiotic spirochetes on protists in the termite gut.
Applied and environmental microbiology, 2003Co-Authors: Satoko Noda, Moriya Ohkuma, Akinori Yamada, Yuichi Hongoh, Toshiaki KudoAbstract:Phylogenetic relationships, diversity, and in situ identification of spirochetes in the gut of the termite Neotermes koshunensis were examined without cultivation, with an emphasis on ectosymbionts attached to flagellated protists. Spirochetes in the gut microbial community investigated so far are related to the genus Treponema and divided into two phylogenetic clusters. In situ hybridizations with a 16S rRNA-targeting consensus oligonucleotide probe for one cluster (known as termite Treponema cluster I) detected both the ectosymbiotic spirochetes on gut protists and the free-swimming spirochetes in the gut fluid of N. koshunensis. The probe for the other cluster (cluster II), which has been identified as ectosymbionts on gut protists of two other termite species, Reticulitermes speratus and Hodotermopsis sjoestedti, failed to detect any spirochete population. The absence of cluster II spirochetes in N. koshunensis was confirmed by intensive 16S ribosomal DNA (rDNA) clone analysis, in which remarkably diverse spirochetes of 45 phylotypes were identified, almost all belonging to cluster I. Ectosymbiotic spirochetes of the three gut protist species Devescovina sp., Stephanonympha sp., and Oxymonas sp. in N. koshunensis were identified by their 16S rDNA and by in situ hybridizations using specific probes. The probes specific for these ectosymbionts did not receive a signal from the free-swimming spirochetes. The ectosymbionts were dispersed in cluster I of the phylogeny, and they formed distinct phylogenetic lineages, suggesting multiple origins of the spirochete attachment. Each single protist cell harbored multiple spirochete species, and some of the spirochetes were common among protist species. The results indicate complex relationships of the ectosymbiotic spirochetes with the gut protists.
David Bass - One of the best experts on this subject based on the ideXlab platform.
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Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems
Environment International, 2020Co-Authors: David Singer, David Bass, Christophe Seppey, Guillaume Lentendu, Micah Dunthorn, Lassâad Belbahri, Quentin Blandenier, Didier Debroas, G De Groot, Colomban De VargasAbstract:Protists dominate eukaryotic diversity and play key functional roles in all ecosystems, particularly by catalyzing carbon and nutrient cycling. To date, however, a comparative analysis of their taxonomic and functional diversity that compares the major ecosystems on Earth (soil, freshwater and marine systems) is missing. Here, we present a comparison of protist diversity based on standardized high throughput 18S rRNA gene sequencing of soil, freshwater and marine environmental DNA. Soil and freshwater protist communities were more similar to each other than to marine protist communities, with virtually no overlap of Operational Taxonomic Units (OTUs) between terrestrial and marine habitats. Soil protists showed higher γ diversity than aquatic samples. Differences in taxonomic composition of the communities led to changes in a functional diversity among ecosystems, as expressed in relative abundance of consumers, phototrophs and parasites. Phototrophs (eukaryotic algae) dominated freshwater systems (49% of the sequences) and consumers soil and marine ecosystems (59% and 48%, respectively). The individual functional groups were composed of ecosystem- specific taxonomic groups. Parasites were equally common in all ecosystems, yet, terrestrial systems hosted more OTUs assigned to parasites of macro-organisms while aquatic systems contained mostly microbial parasitoids. Together, we show biogeographic patterns of protist diversity across major ecosystems on Earth, preparing the way for more focused studies that will help understanding the multiple roles of protists in the biosphere.
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parasites dominate hyperdiverse soil protist communities in neotropical rainforests
Nature Ecology and Evolution, 2017Co-Authors: Fréderic Mahé, David Bass, Colomban De Vargas, Enrique Lara, Lucas Czech, Alexandros Stamatakis, David SingerAbstract:High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms.
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Benthic protists: the under-charted majority
FEMS Microbiology Ecology, 2016Co-Authors: Dominik Forster, David Bass, Micah Dunthorn, Fréderic Mahé, John R. Dolan, Stéphane Audic, Lucie Bittner, Christophe Boutte, Richard Christen, Jean-michel ClaverieAbstract:Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.
