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High molecular diversity in the functional group of small bacterivorous non-scaled chrysomonad flagellates. Eur J Protistol 2022; 86:125915. [DOI: 10.1016/j.ejop.2022.125915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/21/2022]
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2
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Rybarski AE, Nitsche F, Soo Park J, Filz P, Schmidt P, Kondo R, Gb Simpson A, Arndt H. Revision of the phylogeny of Placididea (Stramenopiles): Molecular and morphological diversity of novel placidid protists from extreme aquatic environments. Eur J Protistol 2021; 81:125809. [PMID: 34673437 DOI: 10.1016/j.ejop.2021.125809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022]
Abstract
Recent studies suggested that the diversity of microbial eukaryotes in hypersaline environments is widely underestimated. Placidids are a group of heterotrophic stramenopile flagellates that are frequently found in these environments, but up to now only very few species were isolated and fully described, mostly from marine or brackish water sites. In this study, we extend the known diversity of Placididea by three new genera (Allegra, Haloplacidia, and Placilonga) compromising nine new species, isolated from athalassic, mostly hypersaline environments (Allegra dunaii, Allegra atacamiensis, Allegra hypersalina, Haloplacidia cosmopolita, Suigetsumonas keniensis) and marine waters (Placilonga atlantica, Placidia azorensis, Placidia abyssalis, Wobblia pacifica) including a description of their morphology and molecular phylogeny. In total, 36 strains were comparatively analysed. Studies from athalassic waters revealed an especially high number of different genotypes. A multigene analysis based on a ten genes dataset revealed a clear separation into marine, athalassic and brackish water clades. Several representatives were found to cope with hypersaline conditions from 20 to 250 PSU, even up to 284 PSU, suggesting that they may form a halotolerant group.
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Affiliation(s)
- Alexandra E Rybarski
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Frank Nitsche
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Jong Soo Park
- Department of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Paulina Filz
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Patricia Schmidt
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui 917-0003, Japan
| | | | - Hartmut Arndt
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany.
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3
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Venter PC, Nitsche F, Arndt H. The Hidden Diversity of Flagellated Protists in Soil. Protist 2018; 169:432-449. [PMID: 29870898 DOI: 10.1016/j.protis.2018.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 11/18/2022]
Abstract
Protists are among the most diverse and abundant eukaryotes in soil. However, gaps between described and sequenced protist morphospecies still present a pending problem when surveying environmental samples for known species using molecular methods. The number of sequences in the molecular PR2 database (∼130,000) is limited compared to the species richness expected (>1 million protist species) - limiting the recovery rate. This is important, since high throughput sequencing (HTS) methods are used to find associative patterns between functional traits, taxa and environmental parameters. We performed HTS to survey soil flagellates in 150 grasslands of central Europe, and tested the recovery rate of ten previously isolated and cultivated cercomonad species, among locally found diversity. We recovered sequences for reference soil flagellate species, but also a great number of their phylogenetically evaluated genetic variants, among rare and dominant taxa with presumably own biogeography. This was recorded among dominant (cercozoans, Sandona), rare (apusozoans) and a large hidden diversity of predominantly aquatic protists in soil (choanoflagellates, bicosoecids) often forming novel clades associated with uncultured environmental sequences. Evaluating the reads, instead of the OTUs that individual reads are usually clustered into, we discovered that much of this hidden diversity may be lost due to clustering.
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Affiliation(s)
- Paul Christiaan Venter
- University of Cologne, Cologne Biocenter, Institute of Zoology, Department of General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany
| | - Frank Nitsche
- University of Cologne, Cologne Biocenter, Institute of Zoology, Department of General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany
| | - Hartmut Arndt
- University of Cologne, Cologne Biocenter, Institute of Zoology, Department of General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany.
