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Acosta E, Fincke V, Nitsche F, Arndt H. Novel cercozoan and heterolobosean protists from the rhizosphere and phyllosphere of two endemic cacti from the Atacama Desert. Eur J Protistol 2023; 91:126034. [PMID: 38006640 DOI: 10.1016/j.ejop.2023.126034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/27/2023]
Abstract
Cercozoans and heterolobose amoebae are found across terrestrial habitats where they feed on other unicellular microbes, including bacteria, fungi and microalgae. They constitute a significant fraction of soil ecosystems and are integral members of plant microbiota. Here, we present the results on the isolation of protozoans from the rhizosphere and phyllosphere of Browningia candelaris (Meyen) in the Andean Altiplano and Eulychnia taltalensis (F. Ritter) from the Coastal Cordillera of the Atacama Desert, both endemic to this ancient desert. We identified a new heterolobose amoeba species of the genus Allovahlkampfia isolated from cactus soil, three new species of the different glissomonad genera Allapsa, Neoheteromita, Neocercomonas and one new thecofilosean amoeba of the genus Rhogostoma isolated from the phyllosphere of one studied cactus. In addition, one bacterivorous flagellate was isolated from cactus spines and identified as a member of the non-scaled imbricatean family Spongomonadidae (Spongomonas). The isolation of protists from cactus spines extends the knowledge on the habitat ranges of taxa typically found on plant leaves or soils. The molecular data presented here is a prerequisite for further investigations on the ecology and diversity of protists including next-generation sequencing of microhabitats in plants and the rhizosphere, allowing for deeper taxonomic classification.
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Affiliation(s)
- Eduardo Acosta
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Victoria Fincke
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Frank Nitsche
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Hartmut Arndt
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany.
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Applications of Blocker Nucleic Acids and Non-Metazoan PCR Improves the Discovery of the Eukaryotic Microbiome in Ticks. Microorganisms 2021; 9:microorganisms9051051. [PMID: 34068298 PMCID: PMC8153336 DOI: 10.3390/microorganisms9051051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/08/2021] [Accepted: 05/09/2021] [Indexed: 01/04/2023] Open
Abstract
Ticks serve as important vectors of a variety of pathogens. Recently, the viral and prokaryotic microbiomes in ticks have been explored using next-generation sequencing to understand the physiology of ticks and their interactions with pathogens. However, analyses of eukaryotic communities in ticks are limited, owing to the lack of suitable methods. In this study, we developed new methods to selectively amplify microeukaryote genes in tick-derived DNA by blocking the amplification of the 18S rRNA gene of ticks using artificial nucleic acids: peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). In addition, another PCR using non-metazoan primers, referred to as UNonMet-PCR, was performed for comparison. We performed each PCR using tick-derived DNA and sequenced the amplicons using the Illumina MiSeq platform. Almost all sequences obtained by conventional PCR were derived from ticks, whereas the proportion of microeukaryotic reads and alpha diversity increased upon using the newly developed method. Additionally, the PNA- or LNA-based methods were suitable for paneukaryotic analyses, whereas the UNonMet-PCR method was particularly sensitive to fungi. The newly described methods enable analyses of the eukaryotic microbiome in ticks. We expect the application of these methods to improve our understanding of the tick microbiome.
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Hujslová M, Gryndlerová H, Bystrianský L, Hršelová H, Gryndler M. Biofilm and planktonic microbial communities in highly acidic soil (pH < 3) in the Soos National Nature Reserve, Czech Republic. Extremophiles 2020; 24:577-591. [PMID: 32449144 DOI: 10.1007/s00792-020-01177-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/07/2020] [Indexed: 10/24/2022]
Abstract
Biofilm formation is a typical life strategy used by microorganisms populating acidic water systems. The same strategy might be used by microbes in highly acidic soils that are, however, neglected in this regard. In the present study, the microbial community in such highly acidic soil in the Soos National Nature Reserve (Czech Republic) has been investigated using high-throughput DNA sequencing and the organisms associated with biofilm life mode and those preferring planktonic life were distinguished using the biofilm trap technique. Our data show the differences between biofilm and planktonic microbiota fraction, although the majority of the organisms were capable of using both life modes. The by far most abundant prokaryotic genus was Acidiphilium and fungi were identified among the most abundant eukaryotic elements in biofilm formations. On the other hand, small flagellates from diverse taxonomical groups predominated in plankton. The application of cellulose amendment as well as the depth of sampling significantly influenced the composition of the detected microbial community.
