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Bharti D, Kumar S, Buonanno F, Ortenzi C, Montanari A, Quintela-Alonso P, La Terza A. Free living ciliated protists from the chemoautotrophic cave ecosystem of Frasassi (Italy). SUBTERRANEAN BIOLOGY 2022. [DOI: 10.3897/subtbiol.44.96545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
This study provides the first report on a community of free-living ciliated protists from the chemoautotrophic cave ecosystem of Frasassi, Italy. This subterranean groundwater ecosystem represents a hotspot of biodiversity that still needs to be fully explored with particular reference to microbial eukaryotes such as protist ciliates. A total of 33 taxa of ciliates were identified along with one species each of flagellate, heliozoans and naked amoebae, from four main sampling sites, namely, Grotta Solfurea (GSO), Lago Verde (LVE), Ramo Solfureo (RSO), and Pozzo dei Cristalli (PDC). The last consists of small microhabitats/ponds presenting different chemical–physical and biological parameters, such as sulfur and nutrient contents and the presence of bacterial biofilms. Furthermore, an analysis of the cryptic ciliate species biosphere as a ‘seedbank’ of diversity against cave ecosystem disturbance was also performed. This study also highlights some peculiar adaptations of cave-dwelling ciliates not described in their noncave-dwelling conspecifics, such as the extreme photosensitivity of Urocentrum turbo, the cannibalism of Coleps hirtus, the variable number of thorns in Aspidisca species as a defensive response to predation, and the frequent reorganization of ciliary structures in Euplotes aediculatus. The 18S rDNA sequences were generated for five species and were compared with those of the noncave-dwelling conspecifics. Finally, our results shed light on the still largely unknown ciliate diversity in the chemosynthesis-based sulfidic groundwater ecosystem of Frasassi.
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Wang C, Gao Y, Lu B, Chi Y, Zhang T, El-Serehy HA, Al-Farraj SA, Li L, Song W, Gao F. Large-scale phylogenomic analysis provides new insights into the phylogeny of the class Oligohymenophorea (Protista, Ciliophora) with establishment of a new subclass Urocentria nov. subcl. Mol Phylogenet Evol 2021; 159:107112. [PMID: 33609708 DOI: 10.1016/j.ympev.2021.107112] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/28/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
The class Oligohymenophorea is one of the most diverse assemblage of ciliated protists, which are particularly important in fundamental biological studies including understanding the evolutionary relationships among the lineages. Phylogenetic relationships within the class remain largely elusive, especially within the subclass Peniculia, which contains the long-standing problematic taxa Urocentrum and Paranassula. In the present study, we sequenced the genomes and/or transcriptomes of six non-culturable oligohymenophoreans using single-cell sequencing techniques. Phylogenomic analysis was performed based on expanded taxon sampling of 85 taxa, including 157 nuclear genes encoding 36,953 amino acids. The results indicate that: (1) urocentrids form an independent branch that is sister to the clade formed by Scuticociliatia and Hymenostomatia, which, together with the morphological data, supports the establishment of a new subclass, Urocentria n. subcl., within Oligohymenophorea; (2) phylogenomic analysis and ortholog comparison reveal a close relationship between Paranassula and peniculines, providing corroborative evidence for removing Paranassula from Nassulida and elevating it as an order, Paranassulida, within the subclass Peniculia; (3) based on the phylogenomic analyses and morphological data, we hypothesize that Peritrichia is the earliest diverging clade within Oligohymenophorea while Scuticociliatia and Hymenostomatia share the most common ancestor, followed successively by Urocentria and Peniculia. In addition, stop codon analyses indicate that oligohymenophoreans widely use UGA as the stop codon, while UAR are reassigned to glutamate (peritrichs) or glutamine (others), supporting the evolutionary hypothesis.
