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Roth L, Eviatar G, Schmidt LM, Bonomo M, Feldstein-Farkash T, Schubert P, Ziegler M, Al-Sawalmih A, Abdallah IS, Quod JP, Bronstein O. Mass mortality of diadematoid sea urchins in the Red Sea and Western Indian Ocean. Curr Biol 2024; 34:2693-2701.e4. [PMID: 38788707 DOI: 10.1016/j.cub.2024.04.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 04/07/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Sea urchins are primary herbivores on coral reefs, regulating algal biomass and facilitating coral settlement and growth.1,2,3,4,5,6,7,8,9,10,11,12 Recurring mass mortality events (MMEs) of Diadema species Gray, 1825 have been recorded globally,13,14,15,16,17,18,19,20,21,22,23 the most notorious and ecologically significant of which occurred in the Caribbean in 1983,14,17,19,20 contributing to the shift from coral to algal-dominated ecosystems.17,24,25 Recently, first evidence of Diadema setosum mass mortality was reported from the eastern Mediterranean Sea.23 Here, we report extensive mass mortalities of several diadematoid species inhabiting the Red Sea and Western Indian Ocean (WIO)26,27,28 including first evidence of mortalities in the genus Echinothrix Peters, 1853. Mortalities initiated in the Gulf of Aqaba on December 2022 and span the Red Sea, the Gulf of Oman, and the Western Indian Ocean (Réunion Island), with population declines reaching 100% at some sites. Infected individuals are characterized by spine loss and tissue necrosis, resulting in exposed skeletons (i.e., tests) and mortality. Molecular diagnostics of the 18S rRNA gene confirm the presence of a waterborne scuticociliate protozoan most closely related to Philaster apodigitiformis in infected specimens-identical to the pathogen found in the 2022 Caribbean mass mortality of Diadema antillarum.13,15,18 Collapse of these key benthic grazers in the Red Sea and Western Indian Ocean may lead to algal dominance over corals, threatening the stability of coral reefs on a regional scale.29,30,31,32 We issue a warning regarding the further expansion of mortalities and call for immediate monitoring and conservation efforts for these key ecological species.
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Affiliation(s)
- Lachan Roth
- School of Zoology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel; Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv 69978, Israel; The Inter-University Institute for Marine Sciences in Eilat, Eilat 8810302, Israel
| | - Gal Eviatar
- School of Zoology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel; Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv 69978, Israel; The Inter-University Institute for Marine Sciences in Eilat, Eilat 8810302, Israel
| | - Lisa-Maria Schmidt
- School of Zoology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel; Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv 69978, Israel; The Inter-University Institute for Marine Sciences in Eilat, Eilat 8810302, Israel
| | - Mai Bonomo
- School of Zoology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel; Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv 69978, Israel
| | | | - Patrick Schubert
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Ali Al-Sawalmih
- Marine Science Station, University of Jordan, Aqaba 77110, Jordan
| | | | - Jean-Pascal Quod
- Arvam, Technopole de la Réunion, le Kub, 6 rue Albert Lougnon, 97438 Réunion Island, France
| | - Omri Bronstein
- School of Zoology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel; Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv 69978, Israel.
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2
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Ahmed Shazib SU, Cote-L’Heureux A, Ahsan R, Muñoz-Gómez SA, Lee J, Katz LA, Shin MK. Phylogeny and species delimitation of ciliates in the genus Spirostomum (Class, Heterotrichea) using single-cell transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596006. [PMID: 38854132 PMCID: PMC11160781 DOI: 10.1101/2024.05.29.596006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Ciliates are single-celled microbial eukaryotes that diverged from other eukaryotic lineages over a billion years ago. The extensive evolutionary timespan of ciliate has led to enormous genetic and phenotypic changes, contributing significantly to their high level of diversity. Recent analyses based on molecular data have revealed numerous cases of cryptic species complexes in different ciliate lineages, demonstrating the need for a robust approach to delimit species boundaries and elucidate phylogenetic relationships. Heterotrich ciliate species of the genus Spirostomum are abundant in freshwater and brackish environments and are commonly used as biological indicators for assessing water quality. However, some Spirostomum species are difficult to identify due to a lack of distinguishable morphological characteristics, and the existence of cryptic species in this genus remains largely unexplored. Previous phylogenetic studies have focused on only a few loci, namely the ribosomal RNA genes, alpha-tubulin, and mitochondrial CO1. In this study, we obtained single-cell transcriptome of 25 Spirostomum species populations (representing six morphospecies) sampled from South Korea and the USA, and used concatenation- and coalescent-based methods for species tree inference and delimitation. Phylogenomic analysis of 37 Spirostomum populations and 265 protein-coding genes provided a robustious insight into the evolutionary relationships among Spirostomum species and confirmed that species with moniliform and compact macronucleus each form a distinct monophyletic lineage. Furthermore, the multispecies coalescent (MSC) model suggests that there are at least nine cryptic species in the Spirostomum genus, three in S. minus, two in S. ambiguum, S. subtilis, and S. teres each. Overall, our fine sampling of closely related Spirostomum populations and wide scRNA-seq allowed us to demonstrate the hidden crypticity of species within the genus Spirostomum, and to resolve and provide much stronger support than hitherto to the phylogeny of this important ciliate genus.
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Affiliation(s)
- Shahed Uddin Ahmed Shazib
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
| | - Ragib Ahsan
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Sergio A. Muñoz-Gómez
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, South Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, South Korea
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
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3
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Hooper PM, Bass D, Feil EJ, Vincent WF, Lovejoy C, Owen CJ, Tsola SL, Jungblut AD. Arctic cyanobacterial mat community diversity decreases with latitude across the Canadian Arctic. FEMS Microbiol Ecol 2024; 100:fiae067. [PMID: 38653723 DOI: 10.1093/femsec/fiae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024] Open
Abstract
Cyanobacterial mats are commonly reported as hotspots of microbial diversity across polar environments. These thick, multilayered microbial communities provide a refuge from extreme environmental conditions, with many species able to grow and coexist despite the low allochthonous nutrient inputs. The visibly dominant phototrophic biomass is dependent on internal nutrient recycling by heterotrophic organisms within the mats; however, the specific contribution of heterotrophic protists remains little explored. In this study, mat community diversity was examined along a latitudinal gradient (55-83°N), spanning subarctic taiga, tundra, polar desert, and the High Arctic ice shelves. The prokaryotic and eukaryotic communities were targeted, respectively, by V4 16S ribosomal RNA (rRNA) and V9 18S rRNA gene amplicon high-throughput sequencing. Prokaryotic and eukaryotic richness decreased, in tandem with decreasing temperatures and shorter seasons of light availability, from the subarctic to the High Arctic. Taxonomy-based annotation of the protist community revealed diverse phototrophic, mixotrophic, and heterotrophic genera in all mat communities, with fewer parasitic taxa in High Arctic communities. Co-occurrence network analysis identified greater heterogeneity in eukaryotic than prokaryotic community structure among cyanobacterial mats across the Canadian Arctic. Our findings highlight the sensitivity of microbial eukaryotes to environmental gradients across northern high latitudes.
