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Michael Bonkowski - One of the best experts on this subject based on the ideXlab platform.
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taxonomic and functional diversity of heterotrophic protists Cercozoa and endomyxa from biological soil crusts
Microorganisms, 2021Co-Authors: Samira Khanipour Roshan, Kenneth Dumack, Michael Bonkowski, Peter Leinweber, Ulf Karsten, Karin GlaserAbstract:Biological soil crusts (biocrusts) accommodate diverse communities of phototrophic and heterotrophic microorganisms. Heterotrophic protists have critical roles in the microbial food webs of soils, with Cercozoa and Endomyxa often being dominant groups. Still, the diversity, community composition, and functions of Cercozoa and Endomyxa in biocrusts have been little explored. In this study, using a high-throughput sequencing method with taxon-specific barcoded primers, we studied Cercozoan and endomyxan communities in biocrusts from two unique habitats (subarctic grassland and temperate dunes). The communities differed strongly, with the grassland and dunes being dominated by Sarcomonadea (69%) and Thecofilosea (43%), respectively. Endomyxa and Phytomyxea were the minor components in dunes. Sandonidae, Allapsidae, and Rhogostomidae were the most abundant taxa in both habitats. In terms of functionality, up to 69% of the grassland community was constituted by bacterivorous Cercozoa. In contrast, Cercozoan and endomyxan communities in dunes consisted of 31% bacterivores, 25% omnivores, and 20% eukaryvores. Facultative and obligate eukaryvores mostly belonged to the families Rhogostomidae, Fiscullidae, Euglyphidae, Leptophryidae, and Cercomonadidae, most of which are known to feed mainly on algae. Biocrust edaphic parameters such as pH, total organic carbon, nitrogen, and phosphorus did not have any significant influence on shaping Cercozoan communities within each habitat, which confirms previous results from dunes.
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from forest soil to the canopy increased habitat diversity does not increase species richness of Cercozoa and oomycota in tree canopies
Frontiers in Microbiology, 2020Co-Authors: Robintobias Jauss, Martin Schlegel, Kenneth Dumack, Susanne Walden, Ronny Wolf, Stefan Schaffer, Anna Maria Fioredonno, Michael BonkowskiAbstract:Tree canopies provide habitats for diverse and until now, still poorly characterized communities of microbial eukaryotes. One of the most general patterns in community ecology is the increase in species richness with increasing habitat diversity. Thus, environmental heterogeneity of tree canopies should be an important factor governing community structure and diversity in this subsystem of forest ecosystems. Nevertheless, it is unknown if similar patterns are reflected at the microbial scale within unicellular eukaryotes (protists). In this study, high-throughput sequencing of two prominent protistan taxa, Cercozoa (Rhizaria) and Oomycota (Stramenopiles), was performed. Group specific primers were used to comprehensively analyze their diversity in various microhabitats of a floodplain forest from the forest floor to the canopy region. Beta diversity indicated highly dissimilar protistan communities in the investigated microhabitats. However, the majority of operational taxonomic units (OTUs) was present in all samples, and therefore differences in beta diversity were mainly related to species performance (i.e., relative abundance). Accordingly, habitat diversity strongly favored distinct protistan taxa in terms of abundance, but due to their almost ubiquitous distribution the effect of species richness on community composition was negligible.
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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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stramenopiles and Cercozoa dominate the heterotrophic protist community of biological soil crusts irrespective of edaphic factors
Pedobiologia, 2020Co-Authors: Samira Khanipour Roshan, Kenneth Dumack, Michael Bonkowski, Ulf Karsten, Karin GlaserAbstract:Abstract Biological soil crusts (biocrusts) are terrestrial micro-habitats distributed in drylands and also in temperate coastal dunes. Biocrusts harbor phototrophic and heterotrophic microorganisms in the upper soil layer, which fulfil important ecological functions such as primary production and energy channelling via the microbial loop. Heterotrophic protists, although being an essential component of the microbial food web of biocrusts, have rarely been investigated. Therefore, in the present study, we used the liquid aliquot method (LAM) to assess the abundance and diversity of protists in biocrusts from coastal dunes at the Baltic Sea for the first time. The total abundance of protists ranged between 10 × 103 and 128 × 103 individuals g−1 dry weight. The community was dominated by naked amoebae (54 %) and flagellates (44 %). The most common taxa were Spumella-like flagellates (Stramenopiles), Paracercomonas-like amoeboflagellates, and Sandonidae-like glissomonads (both from the phylum Cercozoa) as well as heteroloboseans. Despite significant differences in the beta diversity of protist morphotypes, the measured environmental drivers, such as pH, total organic carbon, nitrogen, and phosphorus did not explain these differences. Also, the geographical distance could not predict the community dissimilarity, suggesting that the diversity of protists in biocrusts is controlled by biotic or other physicochemical parameters.