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Affiliation(s)
- Chundi Wang
- Laboratory of Marine Protozoan Biodiversity & Evolution, Ocean College, Shandong University, Weihai 264209, China; Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Yunyi Gao
- Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Borong Lu
- Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Yong Chi
- Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Tengteng Zhang
- Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Hamed A El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity & Evolution, Ocean College, Shandong University, Weihai 264209, China
| | - Weibo Song
- Laboratory of Marine Protozoan Biodiversity & Evolution, Ocean College, Shandong University, Weihai 264209, China; Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity and College of Fisheries, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Centers of endemism of freshwater protists deviate from pattern of taxon richness on a continental scale. Sci Rep 2020; 10:14431. [PMID: 32879396 PMCID: PMC7468153 DOI: 10.1038/s41598-020-71332-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/13/2020] [Indexed: 11/21/2022] Open
Abstract
Here, we analyzed patterns of taxon richness and endemism of freshwater protists in Europe. Even though the significance of physicochemical parameters but also of geographic constraints for protist distribution is documented, it remains unclear where regional areas of high protist diversity are located and whether areas of high taxon richness harbor a high proportion of endemics. Further, patterns may be universal for protists or deviate between taxonomic groups. Based on amplicon sequencing campaigns targeting the SSU and ITS region of the rDNA we address these patterns at two different levels of phylogenetic resolution. Our analyses demonstrate that protists have restricted geographical distribution areas. For many taxonomic groups the regions of high taxon richness deviate from those having a high proportion of putative endemics. In particular, the diversity of high mountain lakes as azonal habitats deviated from surrounding lowlands, i.e. many taxa were found exclusively in high mountain lakes and several putatively endemic taxa occurred in mountain regions like the Alps, the Pyrenees or the Massif Central. Beyond that, taxonomic groups showed a pronounced accumulation of putative endemics in distinct regions, e.g. Dinophyceae along the Baltic Sea coastline, and Chrysophyceae in Scandinavia. Many other groups did not have pronounced areas of increased endemism but geographically restricted taxa were found across Europe.
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Frühe L, Cordier T, Dully V, Breiner HW, Lentendu G, Pawlowski J, Martins C, Wilding TA, Stoeck T. Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes. Mol Ecol 2020; 30:2988-3006. [PMID: 32285497 DOI: 10.1111/mec.15434] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/02/2023]
Abstract
Increasing anthropogenic impact and global change effects on natural ecosystems has prompted the development of less expensive and more efficient bioassessments methodologies. One promising approach is the integration of DNA metabarcoding in environmental monitoring. A critical step in this process is the inference of ecological quality (EQ) status from identified molecular bioindicator signatures that mirror environmental classification based on standard macroinvertebrate surveys. The most promising approaches to infer EQ from biotic indices (BI) are supervised machine learning (SML) and the calculation of indicator values (IndVal). In this study we compared the performance of both approaches using DNA metabarcodes of bacteria and ciliates as bioindicators obtained from 152 samples collected from seven Norwegian salmon farms. Results from standard macroinvertebrate-monitoring of the same samples were used as reference to compare the accuracy of both approaches. First, SML outperformed the IndVal approach to infer EQ from eDNA metabarcodes. The Random Forest (RF) algorithm appeared to be less sensitive to noisy data (a typical feature of massive environmental sequence data sets) and uneven data coverage across EQ classes (a typical feature of environmental compliance monitoring scheme) compared to a widely used method to infer IndVals for the calculation of a BI. Second, bacteria allowed for a more accurate EQ assessment than ciliate eDNA metabarcodes. For the implementation of DNA metabarcoding into routine monitoring programmes to assess EQ around salmon aquaculture cages, we therefore recommend bacterial DNA metabarcodes in combination with SML to classify EQ categories based on molecular signatures.