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Affiliation(s)
- Patrick M Hooper
- Science Department, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - David Bass
- Science Department, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Barrack Road, Weymouth, DT4 8UB, United Kingdom
- Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Edward J Feil
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Warwick F Vincent
- Département de Biologie, Takuvik International Research Laboratory and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Connie Lovejoy
- Département de Biologie, Takuvik International Research Laboratory and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, G1V 0A6, Canada
- Québec Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Christopher J Owen
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Stephania L Tsola
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Anne D Jungblut
- Science Department, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
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4
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Ritchie IT, Vilanova-Cuevas B, Altera A, Cornfield K, Evans C, Evans JS, Hopson-Fernandes M, Kellogg CA, Looker E, Taylor O, Hewson I, Breitbart M. Transglobal spread of an ecologically relevant sea urchin parasite. THE ISME JOURNAL 2024; 18:wrae024. [PMID: 38366175 PMCID: PMC11021812 DOI: 10.1093/ismejo/wrae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/10/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024]
Abstract
Mass mortality of the dominant coral reef herbivore Diadema antillarum in the Caribbean in the early 1980s contributed to a persistent phase shift from coral- to algal-dominated reefs. In 2022, a scuticociliate most closely related to Philaster apodigitiformis caused further mass mortality of D. antillarum across the Caribbean, leading to >95% mortality at affected sites. Mortality was also reported in the related species Diadema setosum in the Mediterranean in 2022, though the causative agent of the Mediterranean outbreak has not yet been determined. In April 2023, mass mortality of Diadema setosum occurred along the Sultanate of Oman's coastline. Urchins displayed signs compatible with scuticociliatosis including abnormal behavior, drooping and loss of spines, followed by tissue necrosis and death. Here we report the detection of an 18S rRNA gene sequence in abnormal urchins from Muscat, Oman, that is identical to the Philaster strain responsible for D. antillarum mass mortality in the Caribbean. We also show that scuticociliatosis signs can be elicited in Diadema setosum by experimental challenge with the cultivated Philaster strain associated with Caribbean scuticociliatosis. These results demonstrate the Philaster sp. associated with D. antillarum mass mortality has rapidly spread to geographically distant coral reefs, compelling global-scale awareness and monitoring for this devastating condition through field surveys, microscopy, and molecular microbiological approaches, and prompting investigation of long-range transmission mechanisms.
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Affiliation(s)
- Isabella T Ritchie
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, United States
| | | | - Ashley Altera
- Department of Microbiology, Cornell University, Ithaca, NY 14853, United States
| | | | - Ceri Evans
- Five Oceans Environmental Services, Muscat 131, Oman
| | - James S Evans
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL 33701, United States
| | - Maria Hopson-Fernandes
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, United States
| | - Christina A Kellogg
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL 33701, United States
| | - Elayne Looker
- Five Oceans Environmental Services, Muscat 131, Oman
| | - Oliver Taylor
- Five Oceans Environmental Services, Muscat 131, Oman
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, United States
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5
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Bourland W. Morphologic and molecular characterization of Apertospathula pilata n. sp., a novel freshwater spathidiid (Ciliophora, Litostomatea) from Idaho, USA. Eur J Protistol 2023; 89:125990. [PMID: 37207517 DOI: 10.1016/j.ejop.2023.125990] [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: 02/16/2023] [Revised: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 05/21/2023]
Abstract
Order Spathidiida Foissner and Foissner, 1988 comprises a large group of morphologically diverse, primarily predatory, free living ciliates, the phylogeny of which has remained stubbornly unresolved. Families Arcuospathidiidae and Apertospathulidae are two morphologically similar groups established on the basis of differences in the morphology of the oral bulge and circumoral kinety. While Arcuospathidiidae is non-monophyletic in 18S rRNA gene analyses, the Apertospathulidae has been represented by only a single Apertospathula sequence in public databases. In this report, a novel freshwater species, Apertospathula pilata n. sp. is described on the basis of living observation, silver impregnation, and scanning electron microscopy. The phylogeny of the new species is assessed based on the rRNA cistron. The main features distinguishing A. pilata n. sp. from all congeners are: the oral bulge extrusomes (filiform, up to 25 µm long), the combination of body size (130-193 µm) and shape (spatulate), the extensive oral bulge length (41% of the cell length after protargol impregnation), and multiple micronuclei (one to five, two on average). The monophyly of Apertospathulidae Foissner, Xu and Kreutz, 2005 is rejected.
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Affiliation(s)
- William Bourland
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
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6
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Barouillet C, Vasselon V, Keck F, Millet L, Etienne D, Galop D, Rius D, Domaizon I. Paleoreconstructions of ciliate communities reveal long-term ecological changes in temperate lakes. Sci Rep 2022; 12:7899. [PMID: 35551223 PMCID: PMC9098483 DOI: 10.1038/s41598-022-12041-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Ciliates are unicellular heterotrophic organisms that play a key role in aquatic planktonic and benthic food webs. Advances in sedimentary DNA (sed-DNA) analysis offer the possibility to integrate these bioindicators in paleoenvironmental reconstructions. In this study, we used the top–bottom paleolimnological approach and metabarcoding techniques applied to sed-DNA to compare the recent and past (i.e. prior to major anthropogenic impacts) ciliate communities of 48 lakes located along an elevation gradient. Our results show an overall decline in the β-diversity in recent time, especially in lowland lakes, which are more strongly exposed to local human pressures. Analyses of the functional groups indicate important restructuration of the food web, including the recent increase in mixotrophs. Moreover, changes in the benthic ciliates were consistent with the widespread increase in deep water anoxia. Our results provided evidence that sed-DNA can uncover information about past ciliate communities on a wide variety of lakes. Overall, our study demonstrates the potential of using ciliates as new paleoindicators, integrating information from the pelagic to the benthic zones, and providing valuable insights into ecosystem functioning through a trait-based functional community approach. As paleoindicator, they thus offer a more holistic view on the long-term changes of aquatic ecosystems.
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Affiliation(s)
- Cécilia Barouillet
- INRAE, Université Savoie Mont Blanc, CARRTEL, 74200, Thonon-les-Bains, France. .,Pole R&D ECLA, CARRTEL, 74200, Thonon-les-Bains, France.
| | - Valentin Vasselon
- INRAE, Université Savoie Mont Blanc, CARRTEL, 74200, Thonon-les-Bains, France.,Pole R&D ECLA, CARRTEL, 74200, Thonon-les-Bains, France.,OFB, Site INRAE UMR CARRTEL, 74200, Thonon-les-Bains, France
| | - François Keck
- INRAE, Université Savoie Mont Blanc, CARRTEL, 74200, Thonon-les-Bains, France.,Pole R&D ECLA, CARRTEL, 74200, Thonon-les-Bains, France
| | | | - David Etienne
- Pole R&D ECLA, CARRTEL, 74200, Thonon-les-Bains, France.,Université Savoie Mont Blanc, INRAE, CARRTEL, 73370, Le Bourget du Lac, France
| | - Didier Galop
- GEODE UMR 5602 CNRS, Université de Toulouse, 31058, Toulouse, France.,Labex DRIIHM, OHM Pyrénées, CNRS/INEE, Toulouse, France
| | - Damien Rius
- CNRS, Chrono Environnement, 25000, Besançon, France
| | - Isabelle Domaizon
- INRAE, Université Savoie Mont Blanc, CARRTEL, 74200, Thonon-les-Bains, France. .,Pole R&D ECLA, CARRTEL, 74200, Thonon-les-Bains, France.
