1
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Torruella G, Galindo LJ, Moreira D, Ciobanu M, Heiss AA, Yubuki N, Kim E, López-García P. Expanding the molecular and morphological diversity of Apusomonadida, a deep-branching group of gliding bacterivorous protists. J Eukaryot Microbiol 2023; 70:e12956. [PMID: 36453005 DOI: 10.1111/jeu.12956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 09/13/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022]
Abstract
Apusomonads are cosmopolitan bacterivorous biflagellate protists usually gliding on freshwater and marine sediment or wet soils. These nanoflagellates form a sister lineage to opisthokonts and may have retained ancestral features helpful to understanding the early evolution of this large supergroup. Although molecular environmental analyses indicate that apusomonads are genetically diverse, few species have been described. Here, we morphologically characterize 11 new apusomonad strains. Based on molecular phylogenetic analyses of the rRNA gene operon, we describe four new strains of the known species Multimonas media, Podomonas capensis, Apusomonas proboscidea, and Apusomonas australiensis, and rename Thecamonas oxoniensis as Mylnikovia oxoniensis n. gen., n. comb. Additionally, we describe four new genera and six new species: Catacumbia lutetiensis n. gen. n. sp., Cavaliersmithia chaoae n. gen. n. sp., Singekia montserratensis n. gen. n. sp., Singekia franciliensis n. gen. n. sp., Karpovia croatica n. gen. n. sp., and Chelonemonas dolani n. sp. Our comparative analysis suggests that apusomonad ancestor was a fusiform biflagellate with a dorsal pellicle, a plastic ventral surface, and a sleeve covering the anterior flagellum, that thrived in marine, possibly oxygen-poor, environments. It likely had a complex cell cycle with dormant and multiple fission stages, and sex. Our results extend known apusomonad diversity, allow updating their taxonomy, and provide elements to understand early eukaryotic evolution.
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Affiliation(s)
- Guifré Torruella
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.,Barcelona Supercomputing Center (BSC-CNS), Barcelona, Spain.,Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Luis Javier Galindo
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.,Department of Zoology, University of Oxford, Oxford, UK
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Maria Ciobanu
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Aaron A Heiss
- Department of Invertebrate Zoology, American Museum of Natural History, New York City, New York, USA.,Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Naoji Yubuki
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.,Bioimaging Facility, University of British Columbia, Vancouver, BC, Canada
| | - Eunsoo Kim
- Department of Invertebrate Zoology, American Museum of Natural History, New York City, New York, USA.,Department of Life Science & Division of EcoScience, Ewha Womans University, Seoul, South Korea
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2
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Hittorf M, Letsch-Praxmarer S, Windegger A, Bass D, Kirchmair M, Neuhauser S. Revised Taxonomy and Expanded Biodiversity of the Phytomyxea (Rhizaria, Endomyxa). J Eukaryot Microbiol 2020; 67:648-659. [PMID: 32654223 PMCID: PMC7756720 DOI: 10.1111/jeu.12817] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 05/21/2020] [Accepted: 06/25/2020] [Indexed: 12/27/2022]
Abstract
Phytomyxea (phytomyxids) is a group of obligate biotrophic pathogens belonging to the Rhizaria. Some phytomyxids are well studied and include known plant pathogens such as Plasmodiophora brassicae, the causal agent of clubroot disease. Despite this economic importance, the taxonomy and biodiversity of this group are largely cryptic, with many species described in the premolecular area. Some of these species were key for establishing the morphotaxonomic concepts that define most genera to this day, but systematic efforts to include and integrate those species into molecular studies are still lacking. The aim of this study was to expand our understanding of phytomyxid biodiversity in terrestrial environments. Thirty-eight environmental samples from habitats in which novel and known diversity of Phytomyxea was expected were analysed. We were able to generate 18S rRNA sequences from Ligniera verrucosa, a species which is well defined based on ultrastructure. Phylogenetic analyses of the collected sequences rendered the genera Lignera, Plasmodiophora and Spongospora polyphyletic, and identified two novel and apparently diverse lineages (clade 17, clade 18). Based on these findings and on data from previous studies, we formally establish the new genera Pseudoligniera n. gen. for L. verrucosa,Hillenburgia n. gen. for Spongospora nasturtii and revert Plasmodiophora diplantherae to its original name Ostenfeldiella diplantherae.
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Affiliation(s)
- Michaela Hittorf
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | | | - Alexandra Windegger
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | - David Bass
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, DT4 8UB, United Kingdom
| | - Martin Kirchmair
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | - Sigrid Neuhauser
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
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3
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Hirakata Y, Hatamoto M, Oshiki M, Watari T, Araki N, Yamaguchi T. Food selectivity of anaerobic protists and direct evidence for methane production using carbon from prey bacteria by endosymbiotic methanogen. ISME JOURNAL 2020; 14:1873-1885. [PMID: 32341474 DOI: 10.1038/s41396-020-0660-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 01/28/2023]
Abstract
Anaerobic protists are major predators of prokaryotes in anaerobic ecosystems. However, little is known about the predation behavior of anaerobic protists because almost none have been cultured. In particular, these characteristics of anaerobic protists in the phyla Metamonada and Cercozoa have not been reported previously. In this study, we isolated three anaerobic protists, Cyclidium sp., Trichomitus sp., and Paracercomonas sp., from anaerobic granular sludge in an up-flow anaerobic sludge blanket reactor used to treat domestic sewage. Ingestion and digestion of food bacteria by anaerobic protists with or without endosymbiotic methanogens were demonstrated using tracer experiments with green fluorescent protein and a stable carbon isotope. These tracer experiments also demonstrated that Cyclidium sp. supplied CO2 and hydrogen to endosymbiotic methanogens. While Cyclidium sp. and Trichomitus sp. ingested both Gram-negative and -positive bacteria, Paracercomonas sp. could only take up Gram-negative bacteria. Archaeal cells such as Methanobacterium beijingense and Methanospirillum hungatei did not support the growth of these protists. Metabolite patterns of all three protists differed and were influenced by food bacterial species. These reported growth rates, ingestion rates, food selectivity, and metabolite patterns provide important insights into the ecological roles of these protists in anaerobic ecosystems.
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Affiliation(s)
- Yuga Hirakata
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan.
| | - Mamoru Oshiki
- Department of Civil Engineering, Nagaoka College, National Institute of Technology, Nagaoka, Niigata, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Nobuo Araki
- Department of Civil Engineering, Nagaoka College, National Institute of Technology, Nagaoka, Niigata, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan.,Department of Civil and Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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4
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: diversity, taxonomy and phylogeny of the Fungi. Biol Rev Camb Philos Soc 2019; 94:2101-2137. [PMID: 31659870 PMCID: PMC6899921 DOI: 10.1111/brv.12550] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/11/2022]
Abstract
The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely unicellular monopolar organisms to highly complex syncitial filaments that may form macroscopic structures. Fungi emerged as a 'Third Kingdom', embracing organisms that were outside the classical dichotomy of animals versus vegetals. The taxonomy of this group has a turbulent history that is only now starting to be settled with the advent of genomics and phylogenomics. We here review the current status of the phylogeny and taxonomy of fungi, providing an overview of the main defined groups. Based on current knowledge, nine phylum-level clades can be defined: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Basidiomycota and Ascomycota. For each group, we discuss their main traits and their diversity, focusing on the evolutionary relationships among the main fungal clades. We also explore the diversity and phylogeny of several groups of uncertain affinities and the main phylogenetic and taxonomical controversies and hypotheses in the field.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
- Health and Experimental Sciences DepartmentUniversitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREAPg. Lluís Companys 2308010BarcelonaSpain
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5
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Hirakata Y, Hatamoto M, Oshiki M, Watari T, Kuroda K, Araki N, Yamaguchi T. Temporal variation of eukaryotic community structures in UASB reactor treating domestic sewage as revealed by 18S rRNA gene sequencing. Sci Rep 2019; 9:12783. [PMID: 31484981 PMCID: PMC6726610 DOI: 10.1038/s41598-019-49290-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/22/2019] [Indexed: 11/09/2022] Open
Abstract
Eukaryotes are important components of ecosystems in wastewater treatment processes. However, little is known about eukaryotic community in anaerobic wastewater treatment systems. In this study, eukaryotic communities in an up flow anaerobic sludge blanket (UASB) reactor treating domestic sewage during two years of operation were investigated using V4 and V9 regions of 18S rRNA gene for amplicon sequencing. In addition, activated sludge and influent sewage samples were also analyzed and used as the references for aerobic eukaryotic community to characterize anaerobic eukaryotes. The amplicon sequence V4 and V9 libraries detected different taxonomic groups, especially from the UASB samples, suggesting that commonly used V4 and V9 primer pairs could produce a bias for eukaryotic communities analysis. Eukaryotic community structures in the UASB reactor were influenced by the immigration of eukaryotes via influent sewage but were clearly different from the influent sewage and activated sludge. Multivariate statistics indicated that protist genera Cyclidium, Platyophrya and Subulatomonas correlated with chemical oxygen demand and suspended solid concentration, and could be used as bioindicators of treatment performance. Uncultured eukaryotes groups were dominant in the UASB reactor, and their physiological roles need to be examined to understand their contributions to anaerobic processes in future studies.