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Affiliation(s)
- Martina Hujslová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic.
| | - Hana Gryndlerová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Lukáš Bystrianský
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 40096, Ústí nad Labem, Czech Republic
| | - Hana Hršelová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Milan Gryndler
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 40096, Ústí nad Labem, Czech Republic
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4
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Johansen JL, Rønn R, Ekelund F. Toxicity of cadmium and zinc to small soil protists. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:1510-1517. [PMID: 30144724 DOI: 10.1016/j.envpol.2018.08.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/10/2018] [Accepted: 08/12/2018] [Indexed: 06/08/2023]
Abstract
Small heterotrophic protists (flagellates and naked amoebae) are very abundant in soil and play a key role in maintaining soil services. Hence, knowledge on how xenobiotics affect these organisms is essential in ecosystem management. Cadmium (Cd) is an increasing environmental issue as both industrial deposition and recycling of heavy metal rich waste products have led to Cd enrichment of soils. Evaluation of toxicity of Cd to micro-organisms is often performed using a solution of pure Cd (e.g. CdCl) in liquid culture. This approach may be highly misleading as interactions between Cd and other substances, e.g. various ions or inherent soil components often strongly modify Cd toxicity. Hence, we compared the toxic effect of Cd to small heterotrophic protists in soil microcosms and liquid culture. We also evaluated how zinc (Zn) affects Cd toxicity, as Zn usually accompanies Cd in a ratio of c. 100:1, and is known to impede Cd toxicity. In the soil microcosms, we also monitored the primary food source of the protists, i.e. culturable bacteria, and used soil respiration as a proxy of soil functioning. Finally, we examined to what extent Cd actually sorbs to soil. We found 1) that c. 103 times more Cd was required to obtain the same effect in the soil microcosms compared to the liquid culture, 2) that soil sorption explains why Cd, even though highly toxic in aqueous solutions, has very limited effect when applied to soil, and 3) (very surprisingly) that in our experimental systems Zn was as toxic as Cd. Our study suggests that Cd toxicity to soil protists will be small because most Cd in soil will be sorbed to the soil matrix and because the Zn:Cd ratio of 100:1 in most substances, incl. pollutants, will mean that lethal Zn effects will occur before Cd reaches toxic levels.
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Affiliation(s)
- Jesper Liengaard Johansen
- Center for Bioenergy Recycling, ASHBACK, Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, DK2100, Copenhagen, Denmark.
| | - Regin Rønn
- Center for Bioenergy Recycling, ASHBACK, Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, DK2100, Copenhagen, Denmark
| | - Flemming Ekelund
- Center for Bioenergy Recycling, ASHBACK, Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, DK2100, Copenhagen, Denmark
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5
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The Rainwater Rock-pool Dinoflagellate Nottbeckia ochracea gen. et comb. nov. (syn.: Hemidinium ochraceum) - A Fine-structural and Molecular Study with Emphasis on the Motile Stage. Protist 2018; 169:280-306. [DOI: 10.1016/j.protis.2018.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 11/23/2022]
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Geisen S, Mitchell EAD, Adl S, Bonkowski M, Dunthorn M, Ekelund F, Fernández LD, Jousset A, Krashevska V, Singer D, Spiegel FW, Walochnik J, Lara E. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol Rev 2018; 42:293-323. [DOI: 10.1093/femsre/fuy006] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/12/2018] [Indexed: 12/27/2022] Open
Affiliation(s)
- Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
- Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel 2000, Switzerland
| | - Sina Adl
- Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, Canada
| | - Michael Bonkowski
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Straße, 67663 Kaiserslautern, Germany
| | - Flemming Ekelund
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Leonardo D Fernández
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Avenida Viel 1497, Santiago, Chile
| | - Alexandre Jousset
- Department of Ecology and Biodiversity, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Valentyna Krashevska
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, 37073 Göttingen, Germany
| | - David Singer
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
| | - Frederick W Spiegel
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, United States of America
| | - Julia Walochnik
- Molecular Parasitology, Institute of Tropical Medicine, Medical University, 1090 Vienna, Austria
| | - Enrique Lara
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
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Flues S, Blokker M, Dumack K, Bonkowski M. Diversity of Cercomonad Species in the Phyllosphere and Rhizosphere of Different Plant Species with a Description of Neocercomonas epiphylla (Cercozoa, Rhizaria) a Leaf-Associated Protist. J Eukaryot Microbiol 2018; 65:587-599. [PMID: 29377417 DOI: 10.1111/jeu.12503] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/16/2018] [Accepted: 01/16/2018] [Indexed: 12/15/2022]
Abstract
Cercomonads are among the most abundant and diverse groups of heterotrophic flagellates in terrestrial systems and show an affinity to plants. However, we still lack basic knowledge of plant-associated protists. We isolated 75 Cercomonadida strains from the phyllosphere and rhizosphere of plants from three functional groups: grasses (Poa sp.), legumes (Trifolium sp.) and forbs (Plantago sp.), representing 28 OTUs from the genera Cercomonas, Neocercomonas and Paracercomonas. The community composition differed clearly between phyllosphere and rhizosphere, but was not influenced by plant species identity. From these isolates we describe three novel cercomonad species including Neocercomonas epiphylla that was consistently and exclusively isolated from the phyllosphere. For each new species we provide a detailed morphological description as well as an 18S rDNA gene sequence as a distinct marker of species identity. Our data contribute to a better resolution of the systematics of cercomonads and their association with plants, by describing three novel species and adding gene sequences of 10 new cercomonad genotypes and of nine previously described species. In view of the functional importance of cercozoan communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of their composition, function and predator-prey interactions are clearly required.