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7
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Tamminen M, Spaak J, Tlili A, Eggen R, Stamm C, Räsänen K. Wastewater constituents impact biofilm microbial community in receiving streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151080. [PMID: 34678363 DOI: 10.1016/j.scitotenv.2021.151080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/01/2021] [Accepted: 10/15/2021] [Indexed: 05/27/2023]
Abstract
Microbial life in natural biofilms is dominated by prokaryotes and microscopic eukaryotes living in dense association. In stream ecosystems, microbial biofilms influence primary production, elemental cycles, food web interactions as well as water quality. Understanding how biofilm communities respond to anthropogenic impacts, such as wastewater treatment plant (WWTP) effluent, is important given the key role of biofilms in stream ecosystem function. Here, we implemented 16S and 18S rRNA gene sequencing of stream biofilms upstream (US) and downstream (DS) of WWTP effluents in four Swiss streams to test how bacterial and eukaryotic communities respond to wastewater constituents. Stream biofilm composition was strongly affected by geographic location - particularly for bacteria. However, the abundance of certain microbial community members was related to micropollutants in the wastewater - among bacteria, micropollutant-associated members were found e.g. in Alphaproteobacteria, and among eukaryotes e.g. in Bacillariophyta (algal diatoms). This study corroborates several previously characterized responses (e.g. as seen in diatoms), but also reveals previously unknown community responses - such as seen in Alphaproteobacteria. This study advances our understanding of the ecological impact of the current wastewater treatment practices and provides information about potential new marker organisms to assess ecological change in stream biofilms.
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Affiliation(s)
- Manu Tamminen
- Department of Biology, University of Turku, Finland.
| | - Jenny Spaak
- Department of Environmental Microbiology, Eawag, Switzerland
| | - Ahmed Tlili
- Department of Environmental Toxicology, Eawag, Switzerland
| | - Rik Eggen
- Department of Environmental Toxicology, Eawag, Switzerland; Department of Environmental Systems Science, ETH Zürich, Switzerland
| | | | - Katja Räsänen
- Department of Aquatic Ecology, Eawag, Switzerland; Dept. of Biology and Environmental Science, University of Jyväskylä, Finland
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8
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Fregulia P, Cedrola F, Senra MVX, D'Agosto M, Dias RJP. New Finds on the Systematics of Cycloposthiid Ciliates (Ciliophora: Entodiniomorphida: Cycloposthiidae) Based on New 18S-rDNA Sequences from a Brazilian Capybara. Curr Microbiol 2021; 78:3872-3876. [PMID: 34510223 DOI: 10.1007/s00284-021-02651-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022]
Abstract
The family Cycloposthiidae (Entodiniomorphida) comprises ciliated protists that are symbionts of the gastrointestinal tract of several herbivore mammals, such as rodents, elephants, equids, primates, hippopotamus, marsupials, rhinoceros and tapir, where they contribute to the digestion of their host's plant-based diet. Despite the significance of these ciliates to the evolution of their hosts, many characters used in the taxonomy of the group are homoplastic and most of the valid species do not have molecular data available. For these reasons the systematics of this family is poorly understood. Here, we sequenced the 18S-rDNA of ten cycloposthiids, including nine Cycloposthium spp. and Monoposthium cynodontum, all of them isolated from the cecum of a Brazilian capybara. Our phylogenetic analyses indicate that the family Cycloposthiidae might be polyphyletic, while M. cynodontum and Cycloposthium spp. constitute a single monophyletic group. Given the great morphological and molecular similarities between members of M. cynodontum and Cycloposthium ciliates, it is possible that this species, although it has been described in the genus Monoposthium, is actually a Cycloposthium ciliate.
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Affiliation(s)
- Priscila Fregulia
- Laboratório de Protozoologia, Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, Minas Gerais, CEP 36036-900, Brazil. .,Instituto de Recursos Naturais, Universidade Federal de Itajubá, Itajubá, Minas Gerais, , CEP 37500-903, Brazil.
| | - Franciane Cedrola
- Laboratório de Protozoologia, Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, Minas Gerais, CEP 36036-900, Brazil
| | - Marcus V X Senra
- Instituto de Recursos Naturais, Universidade Federal de Itajubá, Itajubá, Minas Gerais, , CEP 37500-903, Brazil
| | - Marta D'Agosto
- Laboratório de Protozoologia, Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, Minas Gerais, CEP 36036-900, Brazil
| | - Roberto J P Dias
- Laboratório de Protozoologia, Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, Minas Gerais, CEP 36036-900, Brazil
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9
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Sun P, Zhang S, Wang Y, Huang B. Biogeographic Role of the Kuroshio Current Intrusion in the Microzooplankton Community in the Boundary Zone of the Northern South China Sea. Microorganisms 2021; 9:1104. [PMID: 34065542 PMCID: PMC8161332 DOI: 10.3390/microorganisms9051104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022] Open
Abstract
Kuroshio Current intrusion (KCI) has significant impacts on the oceanographic conditions and ecological processes of the Pacific-Asian marginal seas. Little is known to which extent and how, specifically, the microzooplankton community can be influenced through the intrusion. Here, we focused on ciliates that often dominated the microzooplankton community and investigated their communities using high-throughput sequencing of 18S rRNA gene transcripts in the northern South China Sea (NSCS), where the Kuroshio Current (KC) intrudes frequently. We first applied an isopycnal mixing model to assess the fractional contribution of the KC to the NSCS. The ciliate community presented a provincial distribution pattern corresponding to more and less Kuroshio-influenced stations. Structural equation modeling revealed a significant impact of the KCI on the community, while environmental variables had a marginal impact. KCI-sensitive OTUs were taxonomically diverse but mainly belonged to classes Spirotrichea and Phyllopharyngea, suggesting the existence of core ciliates responding to the KCI. KCI-sensitive OTUs were grouped into two network modules that showed contrasting abundance behavior with the KC fraction gradient, reflecting differential niches (i.e., winner and loser) in the ciliate community during the Kuroshio intrusion scenarios. Our study showed that the Kuroshio intrusion, rather than environmental control, was particularly detrimental to the oligotrophic microzooplankton community.
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Affiliation(s)
- Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (S.Z.); (Y.W.); (B.H.)
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Silu Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (S.Z.); (Y.W.); (B.H.)
| | - Ying Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (S.Z.); (Y.W.); (B.H.)
| | - Bangqin Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (S.Z.); (Y.W.); (B.H.)
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
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10
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Kaur H, Shashi, Warren A, Kamra K. Spatial variation in ciliate communities with respect to water quality in the Delhi NCR stretch of River Yamuna, India. Eur J Protistol 2021; 79:125793. [PMID: 33975055 DOI: 10.1016/j.ejop.2021.125793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 03/22/2021] [Accepted: 04/08/2021] [Indexed: 11/15/2022]
Abstract
The River Yamuna emerges from Saptarishi Kund, Yamunotri and merge with River Ganges at Allahabad, India. Anthropogenic stress has affected the water quality of the river Yamuna drastically in the stretch traversing Delhi and its satellite towns (National Capital Region, NCR). In the present study, effect of water quality on the microbial life in the River Yamuna was analyzed using ciliate communities (Protista, Ciliophora) as bio-indicators. Water samples were collected from six sampling sites chosen according to the levels of pollution along the river and water quality was analysed using standard physicochemical factors. As the river traverses Delhi NCR, water quality deteriorates considerably as indicated by the Water Quality Index at the selected sampling sites. Seventy-four ciliate species representing nine classes were recorded. Based on the Shannon diversity index, maximum species diversity was found at the point where the river enters Delhi. The saprobity index showed the river water was beta-mesosaprobic when the river enters Delhi and alpha-mesosaprobic at downstream sites after the first major drain outfall. Significant relationship between the spatial variation in ciliate communities and abiotic parameters indicate that ciliates can be used as effective bioindicators of pollution in the River Yamuna.
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Affiliation(s)
- Harpreet Kaur
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, Delhi 110 007, India
| | - Shashi
- Department of Botany, University of Delhi, Delhi 110 007, India
| | - Alan Warren
- Department of Life Sciences, Natural History Museum of London, London SW7 5BD, UK
| | - Komal Kamra
- Department of Zoology, SGTB Khalsa College, University of Delhi, Delhi 110 007, India.