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Affiliation(s)
- Yuga Hirakata
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan.
| | - Mamoru Oshiki
- Department of Civil Engineering, National institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Kyohei Kuroda
- Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, 473-1 Yoshio-cho, Miyakonojo, Miyazaki, 885-8567, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan.,Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
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6
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Wu W, Huang B. Protist diversity and community assembly in surface sediments of the South China Sea. Microbiologyopen 2019; 8:e891. [PMID: 31218846 PMCID: PMC6813438 DOI: 10.1002/mbo3.891] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 11/10/2022] Open
Abstract
Protists are pivotal components of marine ecosystems in terms of their high diversity, but protist communities have been poorly explored in benthic environments. Here, we investigated protist diversity and community assembly in surface sediments in the South China Sea (SCS) at a basin scale. Pyrosequencing of 18S rDNA was performed for a total of six samples taken from the surface seafloor at water depths ranging from 79 to 2,939 m. We found that Cercozoa was the dominant group, accounting for an average of 39.9% and 25.3% of the reads and operational taxonomic units (OTUs), respectively. The Cercozoa taxa were highly diverse, comprising 14 phylogenetic clades, six of which were affiliated with unknown groups belonging to Filosa and Endomyxa. Fungi were also an important group in both read‐ (18.1% on average) and OTU‐derived (9.3% on average) results. Moreover, the turnover patterns of the protist communities were differently explained by species sorting (53.3%), dispersal limitation (33.3%), mass effects (0%), and drift (13.3%). In summary, our findings show that the basin‐wide protist communities in the surface sediments of the SCS are primarily dominated by Cercozoa and are mainly assembled by species sorting and dispersal limitation.
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Affiliation(s)
- Wenxue Wu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Bangqin Huang
- Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
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7
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Elliott JK, Simpson H, Teesdale A, Replogle A, Elliott M, Coats K, Chastagner G. A Novel Phagomyxid Parasite Produces Sporangia in Root Hair Galls of Eelgrass (Zostera marina). Protist 2018; 170:64-81. [PMID: 30710862 DOI: 10.1016/j.protis.2018.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 11/15/2018] [Accepted: 12/02/2018] [Indexed: 10/27/2022]
Abstract
The objective of this study was to identify the parasite causing the formation of root hair galls on eelgrass (Zostera marina) in Puget Sound, WA. Microscopic and molecular analyses revealed that a novel protist formed plasmodia that developed into sporangia in root hair tip galls and released biflagellate swimming zoospores. Root hair galls were also observed in the basal section of root hairs, and contained plasmodia or formed thick-walled structures filled with cells (resting spores). Phylogenetic analyses of 18S rDNA sequence data obtained from cells in sporangia indicated that the closest relative of the parasite with a known taxonomic identification was Plasmodiophora diplantherae (86.9% sequence similarity), a phagomyxid parasite that infects the seagrass Halodule spp. To determine the local geographic distribution of the parasite, root and soil samples were taken from four eelgrass populations in Puget Sound and analyzed for root hair galls and parasite DNA using a newly designed qPCR protocol. The percent of root hairs with galls and amount of parasite DNA in roots and sediment varied among the four eelgrass populations. Future studies are needed to establish the taxonomy of the parasite, its effects on Z. marina, and the factors that determine its distribution and abundance.
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Affiliation(s)
- Joel K Elliott
- Department of Biology, University of Puget Sound, Tacoma, WA 98406, USA.
| | - Hunter Simpson
- Department of Biology, University of Puget Sound, Tacoma, WA 98406, USA
| | - Alex Teesdale
- Department of Biology, University of Puget Sound, Tacoma, WA 98406, USA
| | - Amy Replogle
- Department of Biology, University of Puget Sound, Tacoma, WA 98406, USA
| | - Marianne Elliott
- Department of Plant Pathology, Washington State University Research & Extension Center, Puyallup, WA 98371, USA
| | - Kathryn Coats
- Department of Plant Pathology, Washington State University Research & Extension Center, Puyallup, WA 98371, USA
| | - Gary Chastagner
- Department of Plant Pathology, Washington State University Research & Extension Center, Puyallup, WA 98371, USA
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8
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Grum-Grzhimaylo OA, Debets AJM, Bilanenko EN. Mosaic structure of the fungal community in the Kislo-Sladkoe Lake that is detaching from the White Sea. Polar Biol 2018. [DOI: 10.1007/s00300-018-2347-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Tropidoatractidae fam. nov., a Deep Branching Lineage of Metopida (Armophorea, Ciliophora) Found in Diverse Habitats and Possessing Prokaryotic Symbionts. Protist 2018; 169:362-405. [DOI: 10.1016/j.protis.2018.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/03/2018] [Accepted: 04/11/2018] [Indexed: 11/29/2022]
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10
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Mangot JF, Logares R, Sánchez P, Latorre F, Seeleuthner Y, Mondy S, Sieracki ME, Jaillon O, Wincker P, Vargas CD, Massana R. Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells. Sci Rep 2017; 7:41498. [PMID: 28128359 PMCID: PMC5269757 DOI: 10.1038/srep41498] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/21/2016] [Indexed: 11/30/2022] Open
Abstract
Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promising tools to retrieve genomic information from these uncultured organisms. However, SCG are based on whole genome amplification, which normally introduces amplification biases that limit the amount of genomic data retrieved from a single cell. Here, we increase the recovery of genomic information from two MAST-4 lineages by co-assembling short reads from multiple Single Amplified Genomes (SAGs) belonging to evolutionary closely related cells. We found that complementary genomic information is retrieved from different SAGs, generating co-assembly that features >74% of genome recovery, against about 20% when assembled individually. Even though this approach is not aimed at generating high-quality draft genomes, it allows accessing to the genomic information of microbes that would otherwise remain unreachable. Since most of the picoeukaryotes still remain uncultured, our work serves as a proof-of-concept that can be applied to other taxa in order to extract genomic data and address new ecological and evolutionary questions.
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Affiliation(s)
- Jean-François Mangot
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)–CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E-08003, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)–CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E-08003, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)–CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E-08003, Spain
| | - Fran Latorre
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)–CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E-08003, Spain
| | - Yoann Seeleuthner
- CEA, Institut de Génomique, Génoscope, 2 Rue Gaston Crémieux, Evry F-91000, France
- CNRS, UMR 8030, CP5706, Evry, F-91000, France
- Université d’Evry, UMR 8030, CP5706, Evry, F-91000, France
| | - Samuel Mondy
- CEA, Institut de Génomique, Génoscope, 2 Rue Gaston Crémieux, Evry F-91000, France
- CNRS, UMR 8030, CP5706, Evry, F-91000, France
- Université d’Evry, UMR 8030, CP5706, Evry, F-91000, France
| | - Michael E. Sieracki
- National Science Foundation, 4201 Wilson Boulevard, Arlington, VA 22230, USA
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME 04544, USA
| | - Olivier Jaillon
- CEA, Institut de Génomique, Génoscope, 2 Rue Gaston Crémieux, Evry F-91000, France
- CNRS, UMR 8030, CP5706, Evry, F-91000, France
- Université d’Evry, UMR 8030, CP5706, Evry, F-91000, France
| | - Patrick Wincker
- CEA, Institut de Génomique, Génoscope, 2 Rue Gaston Crémieux, Evry F-91000, France
- CNRS, UMR 8030, CP5706, Evry, F-91000, France
- Université d’Evry, UMR 8030, CP5706, Evry, F-91000, France
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, F-29680, France
- Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, F-29680, France
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)–CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E-08003, Spain
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11
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Kim E, Sprung B, Duhamel S, Filardi C, Kyoon Shin M. Oligotrophic lagoons of the South Pacific Ocean are home to a surprising number of novel eukaryotic microorganisms. Environ Microbiol 2016; 18:4549-4563. [PMID: 27581800 DOI: 10.1111/1462-2920.13523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/30/2016] [Indexed: 12/20/2022]
Abstract
The diversity of microbial eukaryotes was surveyed by environmental sequencing from tropical lagoon sites of the South Pacific, collected through the American Museum of Natural History (AMNH)'s Explore21 expedition to the Solomon Islands in September 2013. The sampled lagoons presented low nutrient concentrations typical of oligotrophic waters, but contained levels of chlorophyll a, a proxy for phytoplankton biomass, characteristic of meso- to eutrophic waters. Two 18S rDNA hypervariable sites, the V4 and V8-V9 regions, were amplified from the total of eight lagoon samples and sequenced on the MiSeq system. After assembly, clustering at 97% similarity, and removal of singletons and chimeras, a total of 2741 (V4) and 2606 (V8-V9) operational taxonomic units (OTUs) were identified. Taxonomic annotation of these reads, including phylogeny, was based on a combination of automated pipeline and manual inspection. About 18.4% (V4) and 13.8% (V8-V9) of the OTUs could not be assigned to any of the known eukaryotic groups. Of these, we focused on OTUs that were not divergent and possessed multiple sources of evidence for their existence. Phylogenetic analyses of these sequences revealed more than ten branches that might represent new deeply-branching lineages of microbial eukaryotes, currently without any cultured representatives or morphological information.
