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J.a.n. Pawlowski - One of the best experts on this subject based on the ideXlab platform.
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Three new species of Gromia (Protista, Rhizaria) from western Greenland fjords
Polar Biology, 2021Co-Authors: Andrew J. Gooday, Tomas Cedhagen, Maria Holzmann, Eleanor Goetz, Sergei Korsun, J.a.n. PawlowskiAbstract:Species of large, testate, Rhizarian protists in the genus Gromia are often common in high-latitude coastal environments, including fjords, but are frequently overlooked and almost all are undescribed. Here, we describe three new gromiid species from the Nuuk fjord system on the west coast of southern Greenland. Morphologically, the new species differ in the size and shape of the test. Gromia cucumiformis sp. nov. is elongate, up to 5.5 mm long, with a length:width (L/W) ratio of 4.3–5.5; Gromia botelliformis sp. nov. is up to 2.1 mm long, with a L/W ratio of 3.0–4.8; Gromia brevis is typically less than 1.0 mm long, with a L/W ratio around 2.0. Genetically, they are well-characterised and split between two clades. Gromia cucumiformis and G. brevis branch with several species of deep-water gromiids from the Arabian Sea and the Weddell Sea, while G. botelliformis branches with deep Weddell Sea species and several unnamed and morphologically uncharacterised gromiids from different parts of the world. Gromia botelliformis and G. brevis are currently known only from the Nuuk fjords, but sequences of G. cucumiformis from Greenland group together with sequences from Svalbard and the White Sea. Our genetic data reveal four additional clades of undescribed Gromia species. One contains sequences from Greenland, Svalbard and the White Sea, two comprises sequence from Greenland and the White Sea and one is limited to sequences from Greenland. These results demonstrate the high genetic diversity of gromiids and their widespread distribution in Arctic as well as in deep-sea environments.
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broad sampling of monothalamids Rhizaria foraminifera gives further insight into diversity of non marine foraminifera
European Journal of Protistology, 2021Co-Authors: Ferry Siemensma, Maria Holzmann, Susanne Walden, Kenneth Dumack, Laure Apothelozperretgentil, Steffen Claus, Eckhard Voelcker, Wolfgang Bettighofer, Samira Khanipour Roshan, J.a.n. PawlowskiAbstract:Non-marine foraminifera are among the least known groups of protists and only a handful of species have been described since the 19th century. We collected one naked and five morphologically almost identical organic-walled monothalamid species from freshwater and terrestrial environments from Germany and Austria. One of the species was identified as Lieberkuehnia wageneriClaparede and Lachmann, 1859. As its original description is ambiguous and its type specimen has been lost, a neotype is proposed. We describe four new organic-walled monothalamous foraminifera and a novel Reticulomyxa species both morphologically and genetically. Analyses of molecular data of the different isolates revealed that they are distributed across six different clades. Two new genera, Claparedellus gen. nov. and Velamentofex gen. nov., and five new monothalamous families, Lacogromiidae fam. nov., Limnogromiidae fam. nov., Lieberkuehniidae fam. nov., Edaphoallogromiidae fam. nov. and Velamentofexidae fam. nov., are established.