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what drives the diversity of the most abundant terrestrial Cercozoan family rhogostomidae Cercozoa rhizaria
Microorganisms, 2020Co-Authors: Husna Oztoprak, Susanne Walden, Michael Bonkowski, Thierry J Heger, Kenneth DumackAbstract:Environmental sequencing surveys of soils and freshwaters revealed high abundance and diversity of the Rhogostomidae, a group of omnivorous thecate amoebae. This is puzzling since only a few Rhogostomidae species have yet been described and only a handful of reports mention them in field surveys. We investigated the putative cryptic diversity of the Rhogostomidae by a critical re-evaluation of published environmental sequencing data and in-depth ecological and morphological trait analyses. The Rhogostomidae exhibit an amazing diversity of genetically distinct clades that occur in a variety of different environments. We further broadly sampled for Rhogostomidae species; based on these isolates, we describe eleven new species and highlight important morphological traits for species delimitation. The most important environmental drivers that shape the Rhogostomidae community were soil moisture, soil pH, and total plant biomass. The length/width ratio of the theca was a morphological trait related to the colonized habitats, but not the shape and size of the aperture that is often linked to moisture adaption in testate and thecate amoebae.
Kenneth Dumack - One of the best experts on this subject based on the ideXlab platform.
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taxonomic and functional diversity of heterotrophic protists Cercozoa and endomyxa from biological soil crusts
Microorganisms, 2021Co-Authors: Samira Khanipour Roshan, Kenneth Dumack, Michael Bonkowski, Peter Leinweber, Ulf Karsten, Karin GlaserAbstract:Biological soil crusts (biocrusts) accommodate diverse communities of phototrophic and heterotrophic microorganisms. Heterotrophic protists have critical roles in the microbial food webs of soils, with Cercozoa and Endomyxa often being dominant groups. Still, the diversity, community composition, and functions of Cercozoa and Endomyxa in biocrusts have been little explored. In this study, using a high-throughput sequencing method with taxon-specific barcoded primers, we studied Cercozoan and endomyxan communities in biocrusts from two unique habitats (subarctic grassland and temperate dunes). The communities differed strongly, with the grassland and dunes being dominated by Sarcomonadea (69%) and Thecofilosea (43%), respectively. Endomyxa and Phytomyxea were the minor components in dunes. Sandonidae, Allapsidae, and Rhogostomidae were the most abundant taxa in both habitats. In terms of functionality, up to 69% of the grassland community was constituted by bacterivorous Cercozoa. In contrast, Cercozoan and endomyxan communities in dunes consisted of 31% bacterivores, 25% omnivores, and 20% eukaryvores. Facultative and obligate eukaryvores mostly belonged to the families Rhogostomidae, Fiscullidae, Euglyphidae, Leptophryidae, and Cercomonadidae, most of which are known to feed mainly on algae. Biocrust edaphic parameters such as pH, total organic carbon, nitrogen, and phosphorus did not have any significant influence on shaping Cercozoan communities within each habitat, which confirms previous results from dunes.
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from forest soil to the canopy increased habitat diversity does not increase species richness of Cercozoa and oomycota in tree canopies
Frontiers in Microbiology, 2020Co-Authors: Robintobias Jauss, Martin Schlegel, Kenneth Dumack, Susanne Walden, Ronny Wolf, Stefan Schaffer, Anna Maria Fioredonno, Michael BonkowskiAbstract:Tree canopies provide habitats for diverse and until now, still poorly characterized communities of microbial eukaryotes. One of the most general patterns in community ecology is the increase in species richness with increasing habitat diversity. Thus, environmental heterogeneity of tree canopies should be an important factor governing community structure and diversity in this subsystem of forest ecosystems. Nevertheless, it is unknown if similar patterns are reflected at the microbial scale within unicellular eukaryotes (protists). In this study, high-throughput sequencing of two prominent protistan taxa, Cercozoa (Rhizaria) and Oomycota (Stramenopiles), was performed. Group specific primers were used to comprehensively analyze their diversity in various microhabitats of a floodplain forest from the forest floor to the canopy region. Beta diversity indicated highly dissimilar protistan communities in the investigated microhabitats. However, the majority of operational taxonomic units (OTUs) was present in all samples, and therefore differences in beta diversity were mainly related to species performance (i.e., relative abundance). Accordingly, habitat diversity strongly favored distinct protistan taxa in terms of abundance, but due to their almost ubiquitous distribution the effect of species richness on community composition was negligible.