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Affiliation(s)
- Sebastian Flues
- Department of Terrestrial Ecology, Institute for Zoology, University of Cologne, Cologne, 50674, Germany
| | - Malte Blokker
- Department of Terrestrial Ecology, Institute for Zoology, University of Cologne, Cologne, 50674, Germany
| | - Kenneth Dumack
- Department of Terrestrial Ecology, Institute for Zoology, University of Cologne, Cologne, 50674, Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Institute for Zoology, University of Cologne, Cologne, 50674, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
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8
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Harder CB, Rønn R, Brejnrod A, Bass D, Al-Soud WA, Ekelund F. Local diversity of heathland Cercozoa explored by in-depth sequencing. ISME JOURNAL 2016; 10:2488-97. [PMID: 26953604 PMCID: PMC5030685 DOI: 10.1038/ismej.2016.31] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/27/2016] [Accepted: 01/08/2016] [Indexed: 11/10/2022]
Abstract
Cercozoa are abundant free-living soil protozoa and quantitatively important in soil food webs; yet, targeted high-throughput sequencing (HTS) has not yet been applied to this group. Here we describe the development of a targeted assay to explore Cercozoa using HTS, and we apply this assay to measure Cercozoan community response to drought in a Danish climate manipulation experiment (two sites exposed to artificial drought, two unexposed). Based on a comparison of the hypervariable regions of the 18S ribosomal DNA of 193 named Cercozoa, we concluded that the V4 region is the most suitable for group-specific diversity analysis. We then designed a set of highly specific primers (encompassing ~270 bp) for 454 sequencing. The primers captured all major cercozoan groups; and >95% of the obtained sequences were from Cercozoa. From 443 350 high-quality short reads (>300 bp), we recovered 1585 operational taxonomic units defined by >95% V4 sequence similarity. Taxonomic annotation by phylogeny enabled us to assign >95% of our reads to order level and ~85% to genus level despite the presence of a large, hitherto unknown diversity. Over 40% of the annotated sequences were assigned to Glissomonad genera, whereas the most common individually named genus was the euglyphid Trinema. Cercozoan diversity was largely resilient to drought, although we observed a community composition shift towards fewer testate amoebae.