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Affiliation(s)
- Eunsoo Kim
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - Ben Sprung
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Solange Duhamel
- Lamont-Doherty Earth Observatory, Division of Biology and Paleo Environment, Columbia University, Palisades, NY, 10964, USA
| | - Christopher Filardi
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY, 10024, USA
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Nam-Gu, Ulsan, 44610, South Korea
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12
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Richards TA, Leonard G, Mahé F, Del Campo J, Romac S, Jones MDM, Maguire F, Dunthorn M, De Vargas C, Massana R, Chambouvet A. Molecular diversity and distribution of marine fungi across 130 European environmental samples. Proc Biol Sci 2016; 282:rspb.2015.2243. [PMID: 26582030 PMCID: PMC4685826 DOI: 10.1098/rspb.2015.2243] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity and in low abundance in many marine environments, especially in the upper water column. Here, we use a dual approach involving high-throughput diversity tag sequencing from both DNA and RNA templates and fluorescent cell counts to evaluate the diversity and relative abundance of fungi across marine samples taken from six European near-shore sites. We removed very rare fungal operational taxonomic units (OTUs) selecting only OTUs recovered from multiple samples for a detailed analysis. This approach identified a set of 71 fungal 'OTU clusters' that account for 66% of all the sequences assigned to the Fungi. Phylogenetic analyses demonstrated that this diversity includes a significant number of chytrid-like lineages that had not been previously described, indicating that the marine environment encompasses a number of zoosporic fungi that are new to taxonomic inventories. Using the sequence datasets, we identified cases where fungal OTUs were sampled across multiple geographical sites and between different sampling depths. This was especially clear in one relatively abundant and diverse phylogroup tentatively named Novel Chytrid-Like-Clade 1 (NCLC1). For comparison, a subset of the water column samples was also investigated using fluorescent microscopy to examine the abundance of eukaryotes with chitin cell walls. Comparisons of relative abundance of RNA-derived fungal tag sequences and chitin cell-wall counts demonstrate that fungi constitute a low fraction of the eukaryotic community in these water column samples. Taken together, these results demonstrate the phylogenetic position and environmental distribution of 71 lineages, improving our understanding of the diversity and abundance of fungi in marine environments.
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Affiliation(s)
- Thomas A Richards
- Biosciences, University of Exeter, Geoffrey Pope Building, Exeter EX4 4QD, UK Canadian Institute for Advanced Research, CIFAR Program in Integrated Microbial Biodiversity, Toronto, Ontario, Canada M5G 1Z8
| | - Guy Leonard
- Biosciences, University of Exeter, Geoffrey Pope Building, Exeter EX4 4QD, UK
| | - Frédéric Mahé
- CNRS, UMR 7144, EPEP-Évolution des Protistes et des Écosystèmes Pélagiques, Station Biologique de Roscoff, Roscoff 29680, France Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Javier Del Campo
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4 Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Sarah Romac
- CNRS, UMR 7144, EPEP-Évolution des Protistes et des Écosystèmes Pélagiques, Station Biologique de Roscoff, Roscoff 29680, France
| | - Meredith D M Jones
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Finlay Maguire
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Colomban De Vargas
- CNRS, UMR 7144, EPEP-Évolution des Protistes et des Écosystèmes Pélagiques, Station Biologique de Roscoff, Roscoff 29680, France
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Aurélie Chambouvet
- Biosciences, University of Exeter, Geoffrey Pope Building, Exeter EX4 4QD, UK
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13
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Aguilar M, Richardson E, Tan B, Walker G, Dunfield PF, Bass D, Nesbø C, Foght J, Dacks JB. Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water. J Eukaryot Microbiol 2016; 63:732-743. [PMID: 27062087 DOI: 10.1111/jeu.12320] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/25/2016] [Accepted: 03/27/2016] [Indexed: 11/27/2022]
Abstract
Tailings ponds in the Athabasca oil sands (Canada) contain fluid wastes, generated by the extraction of bitumen from oil sands ores. Although the autochthonous prokaryotic communities have been relatively well characterized, almost nothing is known about microbial eukaryotes living in the anoxic soft sediments of tailings ponds or in the thin oxic layer of water that covers them. We carried out the first next-generation sequencing study of microbial eukaryotic diversity in oil sands tailings ponds. In metagenomes prepared from tailings sediment and surface water, we detected very low numbers of sequences encoding eukaryotic small subunit ribosomal RNA representing seven major taxonomic groups of protists. We also produced and analysed three amplicon-based 18S rRNA libraries prepared from sediment samples. These revealed a more diverse set of taxa, 169 different OTUs encompassing up to eleven higher order groups of eukaryotes, according to detailed classification using homology searching and phylogenetic methods. The 10 most abundant OTUs accounted for > 90% of the total of reads, vs. large numbers of rare OTUs (< 1% abundance). Despite the anoxic and hydrocarbon-enriched nature of the environment, the tailings ponds harbour complex communities of microbial eukaryotes indicating that these organisms should be taken into account when studying the microbiology of the oil sands.
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Affiliation(s)
- Maria Aguilar
- Department of Cell Biology, University of Alberta, 510 Medical Sciences Building, Edmonton, AB, T6G 2H7, Canada
| | - Elisabeth Richardson
- Department of Cell Biology, University of Alberta, 510 Medical Sciences Building, Edmonton, AB, T6G 2H7, Canada
| | - BoonFei Tan
- Department of Biological Sciences, CW 405, University of Alberta, Biological Sciences Bldg., Edmonton, AB, T6G 2E9, Canada
| | - Giselle Walker
- Department of Cell Biology, University of Alberta, 510 Medical Sciences Building, Edmonton, AB, T6G 2H7, Canada
| | - Peter F Dunfield
- Department of Biological Sciences, 507 Campus Drive NW, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - David Bass
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, DT4 8UB, United Kingdom
| | - Camilla Nesbø
- Department of Biological Sciences, CW 405, University of Alberta, Biological Sciences Bldg., Edmonton, AB, T6G 2E9, Canada.,CEES, Deptartment of Biosciences, University of Oslo, PO Box 1066, Blindern NO-0316, Oslo, Norway
| | - Julia Foght
- Department of Biological Sciences, CW 405, University of Alberta, Biological Sciences Bldg., Edmonton, AB, T6G 2E9, Canada
| | - Joel B Dacks
- Department of Cell Biology, University of Alberta, 510 Medical Sciences Building, Edmonton, AB, T6G 2H7, Canada. .,Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.
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Nagahama T, Nagano Y. Cultured and uncultured fungal diversity in deep-sea environments. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2016; 53:173-87. [PMID: 22222832 DOI: 10.1007/978-3-642-23342-5_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The importance of fungi found in deep-sea extreme environments is becoming increasingly recognized. In this chapter, current scientific findings on the fungal diversity in several deep-sea environments by conventional culture and culture-independent methods are reviewed and discussed, primarily focused on culture-independent approaches. Fungal species detected by conventional culture methods mostly belonged to Ascomycota and Basidiomycota phyla. Culture-independent approaches have revealed the presence of highly novel fungal phylotypes, including new taxonomic groups placed in deep branches within the phylum Chytridiomycota and unknown ancient fungal groups. Future attempts to culture these unknown fungal groups may provide key insights into the early evolution of fungi and their ecological and physiological significance in deep-sea environments.