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cbol protist working group barcoding eukaryotic richness beyond the animal plant and fungal kingdoms
PLOS Biology, 2012Co-Authors: Jan Pawlowski, David Bass, Lassâad Belbahri, Stéphane Audic, Sina M Adl, Cedric Berney, Samuel S Bowser, Ivan Cepicka, Johan Decelle, Micah DunthornAbstract:Animals, plants, and fungi—the three traditional kingdoms of multicellular eukaryotic life—make up almost all of the visible biosphere, and they account for the majority of catalogued species on Earth [1]. The remaining eukaryotes have been assembled for convenience into the protists, a group composed of many diverse lineages, single-celled for the most part, that diverged after Archaea and Bacteria evolved but before plants, animals, or fungi appeared on Earth. Given their single-celled nature, discovering and describing new species has been difficult, and many Protistan lineages contain a relatively small number of formally described species (Figure 1A), despite the critical importance of several groups as pathogens, environmental quality indicators, and markers of past environmental changes. It would seem natural to apply molecular techniques such as DNA barcoding to the taxonomy of protists to compensate for the lack of diagnostic morphological features, but this has been hampered by the extreme diversity within the group. The genetic divergence observed between and within major Protistan groups greatly exceeds that found in each of the three multicellular kingdoms. No single set of molecular markers has been identified that will work in all lineages, but an international working group is now close to a solution. A universal DNA barcode for protists coupled with group-specific barcodes will enable an explosion of taxonomic research that will catalyze diverse applications.
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closely related protist strains have different grazing impacts on natural bacterial communities
Environmental Microbiology, 2010Co-Authors: Edvard Glucksman, Thomas Bell, Robert I Griffiths, David BassAbstract:Heterotrophic protists are abundant in most environments and exert a strong top-down control on bacterial communities. However, little is known about how selective most protists are with respect to their bacterial prey. We conducted feeding trials using cercomonad and glissomonad Cercozoa by assaying them on a standardized, diverse bacterial community washed from beech leaf litter. For each of the nine protist strains assayed here, we measured several phenotypic traits (cell volume, speed, plasticity and protist cell density) that we anticipated would be important for their feeding ecology. We also estimated the genetic relatedness of the strains based on the 18S rRNA gene. We found that the nine protist strains had significantly different impacts on both the abundance and the composition of the bacterial communities. Both the phylogenetic distance between protist strains and differences in protist strain traits were important in explaining variation in the bacterial communities. Of the morphological traits that we investigated, protist cell volume and morphological plasticity (the extent to which cells showed amoeboid cell shape flexibility) were most important in determining bacterial community composition. The results demonstrate that closely related and morphologically similar protist species can have different impacts on their prey base.
Stefan Geisen - One of the best experts on this subject based on the ideXlab platform.
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The global-scale distributions of soil protists and their contributions to belowground systems
Science advances, 2020Co-Authors: Angela M. Oliverio, Stefan Geisen, Manuel Delgado-baquerizo, Fernando T. Maestre, Benjamin L. Turner, Noah FiererAbstract:Protists are ubiquitous in soil, where they are key contributors to nutrient cycling and energy transfer. However, protists have received far less attention than other components of the soil microbiome. We used amplicon sequencing of soils from 180 locations across six continents to investigate the ecological preferences of protists and their functional contributions to belowground systems. We complemented these analyses with shotgun metagenomic sequencing of 46 soils to validate the identities of the more abundant protist lineages. We found that most soils are dominated by consumers, although parasites and phototrophs are particularly abundant in tropical and arid ecosystems, respectively. The best predictors of protist composition (primarily annual precipitation) are fundamentally distinct from those shaping bacterial and archaeal communities (namely, soil pH). Some protists and bacteria co-occur globally, highlighting the potential importance of these largely undescribed belowground interactions. Together, this study allowed us to identify the most abundant and ubiquitous protists living in soil, with our work providing a cross-ecosystem perspective on the factors structuring soil protist communities and their likely contributions to soil functioning.