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xenophyophores Rhizaria foraminifera from the eastern clarion clipperton zone equatorial pacific the genus psammina
Protist, 2018Co-Authors: Andrew J. Gooday, Maria Holzmann, Aurelie Goineau, Olga E Kamenskaya, Vyacheslav F Melnik, Richard B Pearce, Alexandra Anhthu Weber, J.a.n. PawlowskiAbstract:Xenophyophores are important megafaunal organisms in the abyssal Clarion-Clipperton Zone (CCZ; equatorial Pacific), a region hosting commercially significant deposits of polymetallic nodules. Previous studies assigned those with attached, fan-like tests to Psammina limbata, a species described from the central CCZ based on morphology. Here, we redescribe the holotype of P. limbata and then show that limbata-like morphotypes collected in the eastern CCZ include three genetically distinct species. Psammina aff. limbata is closest morphologically to P. limbata. The others are described as P. microgranulata sp. nov. and P. rotunda sp. nov. These fan-shaped species form a well-supported clade with P. tortilis sp. nov., a morphologically variable species exhibiting features typical of both Psammina and Semipsammina. A second clade containing Psammina sp. 3, and two species questionably assigned to Galatheammina branches at the base of this group. The genus Psammina includes another 9 described species for which there are no genetic data, leaving open the question of whether Psammina as a whole is monophyletic. Our study increases the number of xenophyophore species described from the eastern CCZ from 8 to 11, with a further 25 morphotypes currently undescribed. Many additional species of these giant foraminifera undoubtedly await discovery in abyssal settings.
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Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria.
Molecular phylogenetics and evolution, 2016Co-Authors: Roberto Sierra, J.a.n. Pawlowski, Sandra L. BaldaufAbstract:Rhizaria is a major eukaryotic group of tremendous diversity, including amoebae with spectacular skeletons or tests (Radiolaria and Foraminifera), plasmodial parasites (Plasmodiophorida) and secondary endosymbionts (Chlorarachniophyta). Current phylogeny places Rhizaria in an unresolved trichotomy with Stramenopila and Alveolata (supergroup "SAR"). We assembled a 147-protein data set with extensive Rhizarian coverage (M147), including the first transcriptomic data for a euglyphid amoeba. Phylogenetic pre-screening of individual proteins indicated potential problems with radically misplaced sequences due either to contamination of Rhizarian sequences amplified from wild collected material and/or extremely long branches (xLBs). Therefore, two data subsets were extracted containing either all proteins consistently recovering Rhizarian monophyly (M34) or excluding all proteins with ⩾3 xLBs (defined as ⩾2× the average terminal branch length for the tree). Phylogenetic analyses of M147 give conflicting results depending on the outgroup and method of analysis but strongly support an exclusive Rhizaria+Alveolata (R+A) clade with both data subsets (M34 and M37) regardless of phylogenetic method used. Support for an R+A clade is most consistent when a close outgroup is used and decreases with more distant outgroups, suggesting that support for alternative SAR topologies may reflect a long-branch attraction artifact. A survey of xLB distribution among taxa and protein functional category indicates that small "informational" proteins in particular have highly variable evolutionary rates with no consistent pattern among taxa.
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transcriptome analyses to investigate symbiotic relationships between marine protists
Frontiers in Microbiology, 2015Co-Authors: Roberto Sierra, Johan Decelle, Sergio Balzano, Erwan Corre, Patrick Wincker, Corinne Da Silva, Julie Poulain, J.a.n. PawlowskiAbstract:Rhizaria are an important component of oceanic plankton communities worldwide. A number of species harbour eukaryotic microalgal symbionts, which are horizontally acquired in the environment at each generation. Although these photosymbioses are determinant for Rhizaria ability to thrive in oceanic ecosystems, the mechanisms for symbiotic interactions are unclear. Using high-throughput sequencing technology (i.e. 454), we generated large Expressed Sequence Tag (EST) datasets from four uncultured Rhizaria, an acantharian (Amphilonche elongata), two polycystines (Collozoum sp. and Spongosphaera streptacantha), and one phaeodarean (Aulacantha scolymantha). We assessed the main genetic features of the host/symbionts consortium (i.e. the holobiont) transcriptomes and found rRNA sequences affiliated to a wide range of bacteria and protists in all samples, suggesting that diverse microbial communities are associated with the holobionts. A particular focus was then carried out to search for genes potentially involved in symbiotic processes such as the presence of c-type lectins-coding genes, which are proteins that play a role in cell recognition among eukaryotes. Unigenes coding putative c-type lectin domains (CTLD) were found in the species bearing photosynthetic symbionts (A. elongata, Collozoum sp. and S. streptacantha) but not in the non-symbiotic one (A. scolymantha). More particularly, phylogenetic analyses group CTLDs from A. elongata and Collozoum sp. on a distinct branch from S. streptacantha CTLDs, which contained carbohydrate-binding motifs typically observed in other marine photosymbiosis. Our data suggest that similarly to other well-known marine photosymbiosis involving metazoans, the interactions of glycans with c-type lectins is likely involved in modulation of the host/symbiont specific recognition in Radiolaria.