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Affiliation(s)
- Takahiko Nagahama
- Department of Food and Nutrition, Higashi-Chikushi Junior College, 5-1-1 Shimoitozu, Kokurakita-ku, Kitakyusyu, Fukuoka, 800-0351, Japan,
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15
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Dupont AÖC, Griffiths RI, Bell T, Bass D. Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs. Environ Microbiol 2016; 18:2010-24. [DOI: 10.1111/1462-2920.13220] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 12/29/2015] [Accepted: 01/08/2016] [Indexed: 11/30/2022]
Affiliation(s)
- A. Ö. C. Dupont
- Department of Life Sciences; the Natural History Museum; Cromwell Road London SW7 5BD UK
| | - R. I. Griffiths
- Centre for Ecology & Hydrology; Benson Lane; Crowmarsh Gifford; Wallingford OX10 8BB UK
| | - T. Bell
- Imperial College London; Silwood Park Campus; Buckhurst Road Ascot Berkshire SL5 7PY UK
| | - D. Bass
- Department of Life Sciences; the Natural History Museum; Cromwell Road London SW7 5BD UK
- Cefas; Barrack Road The Nothe Weymouth DT4 8UB UK
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16
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Noguchi F, Shimamura S, Nakayama T, Yazaki E, Yabuki A, Hashimoto T, Inagaki Y, Fujikura K, Takishita K. Metabolic Capacity of Mitochondrion-related Organelles in the Free-living Anaerobic Stramenopile Cantina marsupialis. Protist 2015; 166:534-50. [PMID: 26436880 DOI: 10.1016/j.protis.2015.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/06/2015] [Accepted: 08/17/2015] [Indexed: 11/26/2022]
Abstract
Functionally and morphologically degenerate mitochondria, so-called mitochondrion-related organelles (MROs), are frequently found in eukaryotes inhabiting hypoxic or anoxic environments. In the last decade, MROs have been discovered from a phylogenetically broad range of eukaryotic lineages and these organelles have been revealed to possess diverse metabolic capacities. In this study, the biochemical characteristics of an MRO in the free-living anaerobic protist Cantina marsupialis, which represents an independent lineage in stramenopiles, were inferred based on RNA-seq data. We found transcripts for proteins known to function in one form of MROs, the hydrogenosome, such as pyruvate:ferredoxin oxidoreductase, iron-hydrogenase, acetate:succinate CoA-transferase, and succinyl-CoA synthase, along with transcripts for acetyl-CoA synthetase (ADP-forming). These proteins possess putative mitochondrial targeting signals at their N-termini, suggesting dual ATP generation systems through anaerobic pyruvate metabolism in Cantina MROs. In addition, MROs in Cantina were also shown to share several features with canonical mitochondria, including amino acid metabolism and an "incomplete" tricarboxylic acid cycle. Transcripts for all four subunits of complex II (CII) of the electron transport chain were detected, while there was no evidence for the presence of complexes I, III, IV, or F1Fo ATPase. Cantina MRO biochemistry challenges the categories of mitochondrial organelles recently proposed.
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Affiliation(s)
- Fumiya Noguchi
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Minato-ku, Tokyo, Japan; Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Shigeru Shimamura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Takuro Nakayama
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Euki Yazaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Tetsuo Hashimoto
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuji Inagaki
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Katsunori Fujikura
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Minato-ku, Tokyo, Japan; Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Kiyotaka Takishita
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Minato-ku, Tokyo, Japan; Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
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17
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Yubuki N, Pánek T, Yabuki A, Čepička I, Takishita K, Inagaki Y, Leander BS. Morphological Identities of Two Different Marine Stramenopile Environmental Sequence Clades: Bicosoeca kenaiensis
(Hilliard, 1971) and Cantina marsupialis
(Larsen and Patterson, 1990) gen. nov., comb. nov. J Eukaryot Microbiol 2015; 62:532-42. [DOI: 10.1111/jeu.12207] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/09/2014] [Accepted: 12/19/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Naoji Yubuki
- The Departments of Botany and Zoology; Beaty Biodiversity Research Centre and Museum; University of British Columbia; Vancouver British Columbia V6T 1Z4 Canada
| | - Tomáš Pánek
- Department of Zoology; Faculty of Science; Charles University in Prague; Prague 128 44 Czech Republic
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka Kanagawa 237-0061 Japan
| | - Ivan Čepička
- Department of Zoology; Faculty of Science; Charles University in Prague; Prague 128 44 Czech Republic
| | - Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Yokosuka Kanagawa 237-0061 Japan
| | - Yuji Inagaki
- Center for Computational Sciences and Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki 305-8577 Japan
| | - Brian S. Leander
- The Departments of Botany and Zoology; Beaty Biodiversity Research Centre and Museum; University of British Columbia; Vancouver British Columbia V6T 1Z4 Canada
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Manohar CS, Menezes LD, Ramasamy KP, Meena RM. Phylogenetic analyses and nitrate-reducing activity of fungal cultures isolated from the permanent, oceanic oxygen minimum zone of the Arabian Sea. Can J Microbiol 2014; 61:217-26. [PMID: 25688692 DOI: 10.1139/cjm-2014-0507] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Reports on the active role of fungi as denitrifiers in terrestrial ecosystems have stimulated an interest in the study of the role of fungi in oxygen-deficient marine systems. In this study, the culturable diversity of fungi was investigated from 4 stations within the permanent, oceanic, oxygen minimum zone of the Arabian Sea. The isolated cultures grouped within the 2 major fungal phyla Ascomycota and Basidiomycota; diversity estimates in the stations sampled indicated that the diversity of the oxygen-depleted environments is less than that of mangrove regions and deep-sea habitats. Phylogenetic analyses of 18S rRNA sequences revealed a few divergent isolates that clustered with environmental sequences previously obtained by others. This is significant, as these isolates represent phylotypes that so far were known only from metagenomic studies and are of phylogenetic importance. Nitrate reduction activity, the first step in the denitrification process, was recorded for isolates under simulated anoxic, deep-sea conditions showing ecological significance of fungi in the oxygen-depleted habitats. This report increases our understanding of fungal diversity in unique, poorly studied habitats and underlines the importance of fungi in the oxygen-depleted environments.
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Affiliation(s)
- Cathrine Sumathi Manohar
- Biological Oceanography Division, CSIR - National Institute of Oceanography, Dona Paula, Goa 403 004, India
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19
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Xu W, Pang KL, Luo ZH. High fungal diversity and abundance recovered in the deep-sea sediments of the Pacific Ocean. MICROBIAL ECOLOGY 2014; 68:688-98. [PMID: 25004994 DOI: 10.1007/s00248-014-0448-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 06/16/2014] [Indexed: 05/26/2023]
Abstract
Knowledge about the presence and ecological significance of bacteria and archaea in the deep-sea environments has been well recognized, but the eukaryotic microorganisms, such as fungi, have rarely been reported. The present study investigated the composition and abundance of fungal community in the deep-sea sediments of the Pacific Ocean. In this study, a total of 1,947 internal transcribed spacer (ITS) regions of fungal rRNA gene clones were recovered from five sediment samples at the Pacific Ocean (water depths ranging from 5,017 to 6,986 m) using three different PCR primer sets. There were 16, 17, and 15 different operational taxonomic units (OTUs) identified from fungal-universal, Ascomycota-, and Basidiomycota-specific clone libraries, respectively. Majority of the recovered sequences belonged to diverse phylotypes of Ascomycota (25 phylotypes) and Basidiomycota (18 phylotypes). The multiple primer approach totally recovered 27 phylotypes which showed low similarities (≤97 %) with available fungal sequences in the GenBank, suggesting possible new fungal taxa occurring in the deep-sea environments or belonging to taxa not represented in the GenBank. Our results also recovered high fungal LSU rRNA gene copy numbers (3.52 × 10(6) to 5.23 × 10(7)copies/g wet sediment) from the Pacific Ocean sediment samples, suggesting that the fungi might be involved in important ecological functions in the deep-sea environments.