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protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils
Microbiome, 2019Co-Authors: Zhi Bo Zhao, Stefan Geisen, Lili Han, Juntao Wang, Jupei Shen, Wenxue Wei, Yun Ting Fang, Limei ZhangAbstract:Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied to their microbiome as they together form holobionts. The importance of the microbiome for plant performance is, however, notoriously ignored in agricultural systems as fertilization disconnects the dependency of plants for often plant-beneficial microbial processes. Moreover, we lack a holistic understanding of how fertilization regimes affect the soil microbiome. Here, we examined the effect of a 2-year fertilization regime (no nitrogen fertilization control, nitrogen fertilization, and nitrogen fertilization plus straw amendment) on entire soil microbiomes (bacteria, fungi, and protist) in three common agricultural soil types cropped with maize in two seasons. We found that the application of nitrogen fertilizers more strongly affected protist than bacterial and fungal communities. Nitrogen fertilization indirectly reduced protist diversity through changing abiotic properties and bacterial and fungal communities which differed between soil types and sampling seasons. Nitrogen fertilizer plus straw amendment had greater effects on soil physicochemical properties and microbiome diversity than nitrogen addition alone. Moreover, nitrogen fertilization, even more together with straw, increased soil microbiome network complexity, suggesting that the application of nitrogen fertilizers tightened soil microbiomes interactions. Together, our results suggest that protists are the most susceptible microbiome component to the application of nitrogen fertilizers. As protist communities also exhibit the strongest seasonal dynamics, they serve as the most sensitive bioindicators of soil changes. Changes in protist communities might have long-term effects if some of the key protist hubs that govern microbiome complexities as top microbiome predators are altered. This study serves as the stepping stone to promote protists as promising agents in targeted microbiome engineering to help in reducing the dependency on exogenous unsustainably high fertilization and pesticide applications.
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the prey s scent volatile organic compound mediated interactions between soil bacteria and their protist predators
The ISME Journal, 2017Co-Authors: Kristin Schulzbohm, Stefan Geisen, E Jasper R Wubs, Chunxu Song, Wietse De Boer, Paolina GarbevaAbstract:Protists are major predators of bacteria in soils. However, it remains unknown how protists sense their prey in this highly complex environment. Here, we investigated whether volatile organic compounds (VOCs) of six phylogenetic distinct soil bacteria affect the performance of three different soil protists and how that relates to direct feeding interactions. We observed that most bacteria affected protist activity by VOCs. However, the response of protists to the VOCs was strongly dependent on both the bacterial and protist interacting partner. Stimulation of protist activity by volatiles and in direct trophic interaction assays often coincided, suggesting that VOCs serve as signals for protists to sense suitable prey. Furthermore, bacterial terpene synthase mutants lost the ability to affect protists, indicating that terpenes represent key components of VOC-mediated communication. Overall, we demonstrate that volatiles are directly involved in protist−bacterial predator−prey interactions.
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the soil food web revisited diverse and widespread mycophagous soil protists
Soil Biology & Biochemistry, 2016Co-Authors: Stefan Geisen, Robert Koller, Maike Hunninghaus, Kenneth Dumack, Tim Urich, Michael BonkowskiAbstract:Abstract Soil protists are commonly suggested being solely bacterivorous, serving together with bacterivorous nematodes as the main controllers of the bacterial energy channel in soil food webs. In contrast, the fungal energy channel is assumed to be controlled by arthropods and mycophagous nematodes. This perspective accepted by most soil biologists is, however, challenged by functional studies conducted by taxonomists that revealed a range of mycophagous protists. In order to increase the knowledge on the functional importance of mycophagous protists we isolated and initiated cultures of protist taxa and tested eight for facultative feeding on diverse fungi in microcosm experiments. Two different flagellate species of the genus Cercomonas, the testate amoeba Cryptodifflugia operculata and four genera of naked amoebae (Acanthamoeba sp., Leptomyxa sp., two Mayorella spp. and Thecamoeba spp.) fed and grew on yeasts with four taxa (Cercomonas sp., Leptomyxa sp., Mayorella sp., and Thecamoeba sp.) also thriving on spores of the plant pathogenic hyphal-forming fungus Fusarium culmorum. To identify the potential importance of mycophagous protists in the environment we applied a data-mining approach targeting small subunit (SSU) rRNA data obtained in metatranscriptomes of five fundamentally different terrestrial samples. We focused our analyses on the distribution and relative abundances of two well-studied mycophagous protist groups, vampyrellid amoebae and grossglockneriid ciliates. Both groups were detected in all of the highly contrasting terrestrial samples, comprising up to 3% of all protist SSU rRNA transcripts. SSU transcripts of these two groups, in contrast to all remaining protist SSU transcripts, showed strong correlations with the relative abundance of fungal sequences indicating close direct trophic interactions. Taken together, this study provides evidence that mycophagy among soil protists is common and might be of substantial but hitherto overlooked ecological importance in terrestrial ecosystems. Future studies should aim at evaluating taxon-specific (facultative) mycophagy, decipher changes caused in the fungal community and quantitatively evaluate the functional importance of this trophic position in soil ecosystems.