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Affiliation(s)
- Christoffer Bugge Harder
- Section of Terrestrial Ecology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Regin Rønn
- Section of Terrestrial Ecology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Asker Brejnrod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - David Bass
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, UK.,Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Weymouth, Dorset, UK
| | - Waleed Abu Al-Soud
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Ekelund
- Section of Terrestrial Ecology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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9
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Gómez F, Skovgaard A. The molecular phylogeny of the type-species of Oodinium Chatton, 1912 (Dinoflagellata: Oodiniaceae), a highly divergent parasitic dinoflagellate with non-dinokaryotic characters. Syst Parasitol 2015; 90:125-35. [DOI: 10.1007/s11230-014-9538-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 11/20/2014] [Indexed: 12/01/2022]
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10
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Scoble JM, Cavalier-Smith T. Scale evolution, sequence phylogeny, and taxonomy of thaumatomonad Cercozoa: 11 new species and new genera Scutellomonas, Cowlomonas, Thaumatospina and Ovaloplaca. Eur J Protistol 2014; 50:270-313. [DOI: 10.1016/j.ejop.2013.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022]
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11
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Phylogenetic and Morphological Diversity of Novel Soil Cercomonad Species with a Description of Two New Genera (Nucleocercomonas and Metabolomonas). Protist 2012; 163:495-528. [DOI: 10.1016/j.protis.2012.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 02/24/2012] [Accepted: 02/25/2012] [Indexed: 11/18/2022]
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12
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Paracercomonas Kinetid Ultrastructure, Origins of the Body Plan of Cercomonadida, and Cytoskeleton Evolution in Cercozoa. Protist 2012; 163:47-75. [DOI: 10.1016/j.protis.2011.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 06/04/2011] [Indexed: 11/20/2022]
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13
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Ota S, Eikrem W, Edvardsen B. Ultrastructure and molecular phylogeny of thaumatomonads (Cercozoa) with emphasis on Thaumatomastix salina from Oslofjorden, Norway. Protist 2011; 163:560-73. [PMID: 22177453 DOI: 10.1016/j.protis.2011.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 09/16/2011] [Accepted: 10/24/2011] [Indexed: 10/14/2022]
Abstract
A culture of Thaumatomastix was isolated from a sediment sample collected in Oslofjorden and established as a monospecific strain (UIO286). Based on this culture, light and transmission electron microscopy and phylogenetic analyses were carried out. Thaumatomastix species are confined within the order Thaumatomonadida of the class Imbricatea and phylum Cercozoa. They are heterotrophic and their cell bodies are covered with silica scales. Observations of thin sections as well as whole mounts indicate that the morphology and ultrastructure of UIO286 is identical to T. salina, which was initially described from salt pools in Denmark. Detailed examination revealed some new features such as the presence of pseudopodia and silica deposition vesicles producing spine scales. The phylogeny presented here includes ribosomal DNA sequences from both imbricatean cultures and environmental samples. The 18S rDNA phylogenetic tree suggests that (i) Thaumatomastix is paraphyletic within the Thaumatomonadida clade, (ii) there is no close affinity between T. salina and other cultured and sequenced strains, but it is closely related to a sequence obtained from environmental DNA; we propose the present strain to serve as a reference culture of Thaumatomastix species and T. salina. Further, we discuss the distribution, habitats, and evolution of scale formation among euglyphids and thaumatomonads.
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Affiliation(s)
- Shuhei Ota
- Marine Biology, Department of Biology, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway.
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14
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15
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Pedersen AL, Winding A, Altenburger A, Ekelund F. Protozoan growth rates on secondary-metabolite-producing Pseudomonas spp. correlate with high-level protozoan taxonomy. FEMS Microbiol Lett 2011; 316:16-22. [DOI: 10.1111/j.1574-6968.2010.02182.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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16
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Evidence of okadaic acid production in a cultured strain of the marine dinoflagellate Prorocentrum rhathymum from Malaysia. Toxicon 2010; 55:633-7. [DOI: 10.1016/j.toxicon.2009.07.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/15/2009] [Accepted: 07/16/2009] [Indexed: 11/20/2022]
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17
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Howe AT, Bass D, Vickerman K, Chao EE, Cavalier-Smith T. Phylogeny, Taxonomy, and Astounding Genetic Diversity of Glissomonadida ord. nov., The Dominant Gliding Zooflagellates in Soil (Protozoa: Cercozoa). Protist 2009; 160:159-89. [DOI: 10.1016/j.protis.2008.11.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 11/09/2008] [Indexed: 11/30/2022]
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18
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Skovgaard A, Meneses I, Angélico MM. Identifying the lethal fish egg parasite Ichthyodinium chabelardi as a member of Marine Alveolate Group I. Environ Microbiol 2009; 11:2030-41. [PMID: 19453613 DOI: 10.1111/j.1462-2920.2009.01924.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cells of the parasitic, unicellular eukaryote Ichthyodinium chabelardi were isolated from eggs of sardine (Sardina pilchardus) and from a previously unrecognized host, bogue (Boops boops), off the Atlantic coast of Portugal. Immediately after release from the infected fish egg or newly hatched larva, I. chabelardi cells were spherical and non-motile. After few minutes, spherical cells became flagellated and motile. Following 2-3 days of incubation and several divisions, spherical flagellated cells developed a twisted elongate shape and moved vigorously. Sequences of the small-subunit ribosomal RNA gene (SSU rDNA) were identical for I. chabelardi of both hosts and so were sequences of ITS1, ITS2 and the 5.8S rRNA gene. This genetic similarity suggests that eggs of sardine and bogue were infected by one single population of I. chabelardi. The SSU rRNA gene sequence of I. chabelardi was, in turn, 97% similar to those of two identical Asian isolates of Ichthyodinium sp. Phylogenetic analyses showed high support for the inclusion of Ichthyodinium in the so-called Marine Alveolate Group I (MAGI). Two morphologically well-described genera, namely Ichthyodinium and Dubosquella, have now been shown to belong to this group of seemingly exclusively parasitic alveolates.