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Affiliation(s)
- Wei Xu
- School of Life Sciences, Xiamen University, Xiamen, 361005, People's Republic of China
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20
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Neuhauser S, Kirchmair M, Bulman S, Bass D. Cross-kingdom host shifts of phytomyxid parasites. BMC Evol Biol 2014; 14:33. [PMID: 24559266 PMCID: PMC4016497 DOI: 10.1186/1471-2148-14-33] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 02/13/2014] [Indexed: 11/12/2022] Open
Abstract
Background Phytomyxids (plasmodiophorids and phagomyxids) are cosmopolitan, obligate biotrophic protist parasites of plants, diatoms, oomycetes and brown algae. Plasmodiophorids are best known as pathogens or vectors for viruses of arable crops (e.g. clubroot in brassicas, powdery potato scab, and rhizomania in sugar beet). Some phytomyxid parasites are of considerable economic and ecologic importance globally, and their hosts include important species in marine and terrestrial environments. However most phytomyxid diversity remains uncharacterised and knowledge of their relationships with host taxa is very fragmentary. Results Our molecular and morphological analyses of phytomyxid isolates–including for the first time oomycete and sea-grass parasites–demonstrate two cross-kingdom host shifts between closely related parasite species: between angiosperms and oomycetes, and from diatoms/brown algae to angiosperms. Switching between such phylogenetically distant hosts is generally unknown in host-dependent eukaryote parasites. We reveal novel plasmodiophorid lineages in soils, suggesting a much higher diversity than previously known, and also present the most comprehensive phytomyxid phylogeny to date. Conclusion Such large-scale host shifts between closely related obligate biotrophic eukaryote parasites is to our knowledge unique to phytomyxids. Phytomyxids may readily adapt to a wide diversity of new hosts because they have retained the ability to covertly infect alternative hosts. A high cryptic diversity and ubiquitous distribution in agricultural and natural habitats implies that in a changing environment phytomyxids could threaten the productivity of key species in marine and terrestrial environments alike via host shift speciation.
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Affiliation(s)
- Sigrid Neuhauser
- Institute of Microbiology, Leopold-Franzens University Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria.
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21
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Manohar CS, Boekhout T, Müller WH, Stoeck T. Tritirachium candoliense sp. nov., a novel basidiomycetous fungus isolated from the anoxic zone of the Arabian Sea. Fungal Biol 2014; 118:139-49. [DOI: 10.1016/j.funbio.2013.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 10/25/2013] [Accepted: 10/30/2013] [Indexed: 10/26/2022]
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22
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Glockling SL, Marshall WL, Gleason FH. Phylogenetic interpretations and ecological potentials of the Mesomycetozoea (Ichthyosporea). FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2013.03.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Lax G, Simpson AGB. Combining Molecular Data with Classical Morphology for Uncultured Phagotrophic Euglenids (Excavata): A Single-Cell Approach. J Eukaryot Microbiol 2013; 60:615-25. [DOI: 10.1111/jeu.12068] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/13/2013] [Accepted: 06/05/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Gordon Lax
- Department of Ecology; University of Kaiserslautern; Erwin-Schrödinger-Straβe 14 67663 Kaiserslautern Germany
| | - Alastair G. B. Simpson
- Canadian Institute for Advanced Research; Program in Integrated Microbial Diversity and Department of Biology; Dalhousie University; Halifax Nova Scotia B3H 4R2 Canada
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24
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Manohar CS, Raghukumar C. Fungal diversity from various marine habitats deduced through culture-independent studies. FEMS Microbiol Lett 2013; 341:69-78. [PMID: 23363246 DOI: 10.1111/1574-6968.12087] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/09/2013] [Accepted: 01/10/2013] [Indexed: 11/28/2022] Open
Abstract
Studies on the molecular diversity of the micro-eukaryotic community have shown that fungi occupy a central position in a large number of marine habitats. Environmental surveys using molecular tools have shown the presence of fungi from a large number of marine habitats such as deep-sea habitats, pelagic waters, coastal regions, hydrothermal vent ecosystem, anoxic habitats, and ice-cold regions. This is of interest to a variety of research disciplines like ecology, evolution, biogeochemistry, and biotechnology. In this review, we have summarized how molecular tools have helped to broaden our understanding of the fungal diversity in various marine habitats. Majority of the environmental phylotypes could be grouped as novel clades within Ascomycota, Basidiomycota, and Chytridiomycota or as basal fungal lineages. Deep-branching novel environmental clusters could be grouped within Ascomycota as the Pezizomycotina clone group, deep-sea fungal group-I, and soil clone group-I, within Basidiomycota as the hydrothermal and/or anaerobic fungal group, and within Chytridiomycota as Cryptomycota or the Rozella clade. However, a basal true marine environmental cluster is still to be identified as most of the clusters include representatives from terrestrial regions. The challenge for future research is to explore the true marine fungi using molecular techniques.
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Affiliation(s)
- Cathrine Sumathi Manohar
- Biological Oceanography Division, National Institute of Oceanography - Council of Scientific and Industrial Research, Dona Paula, Goa, India.
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25
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Xu Y, Shao C, Miao M, Song W. Redescription of Parasonderia vestita () comb. nov. (Ciliophora, Plagiopylida), with notes on its phylogeny based on SSU rRNA gene. Eur J Protistol 2013; 49:106-13. [DOI: 10.1016/j.ejop.2012.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 03/09/2012] [Accepted: 03/09/2012] [Indexed: 10/28/2022]
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26
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Reconstruction of the feeding apparatus in Postgaardi mariagerensis provides evidence for character evolution within the Symbiontida (Euglenozoa). Eur J Protistol 2013; 49:32-9. [DOI: 10.1016/j.ejop.2012.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/07/2012] [Accepted: 07/13/2012] [Indexed: 11/30/2022]
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27
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28
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Thaler M, Lovejoy C. Distribution and diversity of a protist predator Cryothecomonas (Cercozoa) in Arctic marine waters. J Eukaryot Microbiol 2012; 59:291-9. [PMID: 22703332 DOI: 10.1111/j.1550-7408.2012.00631.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 05/02/2012] [Accepted: 05/12/2012] [Indexed: 11/30/2022]
Abstract
Heterotrophic nanoflagellates (HNFs) are key components in microbial food webs, potentially influencing community composition via top-down control of their favored prey or host. Marine cercozoan Cryothecomonas species are parasitoid and predatory HNFs that have been reported from ice, sediments, and the water column. Although Cryothecomonas is frequently reported from Arctic and subarctic seas, factors determining its occurrence are not known. We investigated the temporal and geographic distribution of Cryothecomonas in Canadian Arctic seas during the summer and autumn periods from 2006 to 2010. We developed a Cryothecomonas-specific fluorescent in situ hybridization (FISH) probe targeting ribosomal 18S rRNA to estimate cell concentrations in natural and manipulated samples. Comparison of simple and partial correlation coefficients showed that salinity, depth, and overall community biomass are important factors determining Cryothecomonas abundance. We found no evidence of parasitism in our samples. Hybridized cells included individuals smaller than any formally described Cryothecomonas, suggesting the presence of novel taxa or unknown life stages in this genus. A positive relationship between Cryothecomonas abundance and ice and meltwater suggests that it is a sensitive indicator of ice melt in Arctic water columns.
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Affiliation(s)
- Mary Thaler
- Département de Biologie, Québec-Océan and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
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29
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Edgcomb VP, Biddle JF. Microbial Eukaryotes in the Marine Subsurface? CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2012. [DOI: 10.1007/978-94-007-1896-8_25] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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30
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Jebaraj CS, Forster D, Kauff F, Stoeck T. Molecular Diversity of Fungi from Marine Oxygen-Deficient Environments (ODEs). PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2012; 53:189-208. [PMID: 22222833 DOI: 10.1007/978-3-642-23342-5_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Molecular diversity surveys of marine fungi have demonstrated that the species richness known to date is just the tip of the iceberg and that there is a large extent of unknown fungal diversity in marine habitats. Reports of novel fungal lineages at higher taxonomic levels are documented from a large number of marine habitats, including the various marine oxygen-deficient environments (ODEs). In the past few years, a strong focus of eukaryote diversity research has been on a variety of ODEs, as these environments are considered to harbor a large number of organisms, which are highly divergent to known diversity and could provide insights into the early eukaryotic evolution. ODEs that have been targeted so far include shallow water sediments, hydrothermal vent systems, deep-sea basins, intertidal habitats, and fjords. Most, if not all, molecular diversity studies in marine ODEs have shown, that contrary to previous assumptions, fungi contribute significantly to the micro-eukaryotic community in such habitats. In this chapter, we have reanalyzed the environmental fungal sequences obtained from the molecular diversity survey in 14 different sites to obtain a comprehensive picture of fungal diversity in these marine habitats. The phylogenetic analysis of the fungal environmental sequences from various ODEs have grouped these sequences into seven distinct clades (Clade 1-7) clustering with well-known fungal taxa. Apart from this, four environmental clades (EnvClade A, B, C, and D) with exclusive environmental sequences were also identified. This has provided information on the positioning of the environmental sequences at different taxonomic levels within the major fungal phylums. The taxonomic distribution of these environmental fungal sequences into clusters and clades has also shown that they are not restricted by geographical boundaries. The distribution pattern together with the reports on the respiratory abilities of fungi under reduced oxygen conditions shows that they are highly adaptive and may have a huge ecological role in these oxygen deficient habitats.