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4
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Discrepancies Between Molecular and Morphological Databases of Soil Ciliates Studied for Temperate Grasslands of Central Europe. Protist 2018; 169:521-538. [PMID: 29936291 DOI: 10.1016/j.protis.2018.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 03/27/2018] [Accepted: 04/08/2018] [Indexed: 01/01/2023]
Abstract
By measuring the change in soil protist communities, the effect of human land use on grasslands can be monitored to promote sustainable ecosystem functioning. Protists form the active link in the rhizosphere between the plant roots and higher trophic organisms; however, only few morphological species and their ecological values have yet been described in this context. To investigate the communicability between morphological and molecular databases used in the molecular barcoding of protists and in the biomonitoring of grassland soil, the present high-throughput sequencing (HTS) study (N=150) covered the area of central Europe (mesoscale) known to be well studied for ciliated protists. HTS delivered 2,404 unique reads identifying taxa in all major ciliophoran classes but exact reference matches were few. The study identified clear discrepancies between databases for well-studied taxa, where molecular databases contained multiple gene variants for single morphospecies of dominant taxa. Gene variants presented own biogeography - the eukaryotic microdiversity along gradients (e.g., land-use intensity, soil water). It is possible that many of the so called novel phylogenetic lineages and hidden diversity pointed out in environmental surveys could be evidence for the severe lack of molecular data for already known and morphologically described species, present in morphological databases.
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5
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Ngo CN, Braithwaite KS, Bass D, Young AJ, Croft BJ. Phytocercomonas venanatans, a New Species of Cercozoa Associated with Chlorotic Streak of Sugarcane. PHYTOPATHOLOGY 2018; 108:479-486. [PMID: 29256830 DOI: 10.1094/phyto-07-17-0237-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Chlorotic streak is a global disease of commercial sugarcane (Saccharum spp. hybrids). The disease is transmitted by wet soil, water, as well as in diseased planting material. Although first recognized almost 90 years ago and despite significant research effort, the identity of the causal agent has been elusive. Metagenomic high throughput sequencing (HTS) facilitated the discovery of novel protistan ribosomal and nuclear genes in chlorotic streak-infected sugarcane. These sequences suggest a possible causal agent belonging to the order Cercomonadida (Rhizaria, phylum Cercozoa). An organism with morphological features similar to cercomonads (=Cercomonadida) was isolated into pure axenic culture from internal stalk tissues of infected sugarcane. The isolated organism contained DNA sequences identical to those identified in infected plants by HTS. The DNA sequences and the morphology of the organism did not match any known species. Here we present a new genus and species, Phytocercomonas venanatans, which is associated with chlorotic streak of sugarcane. Amplicon sequencing also supports that P. venanatans is associated with this disease. This is the first reported member from Cercomonadida showing a probable pathogenic association with higher plants.
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Affiliation(s)
- Chuong N Ngo
- First and second authors: Sugar Research Australia, Indooroopilly, QLD, 4068, Australia; third author: Division of Genomics and Microbial Diversity, Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom and Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom; fourth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia; and fifth author: Sugar Research Australia, Woodford, QLD 4514, Australia
| | - Kathryn S Braithwaite
- First and second authors: Sugar Research Australia, Indooroopilly, QLD, 4068, Australia; third author: Division of Genomics and Microbial Diversity, Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom and Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom; fourth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia; and fifth author: Sugar Research Australia, Woodford, QLD 4514, Australia
| | - David Bass
- First and second authors: Sugar Research Australia, Indooroopilly, QLD, 4068, Australia; third author: Division of Genomics and Microbial Diversity, Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom and Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom; fourth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia; and fifth author: Sugar Research Australia, Woodford, QLD 4514, Australia