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11
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Metz DCG, Hechinger RF. Lynnia grapsolytica n. gen, n. sp. (Ciliophora: Apostomatida: Colliniidae), a Deadly Blood Parasite of Crabs with a Novel Pseudocytopharynx. J Eukaryot Microbiol 2021; 68:e12847. [PMID: 33650262 DOI: 10.1111/jeu.12847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 01/28/2021] [Accepted: 02/19/2021] [Indexed: 11/28/2022]
Abstract
We describe a new genus and species of blood-dwelling apostome ciliate, Lynnia grapsolytica n. gen., n. sp. (Apostomatida: Colliniidae). A distinct kinety "hook" pattern on the tomite's posterior ventral face, coupled with its marine habitat and use of a decapod host, readily distinguishes this ciliate from all known colliniids. We detected the parasite in ~12% of Pachygrapsus crassipes (Brachyura: Grapsidae) crabs in a California estuary and confirmed its presence at a Baja California rocky intertidal site. As existing methods failed to adequately stain this ciliate, we developed a new miniaturized silver carbonate impregnation staining method that produced excellent somatic and nuclear stains in all five observed cell types. A possibly unique trait is the active invagination of the tropho-tomont's anterior to form a temporary "pseudocytopharynx," likely used for feeding. Histological examination revealed that the ciliate invaded and damaged skeletal muscle, the heart, connective tissues, and gonads. Survivorship analysis indicated that infected crabs experienced 2.6 times greater daily mortality than uninfected crabs. Laboratory and field experimental infection attempts failed, suggesting a complex life cycle with outside-host development. Phylogenetic analysis at the 18S and COI loci confirmed the ciliate's placement in the Colliniidae. We emend the diagnosis of Family Colliniidae.
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Affiliation(s)
- Daniel C G Metz
- Scripps Institution of Oceanography Marine Biology Research Division, University of California San Diego, La Jolla, California, USA
| | - Ryan F Hechinger
- Scripps Institution of Oceanography Marine Biology Research Division, University of California San Diego, La Jolla, California, USA
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12
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Graf JS, Schorn S, Kitzinger K, Ahmerkamp S, Woehle C, Huettel B, Schubert CJ, Kuypers MMM, Milucka J. Anaerobic endosymbiont generates energy for ciliate host by denitrification. Nature 2021; 591:445-450. [PMID: 33658719 PMCID: PMC7969357 DOI: 10.1038/s41586-021-03297-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/27/2021] [Indexed: 11/27/2022]
Abstract
Mitochondria are specialized eukaryotic organelles that have a dedicated function in oxygen respiration and energy production. They evolved about 2 billion years ago from a free-living bacterial ancestor (probably an alphaproteobacterium), in a process known as endosymbiosis1,2. Many unicellular eukaryotes have since adapted to life in anoxic habitats and their mitochondria have undergone further reductive evolution3. As a result, obligate anaerobic eukaryotes with mitochondrial remnants derive their energy mostly from fermentation4. Here we describe 'Candidatus Azoamicus ciliaticola', which is an obligate endosymbiont of an anaerobic ciliate and has a dedicated role in respiration and providing energy for its eukaryotic host. 'Candidatus A. ciliaticola' contains a highly reduced 0.29-Mb genome that encodes core genes for central information processing, the electron transport chain, a truncated tricarboxylic acid cycle, ATP generation and iron-sulfur cluster biosynthesis. The genome encodes a respiratory denitrification pathway instead of aerobic terminal oxidases, which enables its host to breathe nitrate instead of oxygen. 'Candidatus A. ciliaticola' and its ciliate host represent an example of a symbiosis that is based on the transfer of energy in the form of ATP, rather than nutrition. This discovery raises the possibility that eukaryotes with mitochondrial remnants may secondarily acquire energy-providing endosymbionts to complement or replace functions of their mitochondria.
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Affiliation(s)
- Jon S Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katharina Kitzinger
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Christian Woehle
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Carsten J Schubert
- Surface Waters - Research and Management, Eawag, Kastanienbaum, Switzerland
| | | | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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13
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Isolation and identification of herbivorous ciliates from contaminated microalgal cultures. Eur J Protistol 2020; 76:125743. [PMID: 33166874 DOI: 10.1016/j.ejop.2020.125743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/15/2020] [Accepted: 10/07/2020] [Indexed: 11/23/2022]
Abstract
Ciliates are a common but understudied group of grazers that can invade microalgal cultures. To estimate the potential impact of ciliates on microalgal culture productivity, the identification of species that can invade these cultures is essential. Furthermore, isolation of these herbivorous ciliates allows to use them in experiments that investigate the impact of ciliate grazing on the productivity of microalgal cultures. The main aims of this study were to isolate and identify ciliates that invade cultures of the freshwater microalgae Chlorella and Chlamydomonas, and to establish a live collection of these ciliates for usage in future experiments. To this end, we optimized a method for isolating ciliates from contaminated microalgal cultures and we developed a new PCR primer set for amplifying the partial 18S rDNA of ciliates belonging to the classes Spirotrichea, Oligohymenophorea and Colpodea. As a result, we isolated 11 ciliates from microalgal enrichment cultures inoculated with non-sterile dust and various freshwater sources. Of these 11 species, 7 were found to be feeding on Chlamydomonas. Ciliate species that fed on Chlorella could not be isolated in this study. Ciliate species feeding on Chlamydomonas were identified based on a combination of morphological observations and molecular analyses of partial 18S rDNA sequences.
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14
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Sun P, Wang Y, Laws E, Huang B. Water mass-driven spatial effects and environmental heterogeneity shape microeukaryote biogeography in a subtropical, hydrographically complex ocean system - A case study of ciliates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135753. [PMID: 31836222 DOI: 10.1016/j.scitotenv.2019.135753] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/21/2019] [Accepted: 11/24/2019] [Indexed: 06/10/2023]
Abstract
The relative importance of geographic distance and depth in shaping microeukaryote community composition on a regional scale remains unclear, especially how that composition is related to the movement of water masses. Here, we collected 156 water samples across the Taiwan Strait, which is characterized by complex topography and dynamic circulation, to investigate the composition of the ciliate community with high-throughput sequencing of the 18S rRNA gene transcript. Ciliate alpha diversity exhibited strong correlations with water chemistry, food abundance, and geographic distance; approximately 50% of the variance of the diversity could be explained by dissolved oxygen concentrations, chlorophyll a concentrations, bacterial abundance, and latitude. The sampling sites could be divided into three provinces based on the compositions of the ciliate communities, which exhibited a distinctly nonuniform spatial distribution pattern on a regional scale (587 km). Geographic distance, environmental conditions, and depth were identified as principal determinants of the ciliate community within the Strait. Geographic distance was the most influential factor. The effect of geographic distance seems to mainly reflect the movement of water masses that strongly constrain dispersal and contribute to environmental heterogeneity that accounts for 86.0% and 5.5%, respectively, of community variance across the Strait. Overall, this study revealed that ciliate biogeography as a function of depth and environmental gradients is linked on a regional scale to the water masses that the ciliates inhabit. This result expands our knowledge of the drivers of microeukaryote community composition across regions within which there are water mass movements and strong spatial and environmental gradients.