Tristan Biard - One of the best experts on this subject based on the ideXlab platform.
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vertical niche definition of test bearing protists Rhizaria into the twilight zone revealed by in situ imaging
Limnology and Oceanography, 2020Co-Authors: Tristan Biard, Mark D OhmanAbstract:Author(s): Biard, T; Ohman, MD | Abstract: © 2020 Association for the Sciences of Limnology and Oceanography The Rhizaria is a super-group of amoeboid protists with ubiquitous distributions, from the euphotic zone to the twilight zone and beyond. While Rhizarians have been recently described as important contributors to both biogenic silica and carbon fluxes, we lack the most basic information about their ecological habitats and preferences. Here, using in situ imaging (Underwater Vision Profiler 5), we characterize the vertical ecological niches of different test-bearing pelagic Rhizarian taxa in the southern California Current Ecosystem. We define three vertical layers between 0 and 500 m occupied, respectively, by (1) surface dwelling and mostly symbiont-bearing Rhizarians (Acantharia and Collodaria), (2) flux-feeding phaeodarians in the lower epipelagic (100–200 m), and (3) Foraminifera and Phaeodaria populations adjacent to the oxygen minimum zone. We then use Generalized Additive Models to analyze the response of each Rhizarian category to a suite of environmental variables. The models explain between 9% and 93% of the total variance observed for the different groups. While temperature and the depth of the deep chlorophyll maximum appear as the main abiotic factors influencing populations in the upper 200 m, dissolved silicon concentration is related to the abundance of mesopelagic phaeodarians, though it explains only a portion of the variance. The importance of biotic interactions (e.g., prey availability, predation, parasitism, symbiosis) is still to be considered, in order to fully incorporate the dynamics of test-bearing pelagic Rhizarians in ecological and biogeochemical models.
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vertical niche definition of test bearing protists Rhizaria into the twilight zone revealed by in situ imaging
bioRxiv, 2019Co-Authors: Tristan Biard, Mark D OhmanAbstract:Abstract The Rhizaria is a super-group of ameoboid protists with ubiquitous distributions, from the euphotic zone to the twilight zone and beyond. While Rhizarians have been recently described as important contributors to both silica and carbon fluxes, we lack the most basic information about their ecological preferences. Here, using the in situ imaging (Underwater Vision Profiler 5), we characterize the vertical ecological niches of different test-bearing Rhizarian taxa in the southern California Current Ecosystem. We define three vertical layers between 0-500 m occupied, respectively, by 1) surface dwelling and mostly symbiont-bearing Rhizarians (Acantharia and Collodaria), 2) flux-feeding phaeodarians in the lower epipelagic (100-200 m), and 3) Foraminifera and Phaeodaria populations adjacent to the Oxygen Minimum Zone. We then use Generalized Additive Models to analyze the response of each Rhizarian category to a suite of environmental variables. The models explain between 13 and 93% of the total variance observed for the different groups. While temperature and the depth of the deep chlorophyll maximum, appear as the main factors influencing populations in the upper 200 m, silicic acid concentration is the most important variable related to the abundance of mesopelagic phaeodarians. The relative importance of biotic interactions (e.g., predation, parasitism) is still to be considered, in order to fully incorporate the dynamics of test-bearing pelagic Rhizarians in ecological and biogeochemical models.