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stramenopiles and Cercozoa dominate the heterotrophic protist community of biological soil crusts irrespective of edaphic factors
Pedobiologia, 2020Co-Authors: Samira Khanipour Roshan, Kenneth Dumack, Michael Bonkowski, Ulf Karsten, Karin GlaserAbstract:Abstract Biological soil crusts (biocrusts) are terrestrial micro-habitats distributed in drylands and also in temperate coastal dunes. Biocrusts harbor phototrophic and heterotrophic microorganisms in the upper soil layer, which fulfil important ecological functions such as primary production and energy channelling via the microbial loop. Heterotrophic protists, although being an essential component of the microbial food web of biocrusts, have rarely been investigated. Therefore, in the present study, we used the liquid aliquot method (LAM) to assess the abundance and diversity of protists in biocrusts from coastal dunes at the Baltic Sea for the first time. The total abundance of protists ranged between 10 × 103 and 128 × 103 individuals g−1 dry weight. The community was dominated by naked amoebae (54 %) and flagellates (44 %). The most common taxa were Spumella-like flagellates (Stramenopiles), Paracercomonas-like amoeboflagellates, and Sandonidae-like glissomonads (both from the phylum Cercozoa) as well as heteroloboseans. Despite significant differences in the beta diversity of protist morphotypes, the measured environmental drivers, such as pH, total organic carbon, nitrogen, and phosphorus did not explain these differences. Also, the geographical distance could not predict the community dissimilarity, suggesting that the diversity of protists in biocrusts is controlled by biotic or other physicochemical parameters.
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what drives the diversity of the most abundant terrestrial Cercozoan family rhogostomidae Cercozoa rhizaria
Microorganisms, 2020Co-Authors: Husna Oztoprak, Susanne Walden, Michael Bonkowski, Thierry J Heger, Kenneth DumackAbstract:Environmental sequencing surveys of soils and freshwaters revealed high abundance and diversity of the Rhogostomidae, a group of omnivorous thecate amoebae. This is puzzling since only a few Rhogostomidae species have yet been described and only a handful of reports mention them in field surveys. We investigated the putative cryptic diversity of the Rhogostomidae by a critical re-evaluation of published environmental sequencing data and in-depth ecological and morphological trait analyses. The Rhogostomidae exhibit an amazing diversity of genetically distinct clades that occur in a variety of different environments. We further broadly sampled for Rhogostomidae species; based on these isolates, we describe eleven new species and highlight important morphological traits for species delimitation. The most important environmental drivers that shape the Rhogostomidae community were soil moisture, soil pH, and total plant biomass. The length/width ratio of the theca was a morphological trait related to the colonized habitats, but not the shape and size of the aperture that is often linked to moisture adaption in testate and thecate amoebae.
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from forest soil to the canopy increased habitat diversity does not increase species richness of Cercozoa and oomycota in tree canopies
Authorea Preprints, 2020Co-Authors: Robintobias Jauss, Martin Schlegel, Kenneth Dumack, Susanne Walden, Ronny Wolf, Stefan Schaffer, Anna Maria Fioredonno, Michael BonkowskiAbstract:Tree canopies provide habitats for diverse and until now, still poorly characterised communities of microbial eukaryotes. One of the most general patterns in community ecology is the increase in species richness with increasing habitat diversity. Thus, environmental heterogeneity of tree canopies should be an important factor governing community structure and diversity in this subsystem of forest ecosystems. Nevertheless, it is unknown if similar patterns are reflected at the microbial scale within unicellular eukaryotes (protists). In this study, high-throughput sequencing of two prominent protistan taxa, Cercozoa and Oomycota, was performed. For a comprehensive assessment of their diversity across all ecological compartments from forest soils to the canopy, group specific primers were used. When taking OTU abundances into account, our results showed highly dissimilar protistan communities within the investigated microhabitats. We observed no pattern of nestedness, because the majority of OTUs was present in all sampled microhabitats. According to the microbiological tenet ‘Everything is everywhere, but, the environment selects’, habitat diversity strongly favoured distinct protistan taxa in terms of abundance, but due to their almost ubiquitous distribution the effect of species richness on community composition was negligible.