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Affiliation(s)
- Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China.
| | - Ying Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
| | - Edward Laws
- Department of Environmental Sciences, School of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Bangqin Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
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15
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Shazib SUA, Vďačný P, Slovák M, Gentekaki E, Shin MK. Deciphering phylogenetic relationships and delimiting species boundaries using a Bayesian coalescent approach in protists: A case study of the ciliate genus Spirostomum (Ciliophora, Heterotrichea). Sci Rep 2019; 9:16360. [PMID: 31704993 PMCID: PMC6841689 DOI: 10.1038/s41598-019-52722-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 10/22/2019] [Indexed: 11/09/2022] Open
Abstract
The ciliate genus Spirostomum comprises eight morphospecies, inhabiting diverse aquatic environments worldwide, where they can be used as water quality indicators. Although Spirostomum species are relatively easily identified using morphological methods, the previous nuclear rDNA-based phylogenies indicated several conflicts in morphospecies delineation. Moreover, the single locus phylogenies and previous analytical approaches could not unambiguously resolve phylogenetic relationships among Spirostomum morphospecies. Here, we attempt to investigate species boundaries and evolutionary history of Spirostomum taxa, using 166 new sequences from multiple populations employing one mitochondrial locus (CO1 gene) and two nuclear loci (rRNA operon and alpha-tubulin gene). In accordance with previous studies, relationships among the eight Spirostomum morphospecies were poorly supported statistically in individual gene trees. To overcome this problem, we utilised for the first time in ciliates the Bayesian coalescent approach, which accounts for ancestral polymorphisms, incomplete lineage sorting, and recombination. This strategy enabled us to robustly resolve deep relationships between Spirostomum species and to support the hypothesis that taxa with compact macronucleus and taxa with moniliform macronucleus each form a distinct lineage. Bayesian coalescent-based delimitation analyses strongly statistically supported the traditional morphospecies concept but also indicated that there are two S. minus-like cryptic species and S. teres is non-monophyletic. Spirostomum teres was very likely defined by a set of ancestral features of lineages that also gave rise to S. yagiui and S. dharwarensis. However, molecular data from type populations of the morphospecies S. minus and S. teres are required to unambiguously resolve the taxonomic problems.
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Affiliation(s)
| | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, 842 15, Bratislava, Slovakia
| | - Marek Slovák
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, 845 23, Bratislava, Slovakia.,Department of Botany, Charles University, 128 01, Prague, Czech Republic
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Mann Kyoon Shin
- Department of Biological Science, University of Ulsan, Ulsan, 44610, South Korea.
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16
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McMurtrie J, Verner-Jeffreys DW, Cochrane-Dyet T, White P, van Aerle R, Ryder D, Stone D, Green M, Feist SW, Cano I. Health assessment of the cleaner fish ballan wrasse Labrus bergylta from the British south-west coast. DISEASES OF AQUATIC ORGANISMS 2019; 136:133-146. [PMID: 31621646 DOI: 10.3354/dao03394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Wild-caught ballan wrasse Labrus bergylta are translocated en masse from the British south-west coast to Scotland for use as cleaner fish to tackle Atlantic salmon Salmo salar sea lice infestations; however, very little is known about the background health status of this species. This is the first health assessment of wild ballan wrasse from the British south-west. Wild-caught ballan wrasse (n = 75) from coastal populations off Dorset and Cornwall were subjected to a full health screen for viral, bacterial and parasitic infections and associated pathology. A range of metazoan and protozoan parasites were observed in histological sections, including copepods (sea lice Caligus centrodonti), nematodes, cestodes, digenean metacercariae, Cryptocaryon-like ciliates and an intestinal coccidian (Eimeria sp.) observed in 26.6% of the samples. The mycoplasma Acholeplasma laidlawii was associated with cytopathic effect in cell culture inoculated with tissue homogenates. The opportunistic pathogen Photobacterium damselae damselae was isolated from a single fish with a systemic infection. The isolate was confirmed to possess the virulence factors hlyAch and plpV, previously associated with cell toxicity and pathogenicity to fish. There are no immediate concerns for the continued mass translation of ballan wrasse, however careful monitoring of the population is recommended.
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Affiliation(s)
- Jamie McMurtrie
- Cefas Weymouth Laboratory, Centre for Environment, Fisheries and Aquaculture Science, Weymouth DT4 8UB, UK
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17
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Sun P, Huang L, Xu D, Warren A, Huang B, Wang Y, Wang L, Xiao W, Kong J. Integrated Space-Time Dataset Reveals High Diversity and Distinct Community Structure of Ciliates in Mesopelagic Waters of the Northern South China Sea. Front Microbiol 2019; 10:2178. [PMID: 31616397 PMCID: PMC6768975 DOI: 10.3389/fmicb.2019.02178] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/05/2019] [Indexed: 12/20/2022] Open
Abstract
Little is known about diversity distribution and community structure of ciliates in mesopelagic waters, especially how they are related to spatial and temporal changes. Here, an integrative approach, combining high-throughput cDNA sequencing and quantitative protargol stain, was used to analyze ciliate communities collected temporally along a transect from coastal to oceanic regions at depths ranging from the surface to 1000 m. The mesopelagic zone exhibited comparable alpha diversity to surface water which was consistent over temporal variation, with high diversity occurring at the interface with the euphotic zone. Comparison with the northeastern and the western Pacific Ocean revealed consistency of this vertical distribution of ciliates across oceanic basins. Mesopelagic ciliates harbored distinct community structure without significant seasonal differences, with the vertical variations driven largely by members of the classes Spirotrichea and Oligohymenophorea. Operational taxonomic units (OTUs) affiliated with Scuticociliatia, Astomatida and Apostomatida, members of which are known to be bacterivorous and/or commensal/parasitic species, were more abundant in mesopelagic waters than above, implying they are an important component of food webs in the mesopelagic zone. A combination of depth, geographic distance and environment shaped the ciliate communities, with depth being the most influential factor. Phylogenetic null modeling analysis further indicated that 57.1 and 33.3% of mesopelagic community variation was governed by dispersal limitation and heterogeneous selection, respectively, probably due to the marked biochemical and physical gradients down the water column. This suggests that ciliate community structure in the mesopelagic zone is mainly controlled by stochastic processes. Collectively, this study reports mesopelagic ciliates exhibited high diversity and distinct community structure across spatiotemporal scales and informs the processes mediating ciliate assembly in the mesopelagic zone. These should be fully considered in future studies to build a more comprehensive understanding of mesopelagic microbial assemblages.
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Affiliation(s)
- Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
| | - Liying Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Bangqin Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
| | - Ying Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lei Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Wupeng Xiao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jie Kong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
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18
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Wiroonpan P, Purivirojkul W. New record of Trichodina unionis (Ciliophora, Trichodinidae) from freshwater gastropods in Bangkok, Thailand. ACTA ACUST UNITED AC 2019; 26:47. [PMID: 31359860 PMCID: PMC6664677 DOI: 10.1051/parasite/2019047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/22/2019] [Indexed: 11/14/2022]
Abstract
Trichodinids, which are ciliate protists, are causative agents of an aquatic animal disease, trichodiniasis, especially among both captive and wild fish. This disease can adversely affect aquaculture and have economic impacts. The objectives of this study were to evaluate the prevalence and mean intensity of Trichodina unionis infection, describe qualitative and quantitative morphological characters, and perform a molecular phylogenetic analysis. The gastropod samples were randomly collected by hand-picking and a hand net. Trichodina unionis was collected by the crushing method under a stereomicroscope. Among all 4977 examined gastropods, 55 individuals of two gastropod species, Gyraulus siamensis and Physella acuta, were found to be infected by T. unionis, with overall prevalence and mean intensity of infection of 1.11% and 16.65, respectively. The characteristics of the denticles indicated T. unionis as having moderately wide blades and moderately curved blade margins, with distinctive bend angles near the distal end. The quantitative characters showed some variations, which could be due to food availability. Molecular phylogenetic analysis conducted with 18S rRNA provided a monophyletic tree of our specimens and previously identified T. unionis, confirming species identification. This study represents the first record of T. unionis in Thailand.