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the significance of giant phaeodarians Rhizaria to biogenic silica export in the california current ecosystem
Global Biogeochemical Cycles, 2018Co-Authors: Tristan Biard, Michael R. Stukel, Jeffrey W Krause, Mark D OhmanAbstract:Author(s): Biard, T; Krause, JW; Stukel, MR; Ohman, MD | Abstract: ©2018. American Geophysical Union. All Rights Reserved. In marine ecosystems, many planktonic organisms precipitate biogenic silica (bSiO2) to build silicified skeletons. Among them, giant siliceous Rhizarians (g500 μm), including Radiolaria and Phaeodaria, are important contributors to oceanic carbon pools but little is known about their contribution to the marine silica cycle. We report the first analyses of giant phaeodarians to bSiO2 export in the California Current Ecosystem. We measured the silica content of single Rhizarian cells ranging in size from 470 to 3,920 μm and developed allometric equations to predict silica content (0.37–43.42 μg Si/cell) from morphometric measurements. Using sediment traps to measure phaeodarian fluxes from the euphotic zone on four cruises, we calculated bSiO2 export produced by two families, the Aulosphaeridae and Castanellidae. Biogenic silica export ranged from l0.01 to 0.63 mmol Si · m−2 · day−1. These two families alone contributed on average 10% (range 0–80%) of total bSiO2 export from the euphotic zone. Their proportional contributions increased substantially in more oligotrophic regions with lower bSiO2 fluxes. Using the in situ Underwater Vision Profiler 5, we characterized vertical distributions of the giant phaeodarian family Aulosphaeridae to a depth of 500 m and inferred their contribution to bSiO2 export in deeper waters. We found a significant increase of Aulosphaeridae export (l0.01 to 2.82 mmol Si · m−2 · day−1) when extended to mesopelagic depths. Using a global data set of in situ profiles, we estimated the significance of Aulosphaeridae to bSiO2 export and revealed that they can act as major exporters of bSiO2 to the mesopelagic zone in various regions.
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Radiolaria contribution to vertical export in the California Current Ecosystem revealed by DNA metabarcoding - Supplementary data
2018Co-Authors: Andres Gutierrez-rodriguez, Tristan Biard, Michael R. Stukel, Adriana Lopes Dos Santos, Daniel Vaulot, Michael R. Landry, Fabrice NotAbstract:Supplementary data to:Gutierrez-rodriguez, A., Stukel, M.R., Lopes dos Santos, A., Biard, T., Vaulot, D., Landry, M.R. & Not, F. 2018. High contribution of Rhizaria (Radiolaria) to vertical export in the California Current Ecosystem revealed by DNA metabarcoding. ISME J. submitted.Supplementary data :Supplementary Data S1. CCE Samples.xlsx. List of samples with metadata Supplementary Data S2. CCE OTU 0.97.fasta. Fasta file with sequence of OTUs Supplementary Data S2. CCE OTU table.xlsx. Read abundance table of OTUs (rows) vs Samples (Column)
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In situ imaging reveals the biomass of giant protists in the global ocean
Nature, 2016Co-Authors: Tristan Biard, Lars Stemmann, Marc Picheral, Nicolas Mayot, Pieter Vandromme, Helena Hauss, Gabriel Gorsky, Lionel Guidi, Rainer Kiko, Fabrice NotAbstract:Planktonic organisms play crucial roles in oceanic food webs and global biogeochemical cycles1, 2. Most of our knowledge about the ecological impact of large zooplankton stems from research on abundant and robust crustaceans, and in particular copepods3, 4. A number of the other organisms that comprise planktonic communities are fragile, and therefore hard to sample and quantify, meaning that their abundances and effects on oceanic ecosystems are poorly understood. Here, using data from a worldwide in situ imaging survey of plankton larger than 600 μm, we show that a substantial part of the biomass of this size fraction consists of giant protists belonging to the Rhizaria, a super-group of mostly fragile unicellular marine organisms that includes the taxa Phaeodaria and Radiolaria (for example, orders Collodaria and Acantharia). Globally, we estimate that Rhizarians in the top 200 m of world oceans represent a standing stock of 0.089 Pg carbon, equivalent to 5.2% of the total oceanic biota carbon reservoir5. In the vast oligotrophic intertropical open oceans, Rhizarian biomass is estimated to be equivalent to that of all other mesozooplankton (plankton in the size range 0.2–20 mm). The photosymbiotic association of many Rhizarians with microalgae may be an important factor in explaining their distribution. The previously overlooked importance of these giant protists across the widest ecosystem on the planet6 changes our understanding of marine planktonic ecosystems.