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Affiliation(s)
- Larissa Frühe
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Verena Dully
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Hans-Werner Breiner
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Guillaume Lentendu
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,ID-Gene Ecodiagnostics Ltd, Geneva, Switzerland.,Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | | | - Thomas A Wilding
- Scottish Marine Institute, Scottish Association for Marine Science, Oban, Scotland
| | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
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Obert T, Vďačný P. Delimitation of five astome ciliate species isolated from the digestive tube of three ecologically different groups of lumbricid earthworms, using the internal transcribed spacer region and the hypervariable D1/D2 region of the 28S rRNA gene. BMC Evol Biol 2020; 20:37. [PMID: 32171235 PMCID: PMC7071660 DOI: 10.1186/s12862-020-1601-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/03/2020] [Indexed: 01/19/2023] Open
Abstract
Background Various ecological groups of earthworms very likely constitute sharply isolated niches that might permit speciation of their symbiotic ciliates, even though no distinct morphological features appear to be recognizable among ciliates originating from different host groups. The nuclear highly variable ITS1–5.8S-ITS2 region and the hypervariable D1/D2 region of the 28S rRNA gene have proven to be useful tools for the delimitation of species boundaries in closely related free-living ciliate taxa. In the present study, the power of these molecular markers as well as of the secondary structure of the ITS2 molecule were tested for the first time in order to discriminate the species of endosymbiotic ciliates that were isolated from the gastrointestinal tract of three ecologically different groups of lumbricid earthworms. Results Nineteen new ITS1–5.8S-ITS2 region and D1/D2-28S rRNA gene sequences were obtained from five astome species (Anoplophrya lumbrici, A. vulgaris, Metaradiophrya lumbrici, M. varians, and Subanoplophrya nodulata comb. n.), which were living in the digestive tube of three ecological groups of earthworms. Phylogenetic analyses of the rRNA locus and secondary structure analyses of the ITS2 molecule robustly resolved their phylogenetic relationships and supported the distinctness of all five species, although previous multivariate morphometric analyses were not able to separate congeners in the genera Anoplophrya and Metaradiophrya. The occurrence of all five taxa, as delimited by molecular analyses, was perfectly correlated with the ecological groups of their host earthworms. Conclusions The present study indicates that morphology-based taxonomy of astome ciliates needs to be tested in the light of molecular and ecological data as well. The use of morphological identification alone is likely to miss species that are well delimited based on molecular markers and ecological traits and can lead to the underestimation of diversity and overestimation of host range. An integrative approach along with distinctly increased taxon sampling would be helpful to assess the consistency of the eco-evolutionary trend in astome ciliates.
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Affiliation(s)
- Tomáš Obert
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovak Republic
| | - Peter Vďačný
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovak Republic.
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Fenchel T, Finlay BJ, Esteban GF. Cosmopolitan Metapopulations? Protist 2019; 170:314-318. [PMID: 31181472 DOI: 10.1016/j.protis.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 11/15/2022]
Abstract
A "metapopulation" is a group of populations of the same species separated by space but linked by dispersal and migration. Metapopulations of macroscopic organisms tend to have geographically-restricted distributions, but this does not seem to be the case in microbial eukaryotes due to their astronomical abundance. The term "metapopulation" was first applied to protists' biogeography in the article Finlay and Fenchel (2004), published in PROTIST, which contributed to the popularity of the paper. The article considered protist species as consisting of a single, cosmopolitan population. Here, we recall this paper, and assess developments during the last 15 years with respect to the question of protist species distribution on the surface of the earth.
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Affiliation(s)
- Tom Fenchel
- Marine Biological Laboratory, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
| | - Bland J Finlay
- Queen Mary University of London, School of Biological and Chemical Sciences,Mile End Road London E1 4NS, UK
| | - Genoveva F Esteban
- Bournemouth University, Department of Life and Environmental Sciences, Talbot Campus, Poole, BH12 5BB Dorset, UK.