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Metatranscriptomic census of active protists in soils
The ISME Journal, 2015Co-Authors: Stefan Geisen, Michael Bonkowski, Alexander T Tveit, Ian M Clark, Andreas Richter, Mette M Svenning, Tim UrichAbstract: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.
Michael Bonkowski - One of the best experts on this subject based on the ideXlab platform.
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to the canopy and beyond air samples reveal wind dispersal as a driver of ubiquitous Protistan pathogen assembly in tree canopies
bioRxiv, 2020Co-Authors: Robintobias Jauss, Michael Bonkowski, Anne Nowack, Susanne Walden, Ronny Wolf, Stefan Schaffer, Barbara Schellbach, Martin SchlegelAbstract:Abstract We analyzed air dispersal of the Protistan phyla Cercozoa and Oomycota with an air sampler near the ground (~2 m) and in tree crowns (~25 m) of three tree species (oak, linden and ash) in a temperate floodplain forest in March (before leafing) and May (after leaf unfolding) with a cultivation-independent high throughput metabarcoding approach. Both, Cercozoa and Oomycota, contain important pathogens of forest trees and other vegetation. We found a high diversity of Cercozoa and Oomycota in air samples with 122 and 81 OTUs, respectively. Especially oomycetes showed a high temporal variation in beta diversity between both sampling dates. Differences in community composition between air samples in tree canopies and close to the ground were however negligible, and also tree species identity did not affect communities in air samples, indicating that the distribution of Protistan propagules through the air was not spatially restricted in the forest ecosystem. OTUs of plant pathogens, whose host species that did not occur in the forest, demonstrate wind dispersal of propagules from outside the forest biome. Overall, our results lead to a better understanding of the stochastic processes of wind dispersal of protists and Protistan pathogens, a prerequisite to understand the mechanisms of their community assembly in forest ecosystems. Importance Wind dispersal has been shown to play a crucial role in Protistan community assembly. The Protistan taxa Cercozoa and Oomycota contain important plant parasites with a major ecologic and economic impact. However, comprehensive assessments of cercozoan and oomycete diversity in forest air samples were lacking. Using a cultivation-independent high throughput metabarcoding approach, we analyzed cercozoan and oomycete air dispersal in forest floors and the canopy region – a potential filter for microbial propagules. Our study provides insights into the diversity and community assembly of protists within the air, contributing to a better understanding which factors drive the distribution of plant pathogens within forest ecosystems.
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Microplastic and soil protists: A call for research
Environmental Pollution, 2018Co-Authors: Michael BonkowskiAbstract:Abstract Microplastic is an emerging contaminant of concern in soils globally, probably gradually increasing in soil due to slow degradation. Few studies on microplastic effects on soil biota are available, and no study in a microplastic contamination context has specifically addressed soil protists. Soil protists, a phylogenetically and functionally diverse group of eukaryotic, unicellular soil organisms, are major consumers of bacteria in soils and are potentially important vehicles for the delivery of microplastics into the soil food chain. Here we build a case for focusing research on soil protists by drawing on data from previous, older studies of phagocytosis in protist taxa, which have long made use of polystyrene latex beads (microspheres). Various soil-borne taxa, including ciliates, flagellates and amoebae take up microplastic beads in the size range of a few micrometers. This included filter feeders as well as amoebae which engulf their prey. Discrimination in microplastic particle uptake depended on species, physiological state as well as particle size. Based on the results of the studies we review here, there is now a need to study microplastic effects in a pollution ecology context: this means considering a broad range of particle types under realistic conditions in the soil, and exploring longer-term effects on soil protist communities and functions.