Mark D Ohman - One of the best experts on this subject based on the ideXlab platform.
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vertical niche definition of test bearing protists Rhizaria into the twilight zone revealed by in situ imaging
Limnology and Oceanography, 2020Co-Authors: Tristan Biard, Mark D OhmanAbstract:Author(s): Biard, T; Ohman, MD | Abstract: © 2020 Association for the Sciences of Limnology and Oceanography The Rhizaria is a super-group of amoeboid protists with ubiquitous distributions, from the euphotic zone to the twilight zone and beyond. While Rhizarians have been recently described as important contributors to both biogenic silica and carbon fluxes, we lack the most basic information about their ecological habitats and preferences. Here, using in situ imaging (Underwater Vision Profiler 5), we characterize the vertical ecological niches of different test-bearing pelagic Rhizarian taxa in the southern California Current Ecosystem. We define three vertical layers between 0 and 500 m occupied, respectively, by (1) surface dwelling and mostly symbiont-bearing Rhizarians (Acantharia and Collodaria), (2) flux-feeding phaeodarians in the lower epipelagic (100–200 m), and (3) Foraminifera and Phaeodaria populations adjacent to the oxygen minimum zone. We then use Generalized Additive Models to analyze the response of each Rhizarian category to a suite of environmental variables. The models explain between 9% and 93% of the total variance observed for the different groups. While temperature and the depth of the deep chlorophyll maximum appear as the main abiotic factors influencing populations in the upper 200 m, dissolved silicon concentration is related to the abundance of mesopelagic phaeodarians, though it explains only a portion of the variance. The importance of biotic interactions (e.g., prey availability, predation, parasitism, symbiosis) is still to be considered, in order to fully incorporate the dynamics of test-bearing pelagic Rhizarians in ecological and biogeochemical models.
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vertical niche definition of test bearing protists Rhizaria into the twilight zone revealed by in situ imaging
bioRxiv, 2019Co-Authors: Tristan Biard, Mark D OhmanAbstract:Abstract The Rhizaria is a super-group of ameoboid protists with ubiquitous distributions, from the euphotic zone to the twilight zone and beyond. While Rhizarians have been recently described as important contributors to both silica and carbon fluxes, we lack the most basic information about their ecological preferences. Here, using the in situ imaging (Underwater Vision Profiler 5), we characterize the vertical ecological niches of different test-bearing Rhizarian taxa in the southern California Current Ecosystem. We define three vertical layers between 0-500 m occupied, respectively, by 1) surface dwelling and mostly symbiont-bearing Rhizarians (Acantharia and Collodaria), 2) flux-feeding phaeodarians in the lower epipelagic (100-200 m), and 3) Foraminifera and Phaeodaria populations adjacent to the Oxygen Minimum Zone. We then use Generalized Additive Models to analyze the response of each Rhizarian category to a suite of environmental variables. The models explain between 13 and 93% of the total variance observed for the different groups. While temperature and the depth of the deep chlorophyll maximum, appear as the main factors influencing populations in the upper 200 m, silicic acid concentration is the most important variable related to the abundance of mesopelagic phaeodarians. The relative importance of biotic interactions (e.g., predation, parasitism) is still to be considered, in order to fully incorporate the dynamics of test-bearing pelagic Rhizarians in ecological and biogeochemical models.