| | - Anthony J Young
- First and second authors: Sugar Research Australia, Indooroopilly, QLD, 4068, Australia; third author: Division of Genomics and Microbial Diversity, Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom and Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom; fourth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia; and fifth author: Sugar Research Australia, Woodford, QLD 4514, Australia
| | - Barry J Croft
- First and second authors: Sugar Research Australia, Indooroopilly, QLD, 4068, Australia; third author: Division of Genomics and Microbial Diversity, Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom and Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom; fourth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia; and fifth author: Sugar Research Australia, Woodford, QLD 4514, Australia
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Prokina KI, Mylnikov AP, Galanina OV, Philippov DA. First Reports on Heterotrophic Flagellates in the Mires of Arkhangelsk Region, Russia. BIOL BULL+ 2018. [DOI: 10.1134/s1062359017090096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Prokina KI, Mylnikov AP, Zelalem W. First Data on Heterotrophic Flagellates and Heliozoans of Ethiopia. BIOL BULL+ 2018. [DOI: 10.1134/s106235901708012x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Flues S, Blokker M, Dumack K, Bonkowski M. Diversity of Cercomonad Species in the Phyllosphere and Rhizosphere of Different Plant Species with a Description of Neocercomonas epiphylla (Cercozoa, Rhizaria) a Leaf-Associated Protist. J Eukaryot Microbiol 2018; 65:587-599. [PMID: 29377417 DOI: 10.1111/jeu.12503] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/16/2018] [Accepted: 01/16/2018] [Indexed: 12/15/2022]
Abstract
Cercomonads are among the most abundant and diverse groups of heterotrophic flagellates in terrestrial systems and show an affinity to plants. However, we still lack basic knowledge of plant-associated protists. We isolated 75 Cercomonadida strains from the phyllosphere and rhizosphere of plants from three functional groups: grasses (Poa sp.), legumes (Trifolium sp.) and forbs (Plantago sp.), representing 28 OTUs from the genera Cercomonas, Neocercomonas and Paracercomonas. The community composition differed clearly between phyllosphere and rhizosphere, but was not influenced by plant species identity. From these isolates we describe three novel cercomonad species including Neocercomonas epiphylla that was consistently and exclusively isolated from the phyllosphere. For each new species we provide a detailed morphological description as well as an 18S rDNA gene sequence as a distinct marker of species identity. Our data contribute to a better resolution of the systematics of cercomonads and their association with plants, by describing three novel species and adding gene sequences of 10 new cercomonad genotypes and of nine previously described species. In view of the functional importance of cercozoan communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of their composition, function and predator-prey interactions are clearly required.
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Affiliation(s)
- Sebastian Flues
- Department of Terrestrial Ecology, Institute for Zoology, University of Cologne, Cologne, 50674, Germany
| | - Malte Blokker
- Department of Terrestrial Ecology, Institute for Zoology, University of Cologne, Cologne, 50674, Germany
| | - Kenneth Dumack
- Department of Terrestrial Ecology, Institute for Zoology, University of Cologne, Cologne, 50674, Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Institute for Zoology, University of Cologne, Cologne, 50674, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
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9
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Yabuki A, Ishida KI. An Orphan Protist Quadricilia rotundata Finally Finds Its Phylogenetic Home in Cercozoa. J Eukaryot Microbiol 2018; 65:729-732. [PMID: 29345018 DOI: 10.1111/jeu.12502] [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: 09/25/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 11/27/2022]
Abstract
Quadricilia rotundata is a heterotrophic flagellate with four flagella. However, because this species has no clear morphological characteristics or molecular data affiliating it with any known group, Q. rotundata has been treated as a protist incertae sedis, for a long time. Here, we established a clonal culture of Q. rotundata and sequenced its 18S rDNA sequence. Molecular phylogenetic analysis successfully placed Q. rotundata in an environmental clade within Cercozoa, which contributes to expand the morphological and species diversity within Cercozoa. We also discuss morphological evolution within Cercozoa based on this finding.