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Affiliation(s)
- Pichit Wiroonpan
- Animal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart University, Bang Khen Campus, Bangkok, 10900, Thailand
| | - Watchariya Purivirojkul
- Animal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart University, Bang Khen Campus, Bangkok, 10900, Thailand
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19
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Kavazos CRJ, Huggett MJ, Mueller U, Horwitz P. Bacterial and ciliate biofilm community structure at different spatial levels of a salt lake meta-community. FEMS Microbiol Ecol 2019; 94:5066167. [PMID: 30124812 DOI: 10.1093/femsec/fiy148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 08/01/2018] [Indexed: 11/14/2022] Open
Abstract
Meta-communities are assembled along an ecological scale that determines local and regional diversity. Spatial patterns have been detected in planktonic bacterial communities at distances <20 m, but little is known about the occurrence of similar variation for other microbial groups and changes in microbial meta-community assembly at different levels of a meta-community. To examine this variation, the biofilm of eight saline ponds were used to investigate processes shaping diversity within ponds (β) and between ponds (δ). Bacterial and ciliate communities were assessed using ARISA and T-RFLP respectively, while diversity partitioning methods were used to examine the importance of taxonomic turnover and variation partitioning was used to distinguish spatial from environmental determinants. The results show that turnover is important for determining β- and δ-diversity of biofilms. Spatial factors are important drivers of bacterial β-diversity but were unimportant for ciliate β-diversity. Environmental variation was a strong determinant of bacterial and ciliate δ-diversity, suggesting sorting processes are important for assembling pond communities. Determinants of diversity in bacteria are not universal for ciliates, suggesting higher functional redundancy of bacteria or the greater niche breadth of ciliates may be important in discriminating assembly processes between the two organisms.
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Affiliation(s)
- Christopher R J Kavazos
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Megan J Huggett
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia.,School of Environmental and Life Sciences, The University of Newcastle, 10 Chittaway Dr, Ourimbah, NSW 2258, Australia
| | - Ute Mueller
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Pierre Horwitz
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
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20
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Abraham JS, Sripoorna S, Maurya S, Makhija S, Gupta R, Toteja R. Techniques and tools for species identification in ciliates: a review. Int J Syst Evol Microbiol 2019; 69:877-894. [DOI: 10.1099/ijsem.0.003176] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ciliates are highly divergent unicellular eukaryotic organisms with nuclear dualism and a highly specialized ciliary pattern. They inhabit all biotopes and play crucial roles in regulating microbial food webs as they prey on bacteria, protists and even on microscopic animals. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. In the present review, an attempt has been made to elaborate the various approaches used by modern day ciliate taxonomists for species identification. The different approaches involved in taxonomic characterization of ciliates such as classical (using live-cell observations, staining techniques, etc.), molecular (involving various marker genes) and statistical (delimitation of cryptic species) methods have been reviewed. Ecological and behavioural aspects in species identification have also been discussed. In present-day taxonomy, it is important to use a ‘total evidence’ approach in identifying ciliates, relying on both classical and molecular information whenever possible. This integrative approach will help in the mergence of classical methods with modern-day tools for comprehensive species description in future.
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Affiliation(s)
- Jeeva Susan Abraham
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - S. Sripoorna
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Swati Maurya
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Seema Makhija
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Renu Gupta
- Maitreyi College, University of Delhi, Bapu dham, Chanakyapuri, New Delhi 110021, India
| | - Ravi Toteja
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
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21
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Molecular phylogeny and comparative morphology indicate that odontostomatids (Alveolata, Ciliophora) form a distinct class-level taxon related to Armophorea. Mol Phylogenet Evol 2018; 126:382-389. [DOI: 10.1016/j.ympev.2018.04.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/09/2018] [Accepted: 04/17/2018] [Indexed: 11/17/2022]
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22
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Weitere M, Erken M, Majdi N, Arndt H, Norf H, Reinshagen M, Traunspurger W, Walterscheid A, Wey JK. The food web perspective on aquatic biofilms. ECOL MONOGR 2018. [DOI: 10.1002/ecm.1315] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Markus Weitere
- Department River Ecology; Helmholtz Centre of Environmental Research - UFZ; Brückstrasse 3a 39114 Magdeburg Germany
| | - Martina Erken
- Department River Ecology; Helmholtz Centre of Environmental Research - UFZ; Brückstrasse 3a 39114 Magdeburg Germany
| | - Nabil Majdi
- Department of Animal Ecology; University of Bielefeld; Konsequenz 45 33615 Bielefeld Germany
| | - Hartmut Arndt
- General Ecology; Zoological Institute; Cologne Biocenter; University of Cologne; Zülpicher Strasse 47b 50674 Cologne Germany
| | - Helge Norf
- Department River Ecology; Helmholtz Centre of Environmental Research - UFZ; Brückstrasse 3a 39114 Magdeburg Germany
- Department Aquatic Ecosystem Analyses and Management; Helmholtz Centre of Environmental Research - UFZ; Brückstrasse 3a 39114 Magdeburg Germany
| | - Michael Reinshagen
- General Ecology; Zoological Institute; Cologne Biocenter; University of Cologne; Zülpicher Strasse 47b 50674 Cologne Germany
| | - Walter Traunspurger
- Department of Animal Ecology; University of Bielefeld; Konsequenz 45 33615 Bielefeld Germany
| | - Anja Walterscheid
- General Ecology; Zoological Institute; Cologne Biocenter; University of Cologne; Zülpicher Strasse 47b 50674 Cologne Germany
| | - Jennifer K. Wey
- Department River Ecology; Helmholtz Centre of Environmental Research - UFZ; Brückstrasse 3a 39114 Magdeburg Germany
- Department of Animal Ecology; Federal Institute of Hydrology; Am Mainzer Tor 1 56068 Koblenz Germany
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Sahoo PK, Pattanayak S, Paul A, Sahoo MK, Rajesh Kumar P, Panda D, Pillai BR. First record of Metanophrys sinensis (Protozoa: Ciliophora: Scuticociliatida) from India causing large scale mortality in a new host Macrobrachium rosenbergii larvae. JOURNAL OF FISH DISEASES 2018; 41:1303-1307. [PMID: 29882216 DOI: 10.1111/jfd.12809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Affiliation(s)
- P K Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - S Pattanayak
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - A Paul
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - M K Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - P Rajesh Kumar
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - D Panda
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - B R Pillai
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
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24
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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: 8] [Impact Index Per Article: 1.3] [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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25
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Crespo D, Grilo TF, Baptista J, Coelho JP, Lillebø AI, Cássio F, Fernandes I, Pascoal C, Pardal MÂ, Dolbeth M. New climatic targets against global warming: will the maximum 2 °C temperature rise affect estuarine benthic communities? Sci Rep 2017; 7:3918. [PMID: 28634416 PMCID: PMC5478632 DOI: 10.1038/s41598-017-04309-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/12/2017] [Indexed: 11/09/2022] Open
Abstract
The Paris Agreement signed by 195 countries in 2015 sets out a global action plan to avoid dangerous climate change by limiting global warming to remain below 2 °C. Under that premise, in situ experiments were run to test the effects of 2 °C temperature increase on the benthic communities in a seagrass bed and adjacent bare sediment, from a temperate European estuary. Temperature was artificially increased in situ and diversity and ecosystem functioning components measured after 10 and 30 days. Despite some warmness effects on the analysed components, significant impacts were not verified on macro and microfauna structure, bioturbation or in the fluxes of nutrients. The effect of site/habitat seemed more important than the effects of the warmness, with the seagrass habitat providing more homogenous results and being less impacted by warmness than the adjacent bare sediment. The results reinforce that most ecological responses to global changes are context dependent and that ecosystem stability depends not only on biological diversity but also on the availability of different habitats and niches, highlighting the role of coastal wetlands. In the context of the Paris Agreement it seems that estuarine benthic ecosystems will be able to cope if global warming remains below 2 °C.