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the significance of giant phaeodarians Rhizaria to biogenic silica export in the california current ecosystem
Global Biogeochemical Cycles, 2018Co-Authors: Tristan Biard, Michael R. Stukel, Jeffrey W Krause, Mark D OhmanAbstract:Author(s): Biard, T; Krause, JW; Stukel, MR; Ohman, MD | Abstract: ©2018. American Geophysical Union. All Rights Reserved. In marine ecosystems, many planktonic organisms precipitate biogenic silica (bSiO2) to build silicified skeletons. Among them, giant siliceous Rhizarians (g500 μm), including Radiolaria and Phaeodaria, are important contributors to oceanic carbon pools but little is known about their contribution to the marine silica cycle. We report the first analyses of giant phaeodarians to bSiO2 export in the California Current Ecosystem. We measured the silica content of single Rhizarian cells ranging in size from 470 to 3,920 μm and developed allometric equations to predict silica content (0.37–43.42 μg Si/cell) from morphometric measurements. Using sediment traps to measure phaeodarian fluxes from the euphotic zone on four cruises, we calculated bSiO2 export produced by two families, the Aulosphaeridae and Castanellidae. Biogenic silica export ranged from l0.01 to 0.63 mmol Si · m−2 · day−1. These two families alone contributed on average 10% (range 0–80%) of total bSiO2 export from the euphotic zone. Their proportional contributions increased substantially in more oligotrophic regions with lower bSiO2 fluxes. Using the in situ Underwater Vision Profiler 5, we characterized vertical distributions of the giant phaeodarian family Aulosphaeridae to a depth of 500 m and inferred their contribution to bSiO2 export in deeper waters. We found a significant increase of Aulosphaeridae export (l0.01 to 2.82 mmol Si · m−2 · day−1) when extended to mesopelagic depths. Using a global data set of in situ profiles, we estimated the significance of Aulosphaeridae to bSiO2 export and revealed that they can act as major exporters of bSiO2 to the mesopelagic zone in various regions.
Vincent Herve - One of the best experts on this subject based on the ideXlab platform.
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aquatic urban ecology at the scale of a capital community structure and interactions in street gutters
The ISME Journal, 2018Co-Authors: Vincent Herve, Boris Leroy, Albert Da Silva Pires, Pascal J LopezAbstract:In most cities, streets are designed for collecting and transporting dirt, litter, debris, storm water and other wastes as a municipal sanitation system. Microbial mats can develop on street surfaces and form microbial communities that have never been described. Here, we performed the first molecular inventory of the street gutter-associated eukaryotes across the entire French capital of Paris and the non-potable waters sources. We found that the 5782 OTUs (operational taxonomic units) present in the street gutters which are dominated by diatoms (photoautotrophs), fungi (heterotrophs), Alveolata and Rhizaria, includes parasites, consumers of phototrophs and epibionts that may regulate the dynamics of gutter mat microbial communities. Network analyses demonstrated that street microbiome present many species restricted to gutters, and an overlapping composition between the water sources used for street cleaning (for example, intra-urban aquatic networks and the associated rivers) and the gutters. We propose that street gutters, which can cover a significant surface area of cities worldwide, potentially have important ecological roles in the remediation of pollutants or downstream wastewater treatments, might also be a niche for growth and dissemination of putative parasite and pathogens.
Fabien Burki - One of the best experts on this subject based on the ideXlab platform.