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Affiliation(s)
- Alf Skovgaard
- Section for Aquatic Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Kosmala S, Karnkowska-Ishikawa A, Milanowski R, Kwiatowski J, Zakryś B. PHYLOGENY AND SYSTEMATICS OF EUGLENA (EUGLENACEAE) SPECIES WITH AXIAL, STELLATE CHLOROPLASTS BASED ON MORPHOLOGICAL AND MOLECULAR DATA-NEW TAXA, EMENDED DIAGNOSES, AND EPITYPIFICATIONS(1). JOURNAL OF PHYCOLOGY 2009; 45:464-481. [PMID: 27033825 DOI: 10.1111/j.1529-8817.2009.00653.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Morphological and molecular studies, as well as original literature reexamination, necessitate establishment of five Euglena species with a single axial, stellate chloroplast [Euglena viridis (O. F. Müller) Ehrenberg 1830, Euglena pseudoviridis Chadefaud 1937, Euglena stellata Mainx 1926, Euglena pseudostellata sp. nov., and Euglena cantabrica Pringsheim 1956], three species with two chloroplasts (Euglena geniculata Dujardin ex Schmitz 1884, Euglena chadefaudii Bourrelly 1951, and Euglena pseudochadefaudii sp. nov.), and one species with three chloroplasts (Euglena tristella Chu 1946). The primary morphological features, allowing distinction of the considered species are the presence and the shape of mucocysts, as well as the number of chloroplasts. Spherical mucocysts occur in E. cantabrica and E. geniculata, while spindle-shaped mucocysts are present in E. stellata, E. pseudostellata, E. chadefaudii, E. pseudochadefaudii, and E. tristella. No mucocysts are observed in E. viridis and E. pseudoviridis. Two new species (E. pseudochadefaudii sp. nov. and E. pseudostellata sp. nov.) differ from the respective species, E. chadefaudii and E. stellata, only at the molecular level. Molecular signatures and characteristic sequences are designated for nine distinguished species. Emended diagnoses for all and delimitation of epitypes for seven species (except E. viridis and E. tristella) are proposed.
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Affiliation(s)
- Sylwia Kosmala
- Department of Plant Systematics and Geography, University of Warsaw, Al. Ujazdowskie 4, PL-00-478 Warszawa, Poland
| | - Anna Karnkowska-Ishikawa
- Department of Plant Systematics and Geography, University of Warsaw, Al. Ujazdowskie 4, PL-00-478 Warszawa, Poland
| | - Rafał Milanowski
- Department of Plant Systematics and Geography, University of Warsaw, Al. Ujazdowskie 4, PL-00-478 Warszawa, Poland
| | - Jan Kwiatowski
- Department of Plant Systematics and Geography, University of Warsaw, Al. Ujazdowskie 4, PL-00-478 Warszawa, Poland
| | - Bożena Zakryś
- Department of Plant Systematics and Geography, University of Warsaw, Al. Ujazdowskie 4, PL-00-478 Warszawa, Poland
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Pedersen AL, Nybroe O, Winding A, Ekelund F, Bjørnlund L. Bacterial feeders, the nematode Caenorhabditis elegans and the flagellate Cercomonas longicauda, have different effects on outcome of competition among the Pseudomonas biocontrol strains CHA0 and DSS73. MICROBIAL ECOLOGY 2009; 57:501-9. [PMID: 18975025 DOI: 10.1007/s00248-008-9455-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 09/28/2008] [Indexed: 05/17/2023]
Abstract
How bacterial feeding fauna affects colonization and survival of bacteria in soil is not well understood, which constrains the applicability of bacterial inoculants in agriculture. This study aimed to unravel how food quality of bacteria and bacterial feeders with different feeding habits (the selective feeding flagellate Cercomonas longicauda versus the non-selective feeding nematode Caenorhabditis elegans) influence the abundance of two bacteria that compete for resources in simple model communities. Microcosms consisted of either one gfp-tagged bacterial strain (Pseudomonas fluorescens DSM50090 or one of two biocontrol strains P. fluorescens CHA0 or Pseudomonas sp. DSS73) or combinations of two bacterial strains. DSM50090 is a suitable food bacterium, DSS73 is of intermediate food quality, and CHA0 is inedible to the bacterial feeders. Bacterial and protozoan cell numbers were measured by flow cytometry. In the presence of flagellates, CHA0 increased its abundance as compared to the other biocontrol strain DSS73 or to DSM50090, which were both eaten by the flagellates. In contrast, the number of CHA0 declined as compared to DSS73 when the model community was subjected to nematode predation pressure. Hence, the results suggested that the outcome of competition among bacteria depended on their ability to cope with the prevailing bacterial predator.