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Affiliation(s)
- Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Ken-Ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
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10
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Flues S, Bass D, Bonkowski M. Grazing of leaf‐associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function. Environ Microbiol 2017; 19:3297-3309. [DOI: 10.1111/1462-2920.13824] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 06/06/2017] [Accepted: 06/07/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Sebastian Flues
- Department of Terrestrial Ecology, Institute of ZoologyUniversity of CologneZülpicher Straße 47bKöln 50674 Germany
| | - David Bass
- Department of Life SciencesThe Natural History MuseumCromwell RoadLondonSW7 5BD UK
- CefasBarrack Road, The Nothe, Weymouth, Dorset DT4 8UB UK
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Institute of ZoologyUniversity of CologneZülpicher Straße 47bKöln 50674 Germany
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11
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Venter PC, Nitsche F, Domonell A, Heger P, Arndt H. The Protistan Microbiome of Grassland Soil: Diversity in the Mesoscale. Protist 2017; 168:546-564. [PMID: 28961455 DOI: 10.1016/j.protis.2017.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/10/2017] [Accepted: 03/30/2017] [Indexed: 12/22/2022]
Abstract
Genomic data for less than one quarter of ∼1.8 million named species on earth exist in public databases like GenBank. Little information exists on the estimated one million small sized (1-100μm) heterotrophic nanoflagellates and ciliates and their taxa-area relationship. We analyzed environmental DNA from 150 geo-referenced grassland plots representing topographical and land-use ranges typical for Central Europe. High through-put barcoding allowed the identification of operational taxonomic units (OTUs) at species level, with high pairwise identity to reference sequences (≥99.7%), but also the identification of sequences at the genus (≥97%) and class (≥80%) taxonomic level. Species richness analyses revealed, on average, 100 genus level OTUs (332 unique individual read (UIR) and 56 class level OTUs per gram of soil sample in the mesoscale (1-1000km). Database shortfalls were highlighted by increased uncertain taxonomic lineages at lower resolution (≥80% sequence identity). No single barcode occurred ubiquitously across all sites. Taxa-area relationships indicated that OTUs spread over the entire mesoscale were more similar than in the local scale and increased land-use (fertilization, mowing and grazing) promoted taxa-area separation. Only a small fraction of sequences strictly matched reference library sequences, suggesting a large protistan "dark matter" in soil which warrants further research.
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Affiliation(s)
- Paul Christiaan Venter
- University of Cologne, Department of Biology, Institute of Zoology, General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany
| | - Frank Nitsche
- University of Cologne, Department of Biology, Institute of Zoology, General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany
| | - Anne Domonell
- University of Cologne, Department of Biology, Institute of Zoology, General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany
| | - Peter Heger
- University of Cologne, Department of Biology, Institute for Genetics, Bioinformatics & Population Genetics, Zuelpicher Str. 47a, D-50674 Koeln (Cologne), Germany
| | - Hartmut Arndt
- University of Cologne, Department of Biology, Institute of Zoology, General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany.
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12
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Gawryluk RMR, Kamikawa R, Stairs CW, Silberman JD, Brown MW, Roger AJ. The Earliest Stages of Mitochondrial Adaptation to Low Oxygen Revealed in a Novel Rhizarian. Curr Biol 2016; 26:2729-2738. [PMID: 27666965 DOI: 10.1016/j.cub.2016.08.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/21/2016] [Accepted: 08/09/2016] [Indexed: 12/26/2022]
Abstract
Mitochondria exist on a functional and evolutionary continuum that includes anaerobic mitochondrion-related organelles (MROs), such as hydrogenosomes. Hydrogenosomes lack many classical mitochondrial features, including conspicuous cristae, mtDNA, the tricarboxylic acid (TCA) cycle, and ATP synthesis powered by an electron transport chain (ETC); instead, they produce ATP anaerobically, liberating H2 and CO2 gas in the process. However, our understanding of the evolutionary transformation from aerobic mitochondria to various MRO types remains incomplete. Here we describe a novel MRO from a cercomonad (Brevimastigomonas motovehiculus n. sp.; Rhizaria). We have sequenced its 30,608-bp mtDNA and characterized organelle function through a combination of transcriptomic, genomic, and cell biological approaches. B. motovehiculus MROs are metabolically versatile, retaining mitochondrial metabolic pathways, such as a TCA cycle and ETC-driven ATP synthesis, but also possessing hydrogenosomal-type pyruvate metabolism and substrate-level phosphorylation. Notably, the B. motovehiculus ETC is degenerate and appears to be losing cytochrome-based electron transport (complexes III and IV). Furthermore, the F1Fo ATP synthase (complex V) is unique, with the highly conserved Atpα subunit fragmented into four separate pieces. The B. motovehiculus MRO appears to be in the process of losing aerobic metabolic capacities. Our findings shed light on the transition between organelle types, specifically the early stages of mitochondrial adaptation to anaerobiosis.
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Affiliation(s)
- Ryan M R Gawryluk
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan; Graduate School of Global Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Courtney W Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jeffrey D Silberman
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Halifax, NS B3H 4R2, Canada.