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phylogenomics supports the monophyly of the cercozoa
Molecular Phylogenetics and Evolution, 2019Co-Authors: Nicholas A T Irwin, Fabien Burki, Denis V Tikhonenkov, Elisabeth Hehenberger, Alexander P Mylnikov, Patrick J. KeelingAbstract:Abstract The phylum Cercozoa consists of a diverse assemblage of amoeboid and flagellated protists that forms a major component of the supergroup, Rhizaria. However, despite its size and ubiquity, the phylogeny of the Cercozoa remains unclear as morphological variability between cercozoan species and ambiguity in molecular analyses, including phylogenomic approaches, have produced ambiguous results and raised doubts about the monophyly of the group. Here we sought to resolve these ambiguities using a 161-gene phylogenetic dataset with data from newly available genomes and deeply sequenced transcriptomes, including three new transcriptomes from Aurigamonas solis, Abollifer prolabens, and a novel species, Lapot gusevi n. gen. n. sp. Our phylogenomic analysis strongly supported a monophyletic Cercozoa, and approximately-unbiased tests rejected the paraphyletic topologies observed in previous studies. The transcriptome of L. gusevi represents the first transcriptomic data from the large and recently characterized Aquavolonidae-Treumulida-'Novel Clade 12′ group, and phylogenomics supported its position as sister to the cercozoan subphylum, Endomyxa. These results provide insights into the phylogeny of the Cercozoa and the Rhizaria as a whole.
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phylogenomics of the intracellular parasite mikrocytos mackini reveals evidence for a mitosome in Rhizaria
Current Biology, 2013Co-Authors: Fabien Burki, J.a.n. Pawlowski, Roberto Sierra, Nicolas Corradi, Gary R Meyer, Cathryn L Abbott, Patrick J. KeelingAbstract:Summary Mikrocytos mackini is an intracellular protistan parasite of oysters whose position in the phylogenetic tree of eukaryotes has been a mystery for many years [1,2]. M. mackini is difficult to isolate, has not been cultured, and has no defining morphological feature. Furthermore, its only phylogenetic marker that has been successfully sequenced to date (the small subunit ribosomal RNA) is highly divergent and has failed to resolve its evolutionary position [2]. M. mackini is also one of the few eukaryotes that lacks mitochondria [1], making both its phylogenetic position and comparative analysis of mitochondrial function particularly important. Here, we have obtained transcriptomic data for M. mackini from enriched isolates and constructed a 119-gene phylogenomic data set. M. mackini proved to be among the fastest-evolving eukaryote lineages known to date, but, nevertheless, our analysis robustly placed it within Rhizaria. Searching the transcriptome for genetic evidence of a mitochondrion-related organelle (MRO) revealed only four mitochondrion-derived genes: IscS , IscU , mtHsp70 , and FdxR . Interestingly, all four genes are involved in iron-sulfur cluster formation, a biochemical pathway common to other highly reduced "mitosomes" in unrelated MRO-containing lineages [7]. This is the first evidence of MRO in Rhizaria, and it suggests the parallel evolution of mitochondria to mitosomes in this supergroup.
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evolution of Rhizaria new insights from phylogenomic analysis of uncultivated protists
BMC Evolutionary Biology, 2010Co-Authors: Fabien Burki, Simon Bulman, Patrick J. Keeling, Alexander Kudryavtsev, Mikhail V Matz, Galina V Aglyamova, Mark Fiers, J.a.n. PawlowskiAbstract:Recent phylogenomic analyses have revolutionized our view of eukaryote evolution by revealing unexpected relationships between and within the eukaryotic supergroups. However, for several groups of uncultivable protists, only the ribosomal RNA genes and a handful of proteins are available, often leading to unresolved evolutionary relationships. A striking example concerns the supergroup Rhizaria, which comprises several groups of uncultivable free-living protists such as radiolarians, foraminiferans and gromiids, as well as the parasitic plasmodiophorids and haplosporids. Thus far, the relationships within this supergroup have been inferred almost exclusively from rRNA, actin, and polyubiquitin genes, and remain poorly resolved. To address this, we have generated large Expressed Sequence Tag (EST) datasets for 5 species of Rhizaria belonging to 3 important groups: Acantharea (Astrolonche sp., Phyllostaurus sp.), Phytomyxea (Spongospora subterranea, Plasmodiophora brassicae) and Gromiida (Gromia sphaerica). 