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Affiliation(s)
- Annette L Pedersen
- Department of Environmental Chemistry and Microbiology, National Environmental Research Institute, University of Aarhus, Roskilde, Denmark
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21
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Skovgaard A, Daugbjerg N. Identity and systematic position of Paradinium poucheti and other Paradinium-like parasites of marine copepods based on morphology and nuclear-encoded SSU rDNA. Protist 2008; 159:401-13. [PMID: 18485817 DOI: 10.1016/j.protis.2008.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 02/23/2008] [Indexed: 10/22/2022]
Abstract
Paradinium and Paradinium-like parasites were detected in various copepod hosts collected in the NW Mediterranean Sea, the North Atlantic Ocean, and the Godthåbsfjord (Greenland). The identity and systematic position of the parasitic, plasmodial protist Paradinium was investigated on the basis of SSU rDNA and morphology. SSU rDNA sequences were obtained from 3 specimens of Paradinium poucheti isolated from their cyclopoid copepod host, Oithona similis. In addition, a comparable sequence was obtained from a hitherto undescribed species of Paradinium from the harpactacoid copepod Euterpina acutifrons. Finally, SSU rDNA sequences were acquired from 2 specimens of a red plasmodial parasite (RP parasite) isolated from Clausocalanus sp. Both morphological and SSU rDNA sequence data supported that P. poucheti and Paradinium sp. are closely related organisms. In phylogenetic analyses based on SSU rDNA sequences, Paradinium spp. clustered with sequences from an uncultured eukaryote clone from the Pacific Ocean and two sequences from haplosporidian-like parasites of shrimps, Pandalus spp. This Paradinium clade branched as a sister group to a clade comprising the Haplosporidia and the Foraminifera. The RP parasite had a superficial morphological resemblance to Paradinium and has previously been interpreted as a member of this genus. However, several morphological characters contradict this and SSU rDNA sequence data disagree with the RP parasite and Paradinium being related. The phylogenetic analyses suggested that the RP parasite is a fast-evolved alveolate and a member of the so-called marine alveolate Group I (MAGI) and emerging data now suggest that this enigmatic group may, like the syndinian dinoflagellates, consist of heterotrophic parasites.
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Affiliation(s)
- Alf Skovgaard
- Department of Biology, University of Copenhagen, Øster Farimagsgade 2D, DK-1353 Copenhagen K, Denmark.
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22
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Wylezich C, Mylnikov AP, Weitere M, Arndt H. Distribution and phylogenetic relationships of freshwater Thaumatomonads with a description of the new species Thaumatomonas coloniensis n. sp. J Eukaryot Microbiol 2008; 54:347-57. [PMID: 17669160 DOI: 10.1111/j.1550-7408.2007.00274.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The order Thaumatomonadida includes biflagellated heterotrophic flagellates that form filopodia and typically possess siliceous surface scales. We found thaumatomonads to contribute on average about 5%-10% to flagellate abundance in different benthic habitats. A new species of thaumatomonads, Thaumatomonas coloniensis n. sp., is described on the basis of morphological and molecular biological features. This new species was isolated both from groundwater at Appeldorn near Rees (Germany) and from the Rhine River at Cologne (Germany). We have sequenced the small subunit rRNA (ssu rRNA) gene and a fragment of the large subunit rRNA (lsu rRNA) gene (D3-D5 region) from the isolates of the new species, including the first sequence of a representative of the thaumatomonad genus Gyromitus. In agreement with previous studies, the differences in ribosomal genes of different thaumatomonad species are very small. For understanding the phylogenetic relationships of Thaumatomonadida and to explore their sister group relationships, we have created three sequence data sets (ssu rRNA, partial lsu rRNA, concatenated alignment of both) with the same composition of isolates (from Thaumatomonadida, Euglyphida, Cercomonadidae, and Heteromitidae). According to a Kishino-Hasegawa test, Thaumatomonadida evolved within the Cercozoa as a sister taxon to the Heteromitidae. A possibly close relationship to the Euglyphida, recently grouped together with the Thaumatomonadida in the class Imbricatea/Silicofilosea based on the rRNA data sets was not supported by our analyses.