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the soil food web revisited diverse and widespread mycophagous soil protists
Soil Biology & Biochemistry, 2016Co-Authors: Stefan Geisen, Robert Koller, Maike Hunninghaus, Kenneth Dumack, Tim Urich, Michael BonkowskiAbstract:Abstract Soil protists are commonly suggested being solely bacterivorous, serving together with bacterivorous nematodes as the main controllers of the bacterial energy channel in soil food webs. In contrast, the fungal energy channel is assumed to be controlled by arthropods and mycophagous nematodes. This perspective accepted by most soil biologists is, however, challenged by functional studies conducted by taxonomists that revealed a range of mycophagous protists. In order to increase the knowledge on the functional importance of mycophagous protists we isolated and initiated cultures of protist taxa and tested eight for facultative feeding on diverse fungi in microcosm experiments. Two different flagellate species of the genus Cercomonas, the testate amoeba Cryptodifflugia operculata and four genera of naked amoebae (Acanthamoeba sp., Leptomyxa sp., two Mayorella spp. and Thecamoeba spp.) fed and grew on yeasts with four taxa (Cercomonas sp., Leptomyxa sp., Mayorella sp., and Thecamoeba sp.) also thriving on spores of the plant pathogenic hyphal-forming fungus Fusarium culmorum. To identify the potential importance of mycophagous protists in the environment we applied a data-mining approach targeting small subunit (SSU) rRNA data obtained in metatranscriptomes of five fundamentally different terrestrial samples. We focused our analyses on the distribution and relative abundances of two well-studied mycophagous protist groups, vampyrellid amoebae and grossglockneriid ciliates. Both groups were detected in all of the highly contrasting terrestrial samples, comprising up to 3% of all protist SSU rRNA transcripts. SSU transcripts of these two groups, in contrast to all remaining protist SSU transcripts, showed strong correlations with the relative abundance of fungal sequences indicating close direct trophic interactions. Taken together, this study provides evidence that mycophagy among soil protists is common and might be of substantial but hitherto overlooked ecological importance in terrestrial ecosystems. Future studies should aim at evaluating taxon-specific (facultative) mycophagy, decipher changes caused in the fungal community and quantitatively evaluate the functional importance of this trophic position in soil ecosystems.
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Metatranscriptomic census of active protists in soils
The ISME Journal, 2015Co-Authors: Stefan Geisen, Michael Bonkowski, Alexander T Tveit, Ian M Clark, Andreas Richter, Mette M Svenning, Tim UrichAbstract: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.
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not all are free living high throughput dna metabarcoding reveals a diverse community of protists parasitizing soil metazoa
Molecular Ecology, 2015Co-Authors: Stefan Geisen, Michael Bonkowski, I. Laros, Antón Vizcaíno, G.a. De GrootAbstract:Protists, the most diverse eukaryotes, are largely considered to be free-living bacterivores, but vast numbers of taxa are known to parasitize plants or animals. High-throughput sequencing (HTS) approaches now commonly replace cultivation-based approaches in studying soil protists, but insights into common biases associated with this method are limited to aquatic taxa and samples. We created a mock community of common free-living soil protists (amoebae, flagellates, ciliates), extracted DNA and amplified it in the presence of metazoan DNA using 454 HTS. We aimed at evaluating whether HTS quantitatively reveals true relative abundances of soil protists and at investigating whether the expected protist community structure is altered by the co-amplification of metazoan-associated protist taxa. Indeed, HTS revealed fundamentally different protist communities from those expected. Ciliate sequences were highly over-represented, while those of most amoebae and flagellates were under-represented or totally absent. These results underpin the biases introduced by HTS that prevent reliable quantitative estimations of free-living protist communities. Furthermore, we detected a wide range of nonadded protist taxa probably introduced along with metazoan DNA, which altered the protist community structure. Among those, 20 taxa most closely resembled parasitic, often pathogenic taxa. Therewith, we provide the first HTS data in support of classical observational studies that showed that potential protist parasites are hosted by soil metazoa. Taken together, profound differences in amplification success between protist taxa and an inevitable co-extraction of protist taxa parasitizing soil metazoa obscure the true diversity of free-living soil protist communities.