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Affiliation(s)
- Cathrine Sumathi Jebaraj
- National Institute of Oceanography, Council of Scientific and Industrial Research, Dona Paula, 403 004, Goa, India,
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31
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Saccà A. The Role of Eukaryotes in the Anaerobic Food Web of Stratified Lakes. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2012. [DOI: 10.1007/978-94-007-1896-8_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Wylezich C, Jürgens K. Protist diversity in suboxic and sulfidic waters of the Black Sea. Environ Microbiol 2011; 13:2939-56. [DOI: 10.1111/j.1462-2920.2011.02569.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Boere AC, Rijpstra WIC, De Lange GJ, Sinninghe Damsté JS, Coolen MJL. Preservation potential of ancient plankton DNA in Pleistocene marine sediments. GEOBIOLOGY 2011; 9:377-393. [PMID: 21884361 DOI: 10.1111/j.1472-4669.2011.00290.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Recent studies have shown that ancient plankton DNA can be recovered from Holocene lacustrine and marine sediments, including from species that do not leave diagnostic microscopic fossils in the sediment record. Therefore, the analysis of this so-called fossil plankton DNA is a promising approach for refining paleoecological and paleoenvironmental information. However, further studies are needed to reveal whether DNA of past plankton is preserved beyond the Holocene. Here, we identified past eukaryotic plankton members based on 18S rRNA gene profiling in eastern Mediterranean Holocene and Pleistocene sapropels S1 (~9 ka), S3 (~80 ka), S4 (~105 ka), and S5 (~125 ka). The majority of preserved ~400- to 500-bp-long 18S rDNA fragments of microalgae that were studied in detail (i.e. from haptophyte algae and dinoflagellates) were found in the youngest sapropel S1, whereas their specific lipid biomarkers (long-chain alkenones and dinosterol) were also abundant in sediments deposited between 80 and 124 ka BP. The late-Pleistocene sediments mainly contained eukaryotic DNA of marine fungi and from terrestrial plants, which could have been introduced via the river Nile at the time of deposition and preserved in pollen grains. A parallel analysis of Branched and Isoprenoid Tetraethers (i.e. BIT index) showed that most of the organic matter in the eastern Mediterranean sediment record was of marine (e.g. pelagic) origin. Therefore, the predominance of terrestrial plant DNA over plankton DNA in older sapropels suggests a preferential degradation of marine plankton DNA.
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Affiliation(s)
- A C Boere
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
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Katz LA, Grant J, Parfrey LW, Gant A, O'Kelly CJ, Anderson OR, Molestina RE, Nerad T. Subulatomonas tetraspora nov. gen. nov. sp. is a member of a previously unrecognized major clade of eukaryotes. Protist 2011; 162:762-73. [PMID: 21723191 DOI: 10.1016/j.protis.2011.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 04/18/2011] [Indexed: 11/18/2022]
Abstract
While a large number of aerobic free-living protists have been described within the last decade, the number of new anaerobic or microaerophilic microbial eukaryotic taxa has lagged behind. Here we describe a microaerophilic genus and species of amoeboflagellate isolated from a near-shore marine site off the coast at Plymouth, Massachusetts: Subulatomonas tetraspora nov. gen. nov. sp. This taxon is closely related to Breviata anathema based on both microscopical features and phylogenetic analyses of sequences of three genes: SSU-rDNA, actin, and alpha-tubulin. However, Subulatomonas tetraspora nov. gen. nov. sp. and B. anathema are morphologically distinctive, differ by 14.9% at their SSU-rDNA locus, and were isolated from marine and 'slightly brackish' environments, respectively. Phylogenetic analyses of these two taxa plus closely related sequences from environmental surveys provide support for a novel clade of eukaryotes that is distinct from the major clades including the Opisthokonta, Excavata, Amoebozoa and 'SAR' (Stramenopile, Alveolate, Rhizaria).
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Affiliation(s)
- Laura A Katz
- Department of Biological Sciences, Smith College, 44 College Lane, Northampton, Massachusetts 01063, USA.
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Nagahama T, Takahashi E, Nagano Y, Abdel-Wahab MA, Miyazaki M. Molecular evidence that deep-branching fungi are major fungal components in deep-sea methane cold-seep sediments. Environ Microbiol 2011; 13:2359-70. [PMID: 21605311 DOI: 10.1111/j.1462-2920.2011.02507.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The motile cells of chytrids were once believed to be relics from the time before the colonization of land by fungi. However, the majority of chytrids had not been found in marine but freshwater environments. We investigated fungal diversity by a fungal-specific PCR-based analysis of environmental DNA in deep-sea methane cold-seep sediments, identifying a total of 35 phylotypes, 12 of which were early diverging fungi (basal fungi, ex 'lower fungi'). The basal fungi occupied a major portion of fungal clones. These were phylogenetically placed into a deep-branching clade of fungi and the LKM11 clade that was a divergent group comprised of only environmental clones from aquatic environments. As suggested by Lara and colleagues, species of the endoparasitic genus Rozella, being recently considered of the earliest branching taxa of fungi, were nested within the LKM11 clade. In the remaining 23 phylotypes identified as the Dikarya, the majority of which were similar to those which appeared in previously deep-sea studies, but also highly novel lineages associated with Soil Clone Group I (SCGI), Entorrhiza sp. and the agaricomycetous fungi were recorded. The fungi of the Dikarya may play a role in the biodegradation of lignin and lignin-derived materials in deep-sea, because the characterized fungal species related to the frequent phylotypes within the Dikarya have been reported to possess an ability to degrade lignin.
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Affiliation(s)
- Takahiko Nagahama
- Department of Foods and Human Nutrition, Higashi-Chikushi Junior College, 5-1-1 Shimoitozu, Kokurakita-ku, Kitakyusyu, 803-8511, Japan.
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Kolisko M, Silberman JD, Cepicka I, Yubuki N, Takishita K, Yabuki A, Leander BS, Inouye I, Inagaki Y, Roger AJ, Simpson AGB. A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats. Environ Microbiol 2011; 12:2700-10. [PMID: 20482740 DOI: 10.1111/j.1462-2920.2010.02239.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the last 15 years classical culturing and environmental PCR techniques have revealed a modest number of genuinely new major lineages of protists; however, some new groups have greatly influenced our understanding of eukaryote evolution. We used culturing techniques to examine the diversity of free-living protists that are relatives of diplomonads and retortamonads, a group of evolutionary and parasitological importance. Until recently, a single organism, Carpediemonas membranifera, was the only representative of this region of the tree. We report 18 new isolates of Carpediemonas-like organisms (CLOs) from anoxic marine sediments. Only one is a previously cultured species. Eleven isolates are conspecific and were classified within a new genus, Kipferlia n. gen. The remaining isolates include representatives of three other lineages that likely represent additional undescribed genera (at least). Small-subunit ribosomal RNA gene phylogenies show that CLOs form a cloud of six major clades basal to the diplomonad-retortamonad grouping (i.e. each of the six CLO clades is potentially as phylogenetically distinct as diplomonads and retortamonads). CLOs will be valuable for tracing the evolution of diplomonad cellular features, for example, their extremely reduced mitochondrial organelles. It is striking that the majority of CLO diversity was undetected by previous light microscopy surveys and environmental PCR studies, even though they inhabit a commonly sampled environment. There is no reason to assume this is a unique situation - it is likely that undersampling at the level of major lineages is still widespread for protists.
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Affiliation(s)
- Martin Kolisko
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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Neuhauser S, Kirchmair M, Gleason FH. The ecological potentials of Phytomyxea ("plasmodiophorids") in aquatic food webs. HYDROBIOLOGIA 2011; 659:23-35. [PMID: 21339888 PMCID: PMC3040567 DOI: 10.1007/s10750-010-0508-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 09/14/2010] [Accepted: 09/24/2010] [Indexed: 05/18/2023]
Abstract
The Phytomyxea ("plasmodiophorids") including both Plasmodiophorida and Phagomyxida is a monophyletic group of Eukaryotes composed of obligate biotrophic parasites of green plants, brown algae, diatoms and stramenopiles commonly found in many freshwater, soil and marine environments. However, most research on Phytomyxea has been restricted to plant pathogenic species with agricultural importance, thereby missing the huge ecological potential of this enigmatic group of parasites. Members of the Phytomyxea can induce changes in biomass in their hosts (e.g. hypertrophies of the host tissue) under suitable environmental conditions. Upon infection they alter the metabolism of their hosts, consequently changing the metabolic status of their host. This results in an altered chemical composition of the host tissue, which impacts the diversity of species which feed on the tissues of the infected host and on the zoospores produced by the parasites. Furthermore, significant amounts of nutrients derived from the hosts, both primary producers (plants and algae) and primary consumers (litter decomposers and plant parasites [Oomycetes]), can enter the food web at different trophic levels in form of zoospores and resting spores. Large numbers of zoospores and resting spores are produced which can be eaten by secondary and tertiary consumers, such as grazing zooplankton and metazoan filter-feeders. Therefore, these microbes can act as energy-rich nutrient resources which may significantly alter the trophic relationships in fresh water, soil and marine habitats. Based on the presented data, Phytomyxea can significantly contribute to the complexity and energy transfer within food webs.