David Bass - One of the best experts on this subject based on the ideXlab platform.
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phytocercomonas venanatans a new species of Cercozoa associated with chlorotic streak of sugarcane
Phytopathology, 2017Co-Authors: Chuong Nguyen Ngo, David Bass, Kathryn Susan Braithwaite, Anthony Young, B J CroftAbstract:Chlorotic streak is a global disease of commercial sugarcane (Saccharion spp. hybrids). The disease is transmitted by wet soil, water, as well as in diseased planting material. Although first recognized almost 90 years ago and despite significant research effort, the identity of the causal agent has bocn elusive. Metagenomic high throughput sequencing (HTS) facilitated the discovery of novel protistan ribosomal and nuclear genes in chlorotic streak- infcctcd sugarcane. These sequences suggest a possible causal agent belonging to the order Ccrcomonadida (Rhizaria, phylum Cere07.0a). .An organism with morphological features similar to cercomonads (=Cercomonadida) was isolated into pun: Axcnic culture from internal stalk tissues of infected sugarcane. The Isolated organism contained DNA sequences identical to those identified in infected plants by HTS. The DNA sequences and the morphology of the organism did not match any known species. Here we present a new genus and species. Phytocercomonas venanatans, which is associated with chlorotic streak of sugarcane. Amplicon sequencing also supports that P. venanatans is associated with this disease. This is the first reported member from Ccrcomonadida showing a probable pathogenic association with higher plants.
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grazing of leaf associated cercomonads protists rhizaria Cercozoa structures bacterial community composition and function
Environmental Microbiology, 2017Co-Authors: Sebastian Flues, David Bass, Michael BonkowskiAbstract:Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation-induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co-occurrence patterns showed less complex correlations between bacterial taxa in the protist-grazed treatments with a higher proportion of positive correlations than in non-grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator-prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required.
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persistent patterns of high alpha and low beta diversity in tropical parasitic and free living protists
bioRxiv, 2017Co-Authors: Guillaume Lentendu, David Bass, Frederic Mahe, Sonja Rueckert, Thorsten Stoeck, Micah DunthornAbstract:Animal and plant communities in tropical rainforests are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown if the microbial protists inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of soil protists in three lowland Neotropical rainforests using metabarcoding data, we estimated taxa-area and distance-decay relationships for three large protist taxa and their subtaxa, at both the OTU and phylogenetic levels, with presence-absence and abundance based measures, and compared the estimates to null models. High local alpha and low regional beta diversity patterns were persistently found for both the parasitic Apicomplexa and the free-living Cercozoa and Ciliophora, even though they have different ecological functions and different dispersal modes. In comparison to the null models, both OTU and phylogenetic diversities showed spatial structures between forests, but only phylogenetic diversity showed spatial patterns within forests. These results suggest that the biogeographies of macro- and micro-organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes. As with arthropods, the protists' high alpha diversity within forests presents problems for estimating their local diversity, and shows that regional diversity cannot be easily estimated because of low turnover between forests.
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high diversity revealed in leaf associated protists rhizaria Cercozoa of brassicaceae
Journal of Eukaryotic Microbiology, 2016Co-Authors: Sebastian Ploch, David Bass, Laura E Rose, Michael BonkowskiAbstract:The largest biological surface on earth is formed by plant leaves. These leaf surfaces are colonized by a specialized suite of leaf-inhabiting microorganisms, recently termed "phyllosphere microbiome". Microbial prey, however, attract microbial predators. Protists in particular have been shown to structure bacterial communities on plant surfaces, but virtually nothing is known about the community composition of protists on leaves. Using newly designed specific primers targeting the 18S rDNA gene of Cercozoa, we investigated the species richness of this common protist group on leaves of four Brassicaceae species from two different locations in a cloning-based approach. The generated sequences revealed a broad diversity of leaf-associated Cercozoa, mostly bacterial feeders, but also including known plant pathogens and a taxon of potential endophytes that were recently described as algal predators in freshwater systems. This initial study shows that protists must be regarded as an integral part of the microbial diversity in the phyllosphere of plants.