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Affiliation(s)
- Daniel Crespo
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
| | - Tiago Fernandes Grilo
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia - Faculdade de Ciências da Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374, Cascais, Portugal
| | - Joana Baptista
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - João Pedro Coelho
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- Department of Chemistry & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Ana Isabel Lillebø
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Fernanda Cássio
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Isabel Fernandes
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Cláudia Pascoal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Miguel Ângelo Pardal
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Marina Dolbeth
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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26
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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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27
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Remmas N, Melidis P, Paschos G, Statiris E, Ntougias S. Protozoan indicators and extracellular polymeric substances alterations in an intermittently aerated membrane bioreactor treating mature landfill leachate. ENVIRONMENTAL TECHNOLOGY 2017; 38:53-64. [PMID: 27194208 DOI: 10.1080/09593330.2016.1190792] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/12/2016] [Indexed: 06/05/2023]
Abstract
A membrane bioreactor was operated under intermittent aeration and various organic loading rates (OLR: 0.070, 0.159 and 0.291 g COD L-1 d-1) to remove carbon and nitrogen from mature landfill leachate, where external carbon source (glycerol) addition resulted in effective nitrate removal. A relative increase in soluble microbial product (SMP) over extracellular polymeric substances (EPS) was observed at the highest OLR and glycerol addition, whereas no membrane biofouling occurred. SMP (proteins and carbohydrates) and carbohydrate EPS correlated positively and negatively, respectively, with suspended solids and transmembrane pressure (TMP). Moreover, proteinous SMP significantly correlated with carbon and nitrogen load. Principal component analysis also revealed the influence of leachate organic and nitrogen content on biomass production, TMP and sessile ciliate densities. Although filamentous index (FI) was sustained at high levels (3-4), with Haliscomenobacter hydrossis being the main filamentous bacterium identified, no bulking phenomena occurred. High glycerol addition resulted in a rapid increase in sessile ciliate population. Increased Epistylis and Vorticella microstoma population was detected by microscopic examination during high glycerol addition, while a remarkable Rhogostoma population (supergroup Rhizaria) was identified by molecular techniques. The contribution of Rhizaria in nitrogen processes may lead to the dominance of Rhogostoma during landfill leachate treatment.
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Affiliation(s)
- Nikolaos Remmas
- a Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering , Democritus University of Thrace , Xanthi , Greece
| | - Paraschos Melidis
- a Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering , Democritus University of Thrace , Xanthi , Greece
| | - Georgios Paschos
- a Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering , Democritus University of Thrace , Xanthi , Greece
| | - Evangelos Statiris
- a Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering , Democritus University of Thrace , Xanthi , Greece
| | - Spyridon Ntougias
- a Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering , Democritus University of Thrace , Xanthi , Greece
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28
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Cedrola F, Senra MVX, D'Agosto M, Dias RJP. Phylogenetic Analyses Support Validity of Genus Eodinium (Ciliophora, Entodiniomorphida, Ophryoscolecidae). J Eukaryot Microbiol 2016; 64:242-247. [PMID: 27539116 DOI: 10.1111/jeu.12355] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 08/12/2016] [Accepted: 08/12/2016] [Indexed: 11/29/2022]
Abstract
The validity of genus Eodinium has been historically disputed due to morphological similarities with Diplodinium (absence of skeletal plates as well as adoral and dorsal ciliary zones at the same body level). To address this issue, the 18S rDNA of four Eodinium posterovesiculatum morphotypes and four Diplodinium anisacanthum morphotypes were sequenced and phylogenetically analyzed. The different inference methods suggest the existence of a last common ancestor of Eodinium and Ostracodinium that is not shared with Diplodinium, strongly supporting the validity of genus Eodinium. Since skeletal plates are present in all members of genus Ostracodinium, the most parsimonious is a secondary loss of skeletal plates in E. posterovesiculatum. This work represents a breakthrough in the taxonomy and phylogeny of the family Ophryoscolecidae indicating that the skeletal plates may not reflect evolutionary divergence within this group of ciliates as traditionally proposed.
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Affiliation(s)
- Franciane Cedrola
- Laboratório de Protozoologia, Programa de Pós-graduação em Comportamento e Biologia Animal, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, CEP 36036-900, Minas Gerais, Brazil
| | - Marcus Vinicius Xavier Senra
- Laboratório de Protozoologia, Programa de Pós-graduação em Comportamento e Biologia Animal, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, CEP 36036-900, Minas Gerais, Brazil
| | - Marta D'Agosto
- Laboratório de Protozoologia, Programa de Pós-graduação em Comportamento e Biologia Animal, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, CEP 36036-900, Minas Gerais, Brazil
| | - Roberto Júnio Pedroso Dias
- Laboratório de Protozoologia, Programa de Pós-graduação em Comportamento e Biologia Animal, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, CEP 36036-900, Minas Gerais, Brazil
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29
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Mordret S, Romac S, Henry N, Colin S, Carmichael M, Berney C, Audic S, Richter DJ, Pochon X, de Vargas C, Decelle J. The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.). THE ISME JOURNAL 2016; 10:1424-36. [PMID: 26684730 PMCID: PMC5029185 DOI: 10.1038/ismej.2015.211] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 09/29/2015] [Accepted: 10/06/2015] [Indexed: 12/11/2022]
Abstract
Symbiotic partnerships between heterotrophic hosts and intracellular microalgae are common in tropical and subtropical oligotrophic waters of benthic and pelagic marine habitats. The iconic example is the photosynthetic dinoflagellate genus Symbiodinium that establishes mutualistic symbioses with a wide diversity of benthic hosts, sustaining highly biodiverse reef ecosystems worldwide. Paradoxically, although various species of photosynthetic dinoflagellates are prevalent eukaryotic symbionts in pelagic waters, Symbiodinium has not yet been reported in symbiosis within oceanic plankton, despite its high propensity for the symbiotic lifestyle. Here we report a new pelagic photosymbiosis between a calcifying ciliate host and the microalga Symbiodinium in surface ocean waters. Confocal and scanning electron microscopy, together with an 18S rDNA-based phylogeny, showed that the host is a new ciliate species closely related to Tiarina fusus (Colepidae). Phylogenetic analyses of the endosymbionts based on the 28S rDNA gene revealed multiple novel closely related Symbiodinium clade A genotypes. A haplotype network using the high-resolution internal transcribed spacer-2 marker showed that these genotypes form eight divergent, biogeographically structured, subclade types that do not seem to associate with any benthic hosts. Ecological analyses using the Tara Oceans metabarcoding data set (V9 region of the 18S rDNA) and contextual oceanographic parameters showed a global distribution of the symbiotic partnership in nutrient-poor surface waters. The discovery of the symbiotic life of Symbiodinium in the open ocean provides new insights into the ecology and evolution of this pivotal microalga and raises new hypotheses about coastal pelagic connectivity.