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Dumack K, Schuster J, Bass D, Bonkowski M. A Novel Lineage of ‘Naked Filose Amoebae’; Kraken carinae gen. nov. sp. nov. (Cercozoa) with a Remarkable Locomotion by Disassembly of its Cell Body. Protist 2016; 167:268-78. [DOI: 10.1016/j.protis.2016.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 03/30/2016] [Accepted: 04/16/2016] [Indexed: 01/03/2023]
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14
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Bass D, Silberman JD, Brown MW, Pearce RA, Tice AK, Jousset A, Geisen S, Hartikainen H. Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists. Environ Microbiol 2016; 18:1604-19. [PMID: 26914587 DOI: 10.1111/1462-2920.13235] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/15/2016] [Accepted: 01/18/2016] [Indexed: 11/30/2022]
Abstract
A wide diversity of organisms utilize faecal habitats as a rich nutrient source or a mechanism to traverse through animal hosts. We sequenced the 18S rRNA genes of the coprophilic, fruiting body-forming amoeba Guttulinopsis vulgaris and its non-fruiting relatives Rosculus 'ithacus' CCAP 1571/3, R. terrestris n. sp. and R. elongata n. sp. and demonstrate that they are related to the coprophilic flagellate Helkesimastix in a strongly supported, but highly divergent 18S sister clade. PCR primers specific to both clades were used to generate 18S amplicons from a range of environmental and faecal DNA samples. Phylogenetic analysis of the cloned sequences demonstrated a high diversity of uncharacterised sequence types within this clade, likely representing previously described members of the genera Guttulinopsis, Rosculus and Helkesimastix, as well as so-far unobserved organisms. Further, an Illumina MiSeq sequenced set of 18S V4-region amplicons generated from faecal DNAs using universal eukaryote primers showed that core-cercozoan assemblages in faecal samples are as diverse as those found in more conventionally examined habitats. These results reveal many novel lineages, some of which appear to occur preferentially in faecal material, in particular cercomonads and glissomonads. More broadly, we show that faecal habitats are likely untapped reservoirs of microbial eukaryotic diversity.
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Affiliation(s)
- David Bass
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK.,Cefas, Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Jeffrey D Silberman
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, MS State, 39762, MS, USA
| | - Rebecca A Pearce
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, MS State, 39762, MS, USA
| | - Alexandre Jousset
- Department of Ecology and Biodiversity, Utrecht University, 3584, Utrecht, The Netherlands
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, 6708, PB, Wageningen, The Netherlands
| | - Hanna Hartikainen
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
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15
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Scoble JM, Cavalier-Smith T. Scale evolution, sequence phylogeny, and taxonomy of thaumatomonad Cercozoa: 11 new species and new genera Scutellomonas, Cowlomonas, Thaumatospina and Ovaloplaca. Eur J Protistol 2014; 50:270-313. [DOI: 10.1016/j.ejop.2013.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022]
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16
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Jeuck A, Arndt H. A short guide to common heterotrophic flagellates of freshwater habitats based on the morphology of living organisms. Protist 2013; 164:842-60. [PMID: 24239731 DOI: 10.1016/j.protis.2013.08.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 08/21/2013] [Accepted: 08/26/2013] [Indexed: 11/19/2022]
Affiliation(s)
- Alexandra Jeuck
- Department of General Ecology, Zoological Institute, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Hartmut Arndt
- Department of General Ecology, Zoological Institute, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany.
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The Mystery of Clade X: Orciraptor gen. nov. and Viridiraptor gen. nov. are Highly Specialised, Algivorous Amoeboflagellates (Glissomonadida, Cercozoa). Protist 2013; 164:706-47. [DOI: 10.1016/j.protis.2013.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 07/17/2013] [Accepted: 07/18/2013] [Indexed: 11/20/2022]
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Adl SM, Simpson AGB, Lane CE, Lukeš J, Bass D, Bowser SS, Brown MW, Burki F, Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, Le Gall L, Lynn DH, McManus H, Mitchell EAD, Mozley-Stanridge SE, Parfrey LW, Pawlowski J, Rueckert S, Shadwick L, Shadwick L, Schoch CL, Smirnov A, Spiegel FW. The revised classification of eukaryotes. J Eukaryot Microbiol 2013; 59:429-93. [PMID: 23020233 DOI: 10.1111/j.1550-7408.2012.00644.x] [Citation(s) in RCA: 908] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.
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Affiliation(s)
- Sina M Adl
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
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