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a novel lineage of naked filose amoebae kraken carinae gen nov sp nov Cercozoa with a remarkable locomotion by disassembly of its cell body
Protist, 2016Co-Authors: Kenneth Dumack, David Bass, Julia Schuster, Michael BonkowskiAbstract:The term 'filose amoebae' describes a highly polyphyletic assemblage of protists whose phylogenetic placement can be unpredictable based on gross morphology alone. We isolated six filose amoebae from soils of two European countries and describe a new genus and species of naked filose amoebae, Kraken carinae gen. nov. sp. nov. We provide a morphological description based on light microscopy and small subunit rRNA gene sequences (SSU rDNA). In culture, Kraken carinae strains were very slow-moving and preyed on bacteria using a network of filopodia. Phylogenetic analyses of SSU sequences reveal that Kraken are core (filosan) Cercozoa, branching weakly at the base of the cercomonad radiation, most closely related to Paracercomonas, Metabolomonas, and Brevimastigomonas. Some Kraken sequences are >99% similar to an environmental sequence obtained from a freshwater lake in Antarctica, indicating that Kraken is not exclusively soil dwelling, but also inhabits freshwater habitats.
Thomas Cavaliersmith - One of the best experts on this subject based on the ideXlab platform.
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multigene phylogeny and cell evolution of chromist infrakingdom rhizaria contrasting cell organisation of sister phyla Cercozoa and retaria
Protoplasma, 2018Co-Authors: Thomas Cavaliersmith, Ema E. Chao, Rhodri LewisAbstract:Infrakingdom Rhizaria is one of four major subgroups with distinct cell body plans that comprise eukaryotic kingdom Chromista. Unlike other chromists, Rhizaria are mostly heterotrophic flagellates, amoebae or amoeboflagellates, commonly with reticulose (net-like) or filose (thread-like) feeding pseudopodia; uniquely for eukaryotes, cilia have proximal ciliary transition-zone hub-lattices. They comprise predominantly flagellate phylum Cercozoa and reticulopodial phylum Retaria, whose exact phylogenetic relationship has been uncertain. Given even less clear relationships amongst Cercozoan classes, we sequenced partial transcriptomes of seven Cercozoa representing five classes and endomyxan retarian Filoreta marina to establish 187-gene multiprotein phylogenies. Ectoreta (retarian infraphyla Foraminifera, Radiozoa) branch within classical Cercozoa as sister to reticulose Endomyxa. This supports recent transfer of subphylum Endomyxa from Cercozoa to Retaria alongside subphylum Ectoreta which embraces classical retarians where capsules or tests subdivide cells into organelle-containing endoplasm and anastomosing pseudopodial net-like ectoplasm. Cercozoa are more homogeneously filose, often with filose pseudopodia and/or posterior ciliary gliding motility: zooflagellate Helkesimastix and amoeboid Guttulinopsis form a strongly supported clade, order Helkesida. Cercomonads are polyphyletic (Cercomonadida sister to glissomonads; Paracercomonadida deeper). Thecofilosea are a clade, whereas Imbricatea may not be; Sarcomonadea may be paraphyletic. Helkesea and Metromonadea are successively deeper outgroups within Cercozoan subphylum Monadofilosa; subphylum Reticulofilosa (paraphyletic on site-heterogeneous trees) branches earliest, Granofilosea before Chlorarachnea. Our multiprotein trees confirm that Rhizaria are sisters of infrakingdom Halvaria (Alveolata, Heterokonta) within chromist subkingdom Harosa (= SAR); they further support holophyly of chromist subkingdom Hacrobia, and are consistent with holophyly of Chromista as sister of kingdom Plantae. Site-heterogeneous rDNA trees group Kraken with environmental DNA clade ‘eSarcomonad’, not Paracercomonadida. Ectoretan fossil dates evidence ultrarapid episodic stem sequence evolution. We discuss early rhizarian cell evolution and multigene tree coevolutionary patterns, gene-paralogue evidence for chromist monophyly, and integrate this with fossil evidence for the age of Rhizaria and eukaryote cells, and revise rhizarian classification.