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Affiliation(s)
- Sigrid Neuhauser
- Institute of Microbiology, Leopold Franzens-University Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Martin Kirchmair
- Institute of Microbiology, Leopold Franzens-University Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Frank H. Gleason
- School of Biological Sciences A12, University of Sydney, Sydney, NSW 2006 Australia
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Breglia SA, Yubuki N, Hoppenrath M, Leander BS. Ultrastructure and molecular phylogenetic position of a novel euglenozoan with extrusive episymbiotic bacteria: Bihospites bacati n. gen. et sp. (Symbiontida). BMC Microbiol 2010; 10:145. [PMID: 20482870 PMCID: PMC2881021 DOI: 10.1186/1471-2180-10-145] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 05/19/2010] [Indexed: 11/24/2022] Open
Abstract
Background Poorly understood but highly diverse microbial communities exist within anoxic and oxygen-depleted marine sediments. These communities often harbour single-celled eukaryotes that form symbiotic associations with different prokaryotes. During low tides in South-western British Columbia, Canada, vast areas of marine sand become exposed, forming tidal pools. Oxygen-depleted sediments within these pools are distinctively black at only 2-3 cm depth; these layers contain a rich variety of microorganisms, many of which are undescribed. We discovered and characterized a novel (uncultivated) lineage of heterotrophic euglenozoan within these environments using light microscopy, scanning and transmission electron microscopy, serial sectioning and ultrastructural reconstruction, and molecular phylogenetic analyses of small subunit rDNA sequences. Results Bihospites bacati n. gen. et sp. is a biflagellated microbial eukaryote that lives within low-oxygen intertidal sands and dies within a few hours of exposure to atmospheric oxygen. The cells are enveloped by two different prokaryotic episymbionts: (1) rod-shaped bacteria and (2) longitudinal strings of spherical bacteria, capable of ejecting an internal, tightly wound thread. Ultrastructural data showed that B. bacati possesses all of the euglenozoan synapomorphies. Moreover, phylogenetic analyses of SSU rDNA sequences demonstrated that B. bacati groups strongly with the Symbiontida: a newly established subclade within the Euglenozoa that includes Calkinsia aureus and other unidentified organisms living in low-oxygen sediments. B. bacati also possessed novel features, such as a compact C-shaped rod apparatus encircling the nucleus, a cytostomal funnel and a distinctive cell surface organization reminiscent of the pellicle strips in phagotrophic euglenids. Conclusions We characterized the ultrastructure and molecular phylogenetic position of B. bacati n. gen. et sp. Molecular phylogenetic analyses demonstrated that this species belongs to the Euglenozoa and currently branches as the earliest diverging member of the Symbiontida. This is concordant with ultrastructural features of B. bacati that are intermediate between C. aureus and phagotrophic euglenids, indicating that the most recent ancestor of the Symbiontida descended from phagotrophic euglenids. Additionally, the extrusive episymbionts in B. bacati are strikingly similar to so-called "epixenosomes", prokaryotes previously described in a ciliate species and identified as members of the Verrucomicrobia. These parallel symbioses increase the comparative context for understanding the origin(s) of extrusive organelles in eukaryotes and underscores how little we know about the symbiotic communities of marine benthic environments.
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Affiliation(s)
- Susana A Breglia
- Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, Canada
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TAKISHITA KIYOTAKA, KAKIZOE NATSUKI, YOSHIDA TAKAO, MARUYAMA TADASHI. Molecular Evidence that Phylogenetically Diverged Ciliates Are Active in Microbial Mats of Deep-Sea Cold-Seep Sediment. J Eukaryot Microbiol 2010; 57:76-86. [DOI: 10.1111/j.1550-7408.2009.00457.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Jebaraj CS, Raghukumar C, Behnke A, Stoeck T. Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation. FEMS Microbiol Ecol 2009; 71:399-412. [PMID: 20002178 DOI: 10.1111/j.1574-6941.2009.00804.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
In order to study fungal diversity in oxygen minimum zones of the Arabian Sea, we analyzed 1440 cloned small subunit rRNA gene (18S rRNA gene) sequences obtained from environmental samples using three different PCR primer sets. Restriction fragment length polymorphism (RFLP) analyses yielded 549 distinct RFLP patterns, 268 of which could be assigned to fungi (Dikarya and zygomycetes) after sequence analyses. The remaining 281 RFLP patterns represented a variety of nonfungal taxa, even when using putatively fungal-specific primers. A substantial number of fungal sequences were closely related to environmental sequences from a range of other anoxic marine habitats, but distantly related to known sequences of described fungi. Community similarity analyses suggested distinctively different structures of fungal communities from normoxic sites, seasonally anoxic sites and permanently anoxic sites, suggesting different adaptation strategies of fungal communities to prevailing oxygen conditions. Additionally, we obtained 26 fungal cultures from the study sites, most of which were closely related (>97% sequence similarity) to well-described Dikarya. This indicates that standard cultivation mainly produces more of what is already known. However, two of these cultures were highly divergent to known sequences and seem to represent novel fungal groups on high taxonomic levels. Interestingly, none of the cultured isolates is identical to any of the environmental sequences obtained. Our study demonstrates the importance of a multiple-primer approach combined with cultivation to obtain deeper insights into the true fungal diversity in environmental samples and to enable adequate intersample comparisons of fungal communities.
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Affiliation(s)
- Cathrine S Jebaraj
- National Institute of Oceanography (Council of Scientific and Industrial Research), Dona Paula, Goa, India
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Hoppenrath M, Leander BS. Molecular phylogeny of Parvilucifera prorocentri (Alveolata, Myzozoa): Insights into perkinsid character evolution. J Eukaryot Microbiol 2009; 56:251-6. [PMID: 19527352 DOI: 10.1111/j.1550-7408.2009.00395.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Perkinsids and colpodellids are lineages that diverged near the origins of dinoflagellates and apicomplexans, respectively, and provide compelling insights into the earliest stages of alveolate evolution. Perkinsids, including Perkinsus and Parvilucifera, are intracellular parasites of animals and dinoflagellates and possess traits also known in syndineans, dinokaryotes (mainly free living dinoflagellates), and colpodellids. An improved understanding of perkinsid biodiversity and phylogeny is expected to shed considerable light on the evolutionary origins of syndineans and dinokaryotes as well as the cellular identities of environmental sequences derived from marine and freshwater habitats. Accordingly, the small subunit (SSU) rDNA sequence from Parvilucifera prorocentri, a tube-forming intracellular parasite of the marine benthic dinoflagellate Prorocentrum fukuyoi, was determined. Molecular phylogenetic analyses demonstrated, with very high statistical support, that P. prorocentri branched as a sister lineage to a divergent clade consisting of Parvilucifera infectans and Parvilucifera sinerae. The entire Parvilucifera clade was nested within a more inclusive and modestly supported clade consisting of Perkinsus and several environmental sequences. Because P. prorocentri possessed a novel combination of ultrastructural features known in Perkinsus, Parvilucifera, and/or syndineans (i.e. germ tubes, trichocysts, and a syndinean-like nucleus), establishing the molecular phylogenetic position of this species enabled us to build a more comprehensive framework for understanding the earliest stages in the evolution of myzozoans.
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Affiliation(s)
- Mona Hoppenrath
- Department of Botany and Zoology, University of British Columbia, Vancouver, Canada.