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Affiliation(s)
- Claudia Wylezich
- Department of General Ecology and Limnology, Zoological Institute, University of Cologne, Weyertal 119, 50923 Cologne, Germany.
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23
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Hoppenrath M, Leander BS. Dinoflagellate, Euglenid, or Cercomonad? The ultrastructure and molecular phylogenetic position of Protaspis grandis n. sp. J Eukaryot Microbiol 2006; 53:327-42. [PMID: 16968450 DOI: 10.1111/j.1550-7408.2006.00110.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protaspis is an enigmatic genus of marine phagotrophic biflagellates that have been tentatively classified with several different groups of eukaryotes, including dinoflagellates, euglenids, and cercomonads. This uncertainty led us to investigate the phylogenetic position of Protaspis grandis n. sp. with ultrastructural and small subunit (SSU) rDNA sequence data. Our results demonstrated that the cells were dorsoventrally flattened, shaped like elongated ovals with parallel lateral sides, 32.5-55.0 mum long and 20.0-35.0 mum wide. Moreover, two heterodynamic flagella emerged through funnels that were positioned subapically, each within a depression and separated by a distinctive protrusion. A complex multilayered wall surrounded the cell. Like dinoflagellates and euglenids, the nucleus contained permanently condensed chromosomes and a large nucleolus throughout the cell cycle. Pseudopodia containing numerous mitochondria with tubular cristae emerged from a ventral furrow through a longitudinal slit that was positioned posterior to the protrusion and flagellar apparatus. Batteries of extrusomes were present within the cytoplasm and had ejection sites through pores in the cell wall. The SSU rDNA phylogeny demonstrated a very close relationship between the benthic P. grandis n. sp. and the planktonic Cryothecomonas longipes. These ultrastructural and molecular phylogenetic data for Protaspis indicated that the current taxonomy of Protaspis and Crythecomonas is in need of re-evaluation. The composition and identity of Protaspis is reviewed and suggestions for future taxonomic changes are presented. Problems within the genus Cryothecomonas are highlighted as well, and the missing data needed to resolve ambiguities between the two genera are clarified.
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Affiliation(s)
- Mona Hoppenrath
- Canadian Institute for Advanced Research, Program in Evolutionary Biology, Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, Canada.
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Karpov SA, Bass D, Mylnikov AP, Cavalier-Smith T. Molecular phylogeny of Cercomonadidae and kinetid patterns of Cercomonas and Eocercomonas gen. nov. (Cercomonadida, Cercozoa). Protist 2006; 157:125-58. [PMID: 16647880 DOI: 10.1016/j.protis.2006.01.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Accepted: 01/24/2006] [Indexed: 11/23/2022]
Abstract
Cercomonads are among the most abundant and widespread zooflagellates in soil and freshwater. We cultured 22 strains and report their complete 18S rRNA sequences and light microscopic morphology. Phylogenetic analysis of 51 Cercomonas rRNA genes shows in each previously identified major clade (A, B) two very robust, highly divergent, multi-species subclades (A1, A2; B1, B2). We studied kinetid ultrastructure of five clade A representatives by serial sections. All have two closely associated left ventral posterior microtubular roots, an anterior dorsal root, a microtubule-nucleating left anterior root, and a cone of microtubules passing to the nucleus. Anterior centrioles (=basal bodies, kinetosomes) of A1 have cartwheels; the posterior centriole does not, suggesting it is older, and implying flagellar transformation similar to other bikonts. Strain C-80 (subclade A2) differs greatly, having a dorsal posterior microtubule band, but lacking the A1-specific fibrillar striated root, nuclear extension to the centrioles, centriolar diaphragm, extrusomes; both mature centrioles lack cartwheels. For clade A2 we establish Eocercomonas gen. n., with type Eocercomonas ramosa sp. n., and for clade B1 Paracercomonas gen. n. (type Paracercomonas marina sp. n.). We establish Paracercomonas ekelundi sp. n. for culture SCCAP C1 and propose a Cercomonas longicauda neotype and Cercomonas (=Neocercomonas) jutlandica comb. n. and Paracercomonas (=Cercomonas) metabolica comb. n.