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ultrastructure of allapsa vibrans and the body plan of glissomonadida Cercozoa
Protist, 2012Co-Authors: Thomas Cavaliersmith, Brian OatesAbstract:Biciliate, gliding zooflagellate Cercozoa are globally the most abundant and genetically diverse predators in soil (glissomonads and cercomonads). We present the first detailed ultrastructural study of a phylogenetically well-characterized glissomonad, Allapsa vibrans. There are two ventral posterior centriolar roots as in Cercomonadida, but fewer other microtubular roots. Allapsa's centriolar roots and rhizoplast basically resemble those of the less well studied glissomonads Bodomorpha and Neoheteromita. The posterior centriole of Allapsa attaches laterally to the base of the anterior centriole and to the nucleus by striated fibrillar connectors and nests in a shallow cup-like ventrolateral depression; two broad fans of single microtubules line the cup's posterior and inner side. The anterior centriole has a dorsal two-microtubule root and probably also a singlet root. Its medium-length ciliary transition zones have a proximal hub-lattice and a prominent dense distal transverse plate/collar complex. Golgi bodies are anterior/paranuclear; isodiametric extrusomes are anterior mid-ventral. Tubulicristate mitochondria attach to the nucleus, as do prominent microbodies. We characterize the body plan of glissomonads, comparing it with other Sarcomonadea: their sister group (Pansomonadida) and the phylogenetically more distant Cercomonadida. We discuss glissomonad radiation into families Sandonidae, Proleptomonadidae, Dujardinidae, Bodomorphidae and Allapsidae, establishing Aurigamonadidae fam. n. for the amoeboflagellate pansomonad Aurigamonas.
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new genera species and improved phylogeny of glissomonadida Cercozoa
Protist, 2011Co-Authors: Alexis T Howe, Ema E. Chao, David Bass, Thomas CavaliersmithAbstract:Glissomonadida is an important Cercozoan order of predominantly biflagellate gliding bacterivores found largely in soil and freshwater. Their vast diversity is largely undescribed. We studied 23 mostly newly isolated strains by light microscopy and sequenced their 18S rDNA genes; nine represent new species. For two misidentified ATCC ‘Heteromita triangularis’ strains, we establish novel gliding genera and species: the sandonid Mollimonas lacrima, the only glissomonad forming anterior and posterior pseudopodia, and Dujardina stenomorpha, a strongly flattened member of the new family Dujardinidae. A new strain from Oxfordshire grassland soil is the first reliably identified isolate of the virtually uniflagellate, smooth-gliding glissomonad genus, Allantion Sandon, 1924 . Phylogenetic analysis and cytological features reveal Allantion to be a member of Allapsidae. Sandona limna and Bodomorpha prolixa from Lake Baikal and Sandona hexamutans from volcanic Costa Rican soil are described as new species. Fifteen glissomonad strains were from grassland beside Lake Baikal. We describe two as new species of Sandona (S. heptamutans and S. octamutans); the others included strains of Sandona and Allapsa species that have already been described; and three were new species of Sandona and Allapsa but these died before being described. We discuss the ecological and evolutionary significance of these new strains.
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novel cultured protists identify deep branching environmental dna clades of Cercozoa new genera tremula micrometopion minimassisteria nudifila peregrinia
Protist, 2011Co-Authors: Alexis T Howe, Rhodri Lewis, David Bass, Keith Vickerman, Josephine Margaret Scoble, Hartmut Arndt, Thomas CavaliersmithAbstract:We describe three new orders of filosan Cercozoa, five new deep-branching genera, eight new species of Thaumatomonas, Reckertia, Spongomonas, Rhogostoma, Agitata, Neoheteromita and Paracercomonas, sequence their 18S rDNA, and construct 18S rDNA trees for 148 Cercozoa. Our phylogeny indicates that Filosa were ancestrally gliding flagellates; non-flagellate filose amoebae evolved from them five times independently. The new genera are more closely related to environmental DNA sequences than cultured organisms. Tremula longifila, a zooflagellate glider on both flagella (unlike other Cercozoa), is the most divergent filosan (Tremulida ord. n.). Micrometopion nutans is a eukaryote-eating gliding zooflagellate like Metopion and Metromonas. Minimassisteria diva is a widespread trimorphic marine amoeboflagellate granofilosan. Peregrinia clavideferens, a non-testate, scale-bearing, filose amoeba, branches deeply in Thaumatomonadida, which are probably sisters to Spongomonadida. Nudifila producta is a filose amoeboflagellate related to Clautriavia and Marimonadida (ord. n., e.g. Pseudopirsonia, Auranticordis). We substantially revise Imbricatea, now including Spongomonadida, and Thecofilosea to include Phaeodaria. Thecofilosea and Imbricatea and Thecofilosea are sisters, both arguably ancestrally rigid gliding flagellates with ventral pseudopod-emitting grooves. Scale-free Ovulinata parva is sister to Paulinella, so imbricate silica scales can be lost. Internal hollow silica skeletons evolved twice in Thecofilosea (Ebriida, Phaeodaria) or were multiply lost. Protaspa replaces preoccupied ‘Protaspis’.