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Relative diversity and community structure of ciliates in stream biofilms according to molecular and microscopy methods. Appl Environ Microbiol 2009; 75:5261-72. [PMID: 19561192 DOI: 10.1128/aem.00412-09] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ciliates are an important component of aquatic ecosystems, acting as predators of bacteria and protozoa and providing nutrition for organisms at higher trophic levels. Understanding of the diversity and ecological role of ciliates in stream biofilms is limited, however. Ciliate diversity in biofilm samples from four streams subject to different impacts by human activity was assessed using microscopy and terminal restriction fragment length polymorphism (T-RFLP) analysis of 18S rRNA sequences. Analysis of 3' and 5' terminal fragments yielded very similar estimates of ciliate diversity. The diversity detected using microscopy was consistently lower than that suggested by T-RFLP analysis, indicating the existence of genetic diversity not apparent by morphological examination. Microscopy and T-RFLP analyses revealed similar relative trends in diversity between different streams, with the lowest level of biofilm-associated ciliate diversity found in samples from the least-impacted stream and the highest diversity in samples from moderately to highly impacted streams. Multivariate analysis provided evidence of significantly different ciliate communities in biofilm samples from different streams and seasons, particularly between a highly degraded urban stream and less impacted streams. Microscopy and T-RFLP data both suggested the existence of widely distributed, resilient biofilm-associated ciliates as well as ciliate taxa restricted to sites with particular environmental conditions, with cosmopolitan taxa being more abundant than those with restricted distributions. Differences between ciliate assemblages were associated with water quality characteristics typical of urban stream degradation and may be related to factors such as nutrient availability and macroinvertebrate communities. Microscopic and molecular techniques were considered to be useful complementary approaches for investigation of biofilm ciliate communities.
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CHO BYUNGCHEOL, PARK JONGSOO, XU KUIDONG, CHOI JOONGKI. Morphology and Molecular Phylogeny ofTrimyema koreanumn. sp., a Ciliate from the Hypersaline Water of a Solar Saltern. J Eukaryot Microbiol 2008; 55:417-26. [DOI: 10.1111/j.1550-7408.2008.00340.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Mentel M, Martin W. Energy metabolism among eukaryotic anaerobes in light of Proterozoic ocean chemistry. Philos Trans R Soc Lond B Biol Sci 2008; 363:2717-29. [PMID: 18468979 PMCID: PMC2606767 DOI: 10.1098/rstb.2008.0031] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent years have witnessed major upheavals in views about early eukaryotic evolution. One very significant finding was that mitochondria, including hydrogenosomes and the newly discovered mitosomes, are just as ubiquitous and defining among eukaryotes as the nucleus itself. A second important advance concerns the readjustment, still in progress, about phylogenetic relationships among eukaryotic groups and the roughly six new eukaryotic supergroups that are currently at the focus of much attention. From the standpoint of energy metabolism (the biochemical means through which eukaryotes gain their ATP, thereby enabling any and all evolution of other traits), understanding of mitochondria among eukaryotic anaerobes has improved. The mainstream formulations of endosymbiotic theory did not predict the ubiquity of mitochondria among anaerobic eukaryotes, while an alternative hypothesis that specifically addressed the evolutionary origin of energy metabolism among eukaryotic anaerobes did. Those developments in biology have been paralleled by a similar upheaval in the Earth sciences regarding views about the prevalence of oxygen in the oceans during the Proterozoic (the time from ca 2.5 to 0.6 Ga ago). The new model of Proterozoic ocean chemistry indicates that the oceans were anoxic and sulphidic during most of the Proterozoic. Its proponents suggest the underlying geochemical mechanism to entail the weathering of continental sulphides by atmospheric oxygen to sulphate, which was carried into the oceans as sulphate, fueling marine sulphate reducers (anaerobic, hydrogen sulphide-producing prokaryotes) on a global scale. Taken together, these two mutually compatible developments in biology and geology underscore the evolutionary significance of oxygen-independent ATP-generating pathways in mitochondria, including those of various metazoan groups, as a watermark of the environments within which eukaryotes arose and diversified into their major lineages.
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Marshall WL, Celio G, McLaughlin DJ, Berbee ML. Multiple isolations of a culturable, motile Ichthyosporean (Mesomycetozoa, Opisthokonta), Creolimax fragrantissima n. gen., n. sp., from marine invertebrate digestive tracts. Protist 2008; 159:415-33. [PMID: 18539526 DOI: 10.1016/j.protis.2008.03.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 03/22/2008] [Indexed: 10/22/2022]
Abstract
A fragrant, spherical, osmotrophic eukaryote was isolated 27 times from the digestive tracts of marine invertebrates collected from the Northeast Pacific. The isolates were cultured from 7 animal collections over a 2-year period, most from the peanut worm, Phascolosoma agassizii. A small subunit ribosomal DNA phylogeny placed the spherical organism within the ichthyosporea, closest to Sphaeroforma arctica and Pseudoperkinsus tapetis. Supporting the close relationship of isolates, the sequences of ribosomal gene internal transcribed spacers determined for 26 isolates were identical, as were the elongation factor 1-alpha-like gene fragments from 7 isolates. Dispersal via amoeboid cells distinguished this species from its closest relatives and led to the erection of a new genus and species, "Creolimax fragrantissima." Vegetative cells reproduced asexually in vitro after they reached 30-60 microm in diameter by producing amoebae or endospores, which escaped through openings in the parent cell wall. Ultrathin sections of vegetative cells prepared by high-pressure-freeze substitution provided some of the first images of ichthyosporean spindle pole bodies and document, for the first time, tubular extensions of the plasma membrane into an electron-translucent inner layer of the cell wall. Ichthyosporeans are parasites and commensals of animals and culturable species are few. Because "C. fragrantissima" can be isolated regularly and repeatedly from nature and then grown easily through cycles of asexual reproduction, it has the potential to serve as a model organism for further research into marine ichthyosporeans.
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Affiliation(s)
- Wyth L Marshall
- Department of Botany, University of British Columbia, Vancouver, B.C., Canada V6T 1Z4.
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Ultrastructure of a novel tube-forming, intracellular parasite of dinoflagellates: Parvilucifera prorocentri sp. nov. (Alveolata, Myzozoa). Eur J Protistol 2008; 44:55-70. [DOI: 10.1016/j.ejop.2007.08.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 08/16/2007] [Accepted: 08/21/2007] [Indexed: 11/18/2022]
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Leander BS. Marine gregarines: evolutionary prelude to the apicomplexan radiation? Trends Parasitol 2008; 24:60-7. [PMID: 18226585 DOI: 10.1016/j.pt.2007.11.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 10/18/2007] [Accepted: 11/08/2007] [Indexed: 11/25/2022]
Abstract
Gregarine apicomplexans inhabit the intestines, coeloms and reproductive vesicles of invertebrates. An emphasis on specific ancestral characteristics in marine gregarines has given the group a reputation of being 'primitive.' Although some lineages have retained characteristics inferred to be ancestral for the group, and perhaps apicomplexans as a whole, most gregarines represent highly derived parasites with novel ultrastructural and behavioral adaptations. Many marine gregarines have become giants among single-celled organisms and have evolved ornate surface structures. A comparison of gregarine morphology, placed in a modern phylogenetic context, helps clarify the earliest stages of apicomplexan evolution, the origin of Cryptosporidium, and specific cases of convergent evolution within the group and beyond.
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Affiliation(s)
- Brian S Leander
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Takishita K, Yubuki N, Kakizoe N, Inagaki Y, Maruyama T. Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures. Extremophiles 2007; 11:563-76. [PMID: 17426921 DOI: 10.1007/s00792-007-0068-z] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Accepted: 02/19/2007] [Indexed: 10/23/2022]
Abstract
Recent culture-independent surveys of eukaryotic small-subunit ribosomal DNA (SSU rDNA) from many environments have unveiled unexpectedly high diversity of microbial eukaryotes (microeukaryotes) at various taxonomic levels. However, such surveys were most probably biased by various technical difficulties, resulting in underestimation of microeukaryotic diversity. In the present study on oxygen-depleted sediment from a deep-sea methane cold seep of Sagami Bay, Japan, we surveyed the diversity of eukaryotic rDNA in raw sediment samples and in two enrichment cultures. More than half of all clones recovered from the raw sediment samples were of the basidiomycetous fungus Cryptococcus curvatus. Among other clones, phylotypes of eukaryotic parasites, such as Apicomplexa, Ichthyosporea, and Phytomyxea, were identified. On the other hand, we observed a marked difference in phylotype composition in the enrichment samples. Several phylotypes belonging to heterotrophic stramenopiles were frequently found in one enrichment culture, while a phylotype of Excavata previously detected at a deep-sea hydrothermal vent dominated the other. We successfully established a clonal culture of this excavate flagellate. Since these phylotypes were not identified in the raw sediment samples, the approach incorporating a cultivation step successfully found at least a fraction of the "hidden" microeukaryotic diversity in the environment examined.
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Affiliation(s)
- Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan.
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