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Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region. Mol Phylogenet Evol 2016; 102:128-44. [DOI: 10.1016/j.ympev.2016.05.041] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 11/23/2022]
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da Silva-Neto ID, da Silva Paiva T, do Nascimento Borges B, Harada ML. Fine Structure and Molecular Phylogeny of Parametopidium circumlabens
(Ciliophora: Armophorea), Endocommensal of Sea Urchins. J Eukaryot Microbiol 2015; 63:46-61. [DOI: 10.1111/jeu.12247] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/21/2015] [Accepted: 06/21/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Inácio Domingos da Silva-Neto
- Laboratório de Protistologia; Dept. de Zoologia; Inst. de Biologia; CCS A:074; Universidade Federal do Rio de Janeiro - UFRJ; CEP: 21941-590 Ilha do Fundão Rio de Janeiro Brazil
| | - Thiago da Silva Paiva
- Laboratório de Protistologia; Dept. de Zoologia; Inst. de Biologia; CCS A:074; Universidade Federal do Rio de Janeiro - UFRJ; CEP: 21941-590 Ilha do Fundão Rio de Janeiro Brazil
- Laboratório de Biologia Molecular “Francisco Mauro Salzano”; Inst. de Ciências Biológicas; Universidade Federal do Pará - UFPA; CEP: 66075-110 Belém Pará Brazil
| | - Bárbara do Nascimento Borges
- Centro de Tecnologia Agropecuária; Ins. Socioambiental e dos Recursos Hídricos; Universidade Federal Rural da Amazônia - UFRA; CEP: 66077-901 Belém Pará Brazil
| | - Maria Lúcia Harada
- Laboratório de Biologia Molecular “Francisco Mauro Salzano”; Inst. de Ciências Biológicas; Universidade Federal do Pará - UFPA; CEP: 66075-110 Belém Pará Brazil
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Chen X, Miao M, Ma H, Al-Rasheid KAS, Xu K, Lin X. Morphology, Ontogeny, and Phylogeny of Two Brackish Urostylid Ciliates (Protist, Ciliophora, Hypotricha). J Eukaryot Microbiol 2014; 61:594-610. [DOI: 10.1111/jeu.12137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/03/2014] [Accepted: 04/28/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Xumiao Chen
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
- Laboratory of Protozoology; Institute of Evolution and Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Miao Miao
- College of Life Sciences; University of Chinese Academy of Sciences; Beijing 100049 China
| | - Honggang Ma
- Laboratory of Protozoology; Institute of Evolution and Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | | | - Kuidong Xu
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
| | - Xiaofeng Lin
- Laboratory of Protozoology; Key Laboratory of Ecology and Environment Science in Guangdong Higher Education; College of Life Science; South China Normal University; Guangzhou 510631 China
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Scoble JM, Cavalier-Smith T. Scale evolution, sequence phylogeny, and taxonomy of thaumatomonad Cercozoa: 11 new species and new genera Scutellomonas, Cowlomonas, Thaumatospina and Ovaloplaca. Eur J Protistol 2014; 50:270-313. [DOI: 10.1016/j.ejop.2013.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022]
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11
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de Castro LAM, Küppers GC, Schweikert M, Harada ML, Paiva TDS. Ciliates from eutrophized water in the northern Brazil and morphology of Cristigera hammeri Wilbert, 1986 (Ciliophora, Scuticociliatia). Eur J Protistol 2014; 50:122-33. [DOI: 10.1016/j.ejop.2014.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 01/23/2014] [Accepted: 01/27/2014] [Indexed: 11/29/2022]
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da Silva Paiva T, do Nascimento Borges B, da Silva-Neto ID. Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data. Genet Mol Biol 2013; 36:571-85. [PMID: 24385862 PMCID: PMC3873190 DOI: 10.1590/s1415-47572013000400017] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/18/2013] [Indexed: 11/25/2022] Open
Abstract
The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank database. Emphasis was placed on the use of two nucleotide alignment criteria that involved variation in the gap-opening and gap-extension parameters and the use of rRNA secondary structure to orientate multiple-alignment. A sensitivity analysis of 76 data sets was run to assess the effect of variations in indel parameters on tree topologies. Bayesian inference, maximum likelihood and maximum parsimony phylogenetic analyses were used to explore how different analytic frameworks influenced the resulting hypotheses. A sensitivity analysis revealed that the relationships among higher taxa of the Intramacronucleata were dependent upon how indels were determined during multiple-alignment of nucleotides. The phylogenetic analyses rejected the monophyly of the Armophorea most of the time and consistently indicated that the Metopidae and Nyctotheridae were related to the Litostomatea. There was no consensus on the placement of the Caenomorphidae, which could be a sister group of the Metopidae + Nyctorheridae, or could have diverged at the base of the Spirotrichea branch or the Intramacronucleata tree.