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phylogeny and classification of cercomonadida protozoa Cercozoa cercomonas eocercomonas paracercomonas and cavernomonas gen nov
Protist, 2009Co-Authors: David Bass, Ema E. Chao, Alexis T Howe, Alexandre P Mylnikov, Keith Vickerman, James Edwards Smallbone, Jemma Snell, Charles Cabral, Thomas CavaliersmithAbstract:Cercomonads (=Cercomonadida) are biflagellate gliding bacterivorous protozoa, abundant and diverse in soil and freshwater. We establish 56 new species based on 165 cultures, differential interference contrast microscopy, and 18S and ITS2 rDNA sequencing, and a new genus Cavernomonas studied by scanning electron microscopy. We fundamentally revise the phylogeny and classification of cercomonad Cercozoa. We describe 40 Cercomonas species (35 novel), six Eocercomonas (five novel), two Cavernomonas, and 18 Paracercomonas species (14 novel). We obtained additional cercomonad clade A (Cercomonas, Eocercomonas, Cavernomonas) sequences from multiple environmental DNA libraries. The most commonly cultivated genotypes are not the commonest in environmental DNA, suggesting that cercomonad ecology is far more complex than implied by laboratory cultures. Cercomonads have never been isolated from saline environments, although some species can grow in semi-saline media in the laboratory, and environmental DNA libraries regularly detect them in coastal marine sediments. The first ultrastructural study of an anaerobic Cercozoan, Paracercomonas anaerobica sp. nov., a highly divergent cercomonad, shows much simpler ciliary roots than in clade A cercomonads, a ciliary hub-lattice and axosome, and mitochondria with tubular cristae, consistent with it being only facultatively anaerobic. We also describe Agitata tremulans gen. et sp. nov., previously misidentified as Cercobodo (=Dimastigamoeba) agilis Moroff.
J.a.n. Pawlowski - One of the best experts on this subject based on the ideXlab platform.
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polyubiquitin insertions and the phylogeny of Cercozoa and rhizaria
Protist, 2005Co-Authors: David Bass, Ema E. Chao, J.a.n. Pawlowski, David Moreira, Purificacion Lopezgarcia, Stephane Polet, Sophie Von Der Heyden, Thomas CavaliersmithAbstract:A single or double amino acid insertion at the monomer-monomer junction of the universal eukaryotic protein polyubiquitin is unique to Cercozoa and Foraminifera, closely related 'core' phyla in the protozoan infrakingdom Rhizaria. We screened 11 other candidate rhizarians for this insertion: Radiozoa (polycystine and acantharean radiolaria), a 'microheliozoan', and Apusozoa; all lack it, supporting suggestions that Foraminifera are more closely related to Cercozoa than either is to other eukaryotes. The insertion's size was ascertained for 12 additional Cercozoa to help resolve their basal branching order. The earliest branching Cercozoa generally have a single amino acid insertion, like all Foraminifera, but a large derived clade consisting of all Monadofilosa except Metopion, Helk-esimastix, and Cercobodo agilis has two amino acids, suggesting one doubling event and no reversions to a single amino acid. Metromonas and Sainouron, Cercozoans of uncertain position, have a double insertion, suggesting that they belong in Monadofilosa. An alternative interpretation, suggested by the higher positions for Metopion and Cercobodo on Bayesian trees compared with most distance trees, cannot be ruled out, i.e. that the second insertion took place earlier, in the ancestral filosan, and was followed by three independent reversions to a single amino acid in Chlorarachnea, Metopion and Cercobodo.
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small subunit ribosomal rna gene sequences of phaeodarea challenge the monophyly of haeckel s radiolaria
Protist, 2004Co-Authors: Stephane Polet, José Fahrni, Cédric Berney, J.a.n. PawlowskiAbstract:Summary In his grand monograph of Radiolaria, Ernst Haeckel originally included Phaeodarea together with Acantharea and Polycystinea, all three taxa characterized by the presence of a central capsule and the possession of axopodia. Cytological and ultrastructural studies, however, questioned the monophyly of Radiolaria, suggesting an independent evolutionary origin of the three taxa, and the first molecular data on Acantharea and Polycystinea brought controversial results. To test further the monophyly of Radiolaria, we sequenced the complete small subunit ribosomal RNA gene of three phaeodarians and three polycystines. Our analyses reveal that phaeodarians clearly branch among the recently described phylum Cercozoa, separately from Acantharea and Polycystinea. This result enhances the morphological variability within the phylum Cercozoa, which already contains very heterogeneous groups of protists. Our study also confirms the common origin of Acantharea and Polycystinea, which form a sister-group to the Cercozoa, and allows a phylogenetic reinterpretation of the morphological features of the three radiolarian groups.