167 genes were selected for phylogenetic analyses based on the representation of at least one Rhizarian species for each gene. Concatenation of these genes produced a supermatrix composed of 36,735 amino acid positions, including 10 Rhizarians, 9 stramenopiles, and 9 alveolates. Phylogenomic analyses of this large dataset revealed a strongly supported clade grouping Foraminifera and Acantharea. The position of this clade within Rhizaria was sensitive to the method employed and the taxon sampling: Maximum Likelihood (ML) and Bayesian analyses using empirical model of evolution favoured an early divergence, whereas the CAT model and ML analyses with fast-evolving sites or the foraminiferan species Reticulomyxa filosa removed suggested a derived position, closely related to Gromia and Phytomyxea. In contrast to what has been previously reported, our analyses also uncovered the presence of the Rhizarian-specific polyubiquitin insertion in Acantharea. Finally, this work reveals another possible Rhizarian signature in the 60S ribosomal protein L10a. Our study provides new insights into the evolution of Rhizaria based on phylogenomic analyses of ESTs from three groups of previously under-sampled protists. It was enabled through the application of a recently developed method of transcriptome analysis, requiring very small amount of starting material. Our study illustrates the potential of this method to elucidate the early evolution of eukaryotes by providing large amount of data for uncultivable free-living and parasitic protists.
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Untangling the phylogeny of amoeboid protists.
Journal of Eukaryotic Microbiology, 2008Co-Authors: J.a.n. Pawlowski, Fabien BurkiAbstract:The amoebae and amoeboid protists form a large and diverse assemblage of eukaryotes characterized by various types of pseudopodia. For convenience, the traditional morphology-based classification grouped them together in a macrotaxon named Sarcodina. Molecular phylogenies contributed to the dismantlement of this assemblage, placing the majority of sarcodinids into two new supergroups: Amoebozoa and Rhizaria. In this review, we describe the taxonomic composition of both supergroups and present their small subunit rDNA-based phylogeny. We comment on the advantages and weaknesses of these phylogenies and emphasize the necessity of taxon-rich multigene datasets to resolve phylogenetic relationships within Amoebozoa and Rhizaria. We show the importance of environmental sequencing as a way of increasing taxon sampling in these supergroups. Finally, we highlight the interest of Amoebozoa and Rhizaria for understanding eukaryotic evolution and suggest that resolving their phylogenies will be among the main challenges for future phylogenomic analyses.
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phylogenomics reshuffles the eukaryotic supergroups
PLOS ONE, 2007Co-Authors: Fabien Burki, Marianne A Minge, Asmund Skjaeveland, Kamran Shalchiantabrizi, Kjetill S. Jakobsen, Sergey I. Nikolaev, J.a.n. PawlowskiAbstract:Background Resolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, the accumulation of molecular data led to a new evolutionary understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, the composition of these large assemblages and their relationships remain controversial. Methodology/Principle Findings Here, we report the sequencing of expressed sequence tags (ESTs) for two species belonging to the supergroup Rhizaria and present the analysis of a unique dataset combining 29908 amino acid positions and an extensive taxa sampling made of 49 mainly unicellular species representative of all supergroups. Our results show a very robust relationship between Rhizaria and two main clades of the supergroup chromalveolates: stramenopiles and alveolates. We confirm the existence of consistent affinities between assemblages that were thought to belong to different supergroups of eukaryotes, thus not sharing a close evolutionary history. Conclusions This well supported phylogeny has important consequences for our understanding of the evolutionary history of eukaryotes. In particular, it questions a single red algal origin of the chlorophyll-c containing plastids among the chromalveolates. We propose the abbreviated name ‘SAR’ (Stramenopiles+Alveolates+Rhizaria) to accommodate this new super assemblage of eukaryotes, which comprises the largest diversity of unicellular eukaryotes.