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Affiliation(s)
- Thiago da Silva Paiva
- Laboratório de Protistologia, Departamento de Zoologia, Instituto de Biologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ,
Brazil
- Laboratório de Biologia Molecular “Francisco Mauro Salzano”, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA,
Brazil
| | | | - Inácio Domingos da Silva-Neto
- Laboratório de Protistologia, Departamento de Zoologia, Instituto de Biologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ,
Brazil
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Stoeck T, Przybos E, Dunthorn M. The D1-D2 region of the large subunit ribosomal DNA as barcode for ciliates. Mol Ecol Resour 2013; 14:458-68. [DOI: 10.1111/1755-0998.12195] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 10/20/2013] [Accepted: 10/21/2013] [Indexed: 11/26/2022]
Affiliation(s)
- T. Stoeck
- Department of Ecology; University of Kaiserslautern; 67663 Kaiserslautern Germany
| | - E. Przybos
- Institute of Systematics and Evolution of Animals; Polish Academy of Sciences; 31-016 Kraków Poland
| | - M. Dunthorn
- Department of Ecology; University of Kaiserslautern; 67663 Kaiserslautern Germany
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Forster D, Behnke A, Stoeck T. Meta-analyses of environmental sequence data identify anoxia and salinity as parameters shaping ciliate communities. SYST BIODIVERS 2012. [DOI: 10.1080/14772000.2012.706239] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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15
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Genealogical analyses of multiple loci of litostomatean ciliates (Protista, Ciliophora, Litostomatea). Mol Phylogenet Evol 2012; 65:397-411. [PMID: 22789763 PMCID: PMC3461193 DOI: 10.1016/j.ympev.2012.06.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 06/27/2012] [Accepted: 06/28/2012] [Indexed: 11/23/2022]
Abstract
The class Litostomatea is a highly diverse ciliate taxon comprising hundreds of free-living and endocommensal species. However, their traditional morphology-based classification conflicts with 18S rRNA gene phylogenies indicating (1) a deep bifurcation of the Litostomatea into Rhynchostomatia and Haptoria+Trichostomatia, and (2) body polarization and simplification of the oral apparatus as main evolutionary trends in the Litostomatea. To test whether 18S rRNA molecules provide a suitable proxy for litostomatean evolutionary history, we used eighteen new ITS1-5.8S rRNA-ITS2 region sequences from various free-living litostomatean orders. These single- and multiple-locus analyses are in agreement with previous 18S rRNA gene phylogenies, supporting that both 18S rRNA gene and ITS region sequences are effective tools for resolving phylogenetic relationships among the litostomateans. Despite insertions, deletions and mutational saturations in the ITS region, the present study shows that ITS1 and ITS2 molecules can be used to infer phylogenetic relationships not only at species level but also at higher taxonomic ranks when their secondary structure information is utilized to aid alignment.
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Triadó-Margarit X, Casamayor EO. Genetic diversity of planktonic eukaryotes in high mountain lakes (Central Pyrenees, Spain). Environ Microbiol 2012; 14:2445-56. [DOI: 10.1111/j.1462-2920.2012.02797.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Dunthorn M, Stoeck T, Wolf K, Breiner HW, Foissner W. Diversity and endemism of ciliates inhabiting Neotropical phytotelmata. SYST BIODIVERS 2012. [DOI: 10.1080/14772000.2012.685195] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Fritz GB, Pfannkuchen M, Struck U, Hengherr S, Strohmeier S, Brümmer F. Characterizing an Anoxic Habitat: Sulfur Bacteria in a Meromictic Alpine Lake. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/978-94-007-1896-8_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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19
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Beaudoin DJ, Bernhard JM, Edgcomb VP. A Novel Ciliate (Ciliophora: Hypotrichida) Isolated from Bathyal Anoxic Sediments. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/978-94-007-1896-8_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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20
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Nolte V, Pandey RV, Jost S, Medinger R, Ottenwälder B, Boenigk J, Schlötterer C. Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Mol Ecol 2010; 19:2908-15. [PMID: 20609083 PMCID: PMC2916215 DOI: 10.1111/j.1365-294x.2010.04669.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With the advent of molecular methods, it became clear that microbial biodiversity had been vastly underestimated. Since then, species abundance patterns were determined for several environments, but temporal changes in species composition were not studied to the same level of resolution. Using massively parallel sequencing on the 454 GS FLX platform we identified a highly dynamic turnover of the seasonal abundance of protists in the Austrian lake Fuschlsee. We show that seasonal abundance patterns of protists closely match their biogeographic distribution. The stable predominance of few highly abundant taxa, which previously led to the suggestion of a low global protist species richness, is contrasted by a highly dynamic turnover of rare species. We suggest that differential seasonality of rare and abundant protist taxa explains the—so far—conflicting evidence in the ‘everything is everywhere’ dispute. Consequently temporal sampling is basic for adequate diversity and species richness estimates.
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Affiliation(s)
- Viola Nolte
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Vienna, Austria
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Grim JN, Buonanno F. A re-description of the ciliate genus and type species, Balantidium entozoon. Eur J Protistol 2009; 45:174-82. [DOI: 10.1016/j.ejop.2008.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Revised: 10/27/2008] [Accepted: 10/31/2008] [Indexed: 11/28/2022]
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Diversity and geographic distribution of ciliates (Protista: Ciliophora). PROTIST DIVERSITY AND GEOGRAPHICAL DISTRIBUTION 2007. [DOI: 10.1007/978-90-481-2801-3_9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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