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Affiliation(s)
- Serguei A Karpov
- Department of Zoology, Herzen State Pedagogical University of Russia, Moika emb. 48, 191186 St. Petersburg, Russian Federation
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25
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Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, Barta JR, Bowser SS, Brugerolle G, Fensome RA, Fredericq S, James TY, Karpov S, Kugrens P, Krug J, Lane CE, Lewis LA, Lodge J, Lynn DH, Mann DG, McCourt RM, Mendoza L, Moestrup O, Mozley-Standridge SE, Nerad TA, Shearer CA, Smirnov AV, Spiegel FW, Taylor MFJR. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol 2006; 52:399-451. [PMID: 16248873 DOI: 10.1111/j.1550-7408.2005.00053.x] [Citation(s) in RCA: 859] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.
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Affiliation(s)
- Sina M Adl
- Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
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Lefranc M, Thénot A, Lepère C, Debroas D. Genetic diversity of small eukaryotes in lakes differing by their trophic status. Appl Environ Microbiol 2005; 71:5935-42. [PMID: 16204507 PMCID: PMC1266003 DOI: 10.1128/aem.71.10.5935-5942.2005] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small eukaryotes, cells with a diameter of less than 5 mum, are fundamental components of lacustrine planktonic systems. In this study, small-eukaryote diversity was determined by sequencing cloned 18S rRNA genes in three libraries from lakes of differing trophic status in the Massif Central, France: the oligotrophic Lake Godivelle, the oligomesotrophic Lake Pavin, and the eutrophic Lake Aydat. This analysis shows that the least diversified library was in the eutrophic lake (12 operational taxonomic units [OTUs]) and the most diversified was in the oligomesotrophic lake (26 OTUs). Certain groups were present in at least two ecosystems, while the others were specific to one lake on the sampling date. Cryptophyta, Chrysophyceae, and the strictly heterotrophic eukaryotes, Ciliophora and fungi, were identified in the three libraries. Among the small eukaryotes found only in two lakes, Choanoflagellida and environmental sequences (LKM11) were not detected in the eutrophic system whereas Cercozoa were confined to the oligomesotrophic and eutrophic lakes. Three OTUs, linked to the Perkinsozoa, were detected only in the Aydat library, where they represented 60% of the clones of the library. Chlorophyta and Haptophyta lineages were represented by a single clone and were present only in Godivelle and Pavin, respectively. Of the 127 clones studied, classical pigmented organisms (autotrophs and mixotrophs) represented only a low proportion regardless of the library's origin. This study shows that the small-eukaryote community composition may differ as a function of trophic status; certain lineages could be detected only in a single ecosystem.
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Affiliation(s)
- Marie Lefranc
- Université Blaise Pascal, Laboratoire de Biologie des Protistes UMR CNRS 6023, 63177 Aubière cedex, France
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Vickerman K, Appleton PL, Clarke KJ, Moreira D. Aurigamonas solis n. gen., n. sp., a soil-dwelling predator with unusual helioflagellate organisation and belonging to a novel clade within the Cercozoa. Protist 2005; 156:335-54. [PMID: 16325545 DOI: 10.1016/j.protis.2005.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Accepted: 07/15/2005] [Indexed: 11/26/2022]
Abstract
A flagellate predator, Aurigamonas solis n. gen., n. sp., with numerous radiating axopodia-like appendages, has been isolated in culture from soils. Despite its heliozoan-like appearance, Aurigamonas is not a sit-and-wait predator but a mobile hunter and its stiff appendages are not microtubule-supported axopodia but elongate haptopodia, each supported by a cylindrical core of microfilaments and bearing at its capitate tip a single extrusome-like body (haptosome). Prey flagellates are trapped on the sticky tips of the haptopodia and a large funnel-shaped pseudopodium then emerges to engulf the prey or suck out part of it for internal digestion. Pseudopodial contact is accompanied by killing, possibly as a result of the injection of spicules by the predator. Cytoplasmic haptosomes appear to induce formation of a haptopodium on making contact with the plasma membrane. Propulsion of the organism along the substratum is effected by beating of a long trailing flagellum, the short and inconspicuous second flagellum lacks motility. Small subunit rDNA sequencing shows that Aurigamonas arose within the Cercozoa. Its closest relatives are Cercobodo agilis and several flagellates currently known only as environmental sequences. This conclusion is supported further by the presence of only a single amino acid insertion in the polyubiquitin sequence of Aurigamonas solis.
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Affiliation(s)
- Keith Vickerman
- Division of Environmental and Evolutionary Biology, University of Glasgow, Glasgow G12 8QQ, UK.
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