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foraminifera and Cercozoa share a common origin according to rna polymerase ii phylogenies
International Journal of Systematic and Evolutionary Microbiology, 2003Co-Authors: David Longet, John M Archibald, Patrick J. Keeling, J.a.n. PawlowskiAbstract:Phylogenetic analysis of small and large subunits of rDNA genes suggested that Foraminifera originated early in the evolution of eukaryotes, preceding the origin of other rhizopodial protists. This view was recently challenged by the analysis of actin and ubiquitin protein sequences, which revealed a close relationship between Foraminifera and Cercozoa, an assemblage of various filose amoebae and amoeboflagellates that branch in the so-called crown of the SSU rDNA tree of eukaryotes. To further test this hypothesis, we sequenced a fragment of the largest subunit of the RNA polymerase II (RPB1) from five foraminiferans, two Cercozoans and the testate filosean Gromia oviformis. Analysis of our data confirms a close relationship between Foraminifera and Cercozoa and points to Gromia as the closest relative of Foraminifera.
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Revised Small Subunit rRNA Analysis Provides Further Evidence that Foraminifera Are Related to Cercozoa
Journal of Molecular Evolution, 2003Co-Authors: Cédric Berney, J.a.n. PawlowskiAbstract:There is accumulating evidence that the general shape of the ribosomal DNA-based phylogeny of Eukaryotes is strongly biased by the long-branch attraction phenomenon, leading to an artifactual basal clustering of groups that are probably highly derived. Among these groups, Foraminifera are of particular interest, because their deep phylogenetic position in ribosomal trees contrasts with their Cambrian appearance in the fossil record. A recent actin-based phylogeny of Eukaryotes has proposed that Foraminifera might be closely related to Cercozoa and, thus, branch among the so-called crown of Eukaryotes. Here, we reanalyze the small-subunit ribosomal RNA gene (SSU rDNA) phylogeny by removing all long-branching lineages that could artifactually attract foraminiferan sequences to the base of the tree. Our analyses reveal that Foraminifera branch together with the marine testate filosean Gromia oviformis as a sister group to Cercozoa, in agreement with actin phylogeny. Our study confirms the utility of SSU rDNA as a phylogenetic marker of megaevolutionary history, provided that the artifacts due to the heterogeneity of substitution rates in ribosomal genes are circumvented.
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Gymnophrys cometa and Lecythium sp. are core Cercozoa : evolutionary implications
Acta Protozoologica, 2003Co-Authors: Sergey L. Nikolaev, José Fahrni, Nikolai B. Petrov, Alexander P Mylnikov, V. V. Aleshin, Cédric Berney, J.a.n. PawlowskiAbstract:Recent phylogenetic analyses based on different molecular markers have revealed the existence of the Cercozoa, a group of protists including such morphologically diverse taxa as the cercomonad flagellates, the euglyphid testate filose amoebae, the chloroplast-bearing chlorarachniophytes, and the plasmodiophorid plant pathogens. Molecular data also indicate a close relationship between Cercozoa and Foraminifera (Granuloreticulosea). Little is known, however, about the origin of both groups and their phylogenetic relationships. Here we present the complete small-subunit ribosomal RNA (SSU rRNA) sequence of Gymnophrys cometa, formerly included in the athalamid Granuloreticulosea, as well as that of the test-bearing filose amoeba Lecythium sp. Our study shows that the two organisms clearly belong to the Cercozoa, and indicates that Gymnophrys is not closely related to Foraminifera, supporting the view that Granuloreticulosea sensu lato do not form a natural assemblage. Phylogenetic analyses including most available SSU rRNA sequences from Cercozoa suggest that a rigid, external cell envelope appeared several times independently during the evolution of the group. Furthermore, our results bring additional evidence for the wide morphological variety among Cercozoa, which now also include protists bearing granular pseudopodia and exhibiting mitochondria with flattened cristae.