Shigeharu Moriya - One of the best experts on this subject based on the ideXlab platform.
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Multiple alignments of symbiotic protist cellulase and catalytic domains of the members of the glycoside hydrolase family 7.
2013Co-Authors: Nemuri Todaka, Moriya Ohkuma, Toshiaki Kudo, Tetsushi Inoue, Kanako Saita, Christine A Nalepa, Michael Lenz, Shigeharu MoriyaAbstract:Rs, Reticulitermes speratus symbiotic protists; Hs, Hodotermopsis sjostedti symbiotic protists; Nk, Neotermes koshunensis symbiotic protists; Md, Mastotermes darwiniensis symbiotic protists; Cp, Cryptocercus punctulatus symbiotic protists; Numbered clones (for example SM2038A27) are clone names of cellulase genes identified in this study from the symbiotic protists of termites; CBH, cellobiohydrolase; EG, endoglucanase; TrCel7A, a cellobiohydrolase component, Trichoderma reesei Cel7A [Uni Prot. P00725]; PgCBH-homo, Pseudotrichonympha grassii PgCBH-homo1 [Q95YH1]; TrCel7B, an endo-β-1,4-glucanase (EG) component, T. reesei Cel7B [P07981]; FoCel7B, an EG component, Fusarium oxysporum Cel7B [P46237]; HiCel7B, an EG component, Humicola insolens Cel7B [P56680]. The alignments were performed using CLUSTAL_W and subsequent manual refinement based on the three-dimensional structures of reference sequences. Arabic numerals denote the number of residues from each N terminal end. Solid and open circles under the column indicate the sites of putative proton donors and general acids/bases, respectively. Shaded columns represent conserved positions within the sequences. White letters with black shading denote cysteine residues composing the disulfide bond of T. reesei Cel7A. The asterisks represent the putative Protistan GHF7 CBH homologue cysteine residue sites corresponding to the cysteine residue sites of T. reesei Cel7A. The underlined sequences in TrCel7A indicate the loop-forming regions covering the catalytic tunnel [22], [23].
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phylogenetic analysis of cellulolytic enzyme genes from representative lineages of termites and a related cockroach
PLOS ONE, 2010Co-Authors: Nemuri Todaka, Moriya Ohkuma, Toshiaki Kudo, Tetsushi Inoue, Kanako Saita, Christine A Nalepa, Michael Lenz, Shigeharu MoriyaAbstract:The relationship between xylophagous termites and the protists resident in their hindguts is a textbook example of symbiosis. The essential steps of lignocellulose degradation handled by these protists allow the host termites to thrive on a wood diet. There has never been a comprehensive analysis of lignocellulose degradation by protists, however, as it has proven difficult to establish these symbionts in pure culture. The trends in lignocellulose degradation during the evolution of the host lineage are also largely unknown. To clarify these points without any cultivation technique, we performed meta-expressed sequence tag (EST) analysis of cDNA libraries originating from symbiotic Protistan communities in four termite species and a wood-feeding cockroach. Our results reveal the establishment of a degradation system with multiple enzymes at the ancestral stage of termite-Protistan symbiosis, especially GHF5 and 7. According to our phylogenetic analyses, the enzymes comprising the Protistan lignocellulose degradation system are coded not only by genes innate to the protists, but also genes acquired by the protists via lateral transfer from bacteria. This gives us a fresh perspective from which to understand the evolutionary dynamics of symbiosis.
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two different size distributions of engulfment related vesicles among symbiotic protists of the lower termite reticulitermes speratus
Microbes and Environments, 2004Co-Authors: Isao Kiuchi, Shigeharu Moriya, Toshiaki KudoAbstract:We analyzed symbiotic Protistan engulfment systems using the method of fluorescent imaging. Symbiotic protists can be divided into two Protistan groups, Type S (protists that contain uniformly small and spherical vesicles) and Type L (protists that contain vesicles that vary in both size and form). This classification corresponds not to the taxonomic classification, but to the micro-habitats of the protists. Our results suggested that these protists might have adapted to different resources in the hindgut environment of lower termites.