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Affiliation(s)
- Solenn Mordret
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Sarah Romac
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Nicolas Henry
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Sébastien Colin
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Margaux Carmichael
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Cédric Berney
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Stéphane Audic
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Daniel J Richter
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Colomban de Vargas
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Johan Decelle
- EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
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30
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Battin TJ, Besemer K, Bengtsson MM, Romani AM, Packmann AI. The ecology and biogeochemistry of stream biofilms. Nat Rev Microbiol 2016; 14:251-63. [DOI: 10.1038/nrmicro.2016.15] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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31
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An integrative approach to phylogeny reveals patterns of environmental distribution and novel evolutionary relationships in a major group of ciliates. Sci Rep 2016; 6:21695. [PMID: 26880590 PMCID: PMC4754944 DOI: 10.1038/srep21695] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/29/2016] [Indexed: 12/19/2022] Open
Abstract
Peritrichs are a major group of ciliates with worldwide distribution. Yet, its internal phylogeny remains unresolved owing to limited sampling. Additionally, ecological distributions of peritrichs are poorly known. We performed substantially expanded phylogenetic analyses of peritrichs that incorporated SSU rDNA sequences of samples collected from three continents, revealing a number of new relationships between and within major lineages that greatly challenged the classic view of the group. Interrogation of a dataset comprising new environmental sequences from an estuary and the open ocean generated with high throughput sequencing and clone libraries plus putative environmental peritrich sequences at Genbank, produced a comprehensive tree of peritrichs from a variety of habitats and revealed unique ecological distribution patterns of several lineages for the first time. Also, evidence of adaptation to extreme environments in the Astylozoidae clade greatly broadened the phylogenetic range of peritrichs capable of living in extreme environments. Reconstruction of ancestral states revealed that peritrichs may have transitioned repeatedly from freshwater to brackish/marine/hypersaline environments. This work establishes a phylogenetic framework for more mature investigations of peritrichs in the future, and the approach used here provides a model of how to elucidate evolution in the context of ecological niches in any lineage of microbial eukaryotes.
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32
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Chavatte N, Lambrecht E, Van Damme I, Sabbe K, Houf K. Abundance, diversity and community composition of free-living protozoa on vegetable sprouts. Food Microbiol 2015; 55:55-63. [PMID: 26742616 DOI: 10.1016/j.fm.2015.11.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 11/09/2015] [Accepted: 11/20/2015] [Indexed: 01/20/2023]
Abstract
Interactions with free-living protozoa (FLP) have been implicated in the persistence of pathogenic bacteria on food products. In order to assess the potential involvement of FLP in this contamination, detailed knowledge on their occurrence, abundance and diversity on food products is required. In the present study, enrichment and cultivation methods were used to inventory and quantify FLP on eight types of commercial vegetable sprouts (alfalfa, beetroot, cress, green pea, leek, mung bean, red cabbage and rosabi). In parallel, total aerobic bacteria and Escherichia coli counts were performed. The vegetable sprouts harbored diverse communities of FLP, with Tetrahymena (ciliate), Bodo saltans and cercomonads (flagellates), and Acanthamoeba and Vannella (amoebae) as the dominant taxa. Protozoan community composition and abundance significantly differed between the sprout types. Beetroot harbored the most abundant and diverse FLP communities, with many unique species such as Korotnevella sp., Vannella sp., Chilodonella sp., Podophrya sp. and Sphaerophrya sp. In contrast, mung bean sprouts were species-poor and had low FLP numbers. Sampling month and company had no significant influence, suggesting that seasonal and local factors are of minor importance. Likewise, no significant relationship between protozoan community composition and bacterial load was observed.
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Affiliation(s)
- N Chavatte
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - E Lambrecht
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - I Van Damme
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - K Sabbe
- Department of Biology, Faculty of Sciences, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium.
| | - K Houf
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
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33
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Jung JH, Park KM, Yang EJ, Joo HM, Jeon M, Kang SH, Choi HG, Park MH, Min GS, Kim S. Patchy-distributed ciliate (Protozoa) diversity of eight polar communities as determined by 454 amplicon pyrosequencing. Anim Cells Syst (Seoul) 2015. [DOI: 10.1080/19768354.2015.1082931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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34
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Rossi MF, Dias RJP, Senra MVX, Martinele I, Soares CAG, D'Agosto M. Molecular Phylogeny of the Family Ophryscolecidae (Ciliophora, Litostomatea) Inferred from 18S rDNA Sequences. J Eukaryot Microbiol 2015; 62:584-90. [PMID: 25712321 DOI: 10.1111/jeu.12211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 01/07/2015] [Accepted: 01/07/2015] [Indexed: 11/30/2022]
Abstract
The 18S rDNA was used to infer oral ciliature patterns of evolution within the family Ophryoscolecidae, with the addition of five new sequences of ciliates from the genus Ostracodinium. Our data confirmed the monophyly of the subfamilies Entodiniinae and Ophryoscolecinae, but more analysis would be required for the definition of the status of the subfamily Diplodiniinae. The oral infraciliature patterns reflect evolutionary divergence in the family Ophryscolecidae, observing monophyly on Entodinium-type, Diplodinium-type, Ostracodinium-type, Epidinium-type, and Ophryoscolex-type. The ancestral infraciliature of Entodinium-type cannot be proven, however, the position of Entodinium-type showed closer of Diplodinium-type than Ophryoscolex-type, corroborating previous studies using morphological characters. The observed inconsistencies reflect the need to increase the number of 18S rDNA sequences to family Ophryoscolecidae and investigate the evolution of this group using other molecular markers.
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Affiliation(s)
- Mariana F Rossi
- Laboratory of Protozoology, Postgraduate Program in Animal Behavior and Biology, Federal University of Juiz de Fora, Juiz de Fora, CEP: 36036-900, Minas Gerais, Brazil
| | - Roberto Júnio P Dias
- Laboratory of Protozoology, Postgraduate Program in Animal Behavior and Biology, Federal University of Juiz de Fora, Juiz de Fora, CEP: 36036-900, Minas Gerais, Brazil
| | - Marcus V X Senra
- Laboratory of Protozoology, Postgraduate Program in Animal Behavior and Biology, Federal University of Juiz de Fora, Juiz de Fora, CEP: 36036-900, Minas Gerais, Brazil.,Laboratory of Molecular Genetics of Eukaryotes and Simbionts, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, CEP: 21941-590, Rio de Janeiro, Brazil
| | - Isabel Martinele
- Laboratory of Protozoology, Postgraduate Program in Animal Behavior and Biology, Federal University of Juiz de Fora, Juiz de Fora, CEP: 36036-900, Minas Gerais, Brazil
| | - Carlos A G Soares
- Laboratory of Molecular Genetics of Eukaryotes and Simbionts, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, CEP: 21941-590, Rio de Janeiro, Brazil
| | - Marta D'Agosto
- Laboratory of Protozoology, Postgraduate Program in Animal Behavior and Biology, Federal University of Juiz de Fora, Juiz de Fora, CEP: 36036-900, Minas Gerais, Brazil
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Rubinstein RL, Kadilak AL, Cousens VC, Gage DJ, Shor LM. Protist-facilitated particle transport using emulated soil micromodels. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:1384-91. [PMID: 25565107 DOI: 10.1021/es503424z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Microbial processes in the subsurface can be visualized directly using micromodels to emulate pore-scale geometries. Here, emulated soil micromodels were used to measure transport of fluorescent beads in the presence and absence of the soil ciliate Colpoda sp. under quiescent conditions. Beads alone or beads with protists were delivered to the input wells of replicate micromodels that contained three 20 mm(2) channels emulating a sandy loam microstructure. Bead abundance in microstructured channels was measured by direct counts of tiled confocal micrographs. For channels with protists, average bead abundances were approximately 320, 560, 710, 830, and 790 mm(-2) after 1, 2, 3, 5, and 10 days, respectively, versus 0, 0, 0.3, 7.8, and 45 mm(-2) without protists. Spatial and temporal patterns of bead abundance indicate that protist-facilitated transport is not a diffusive-type process but rather a function of more complex protist behaviors, including particle uptake and egestion and motility in a microstructured habitat. Protist-facilitated transport may enhance particle mixing in the soil subsurface and could someday be used for targeted delivery of nanoparticles, encapsulated chemicals, or bacteria for remediation and agriculture applications.
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Affiliation(s)
- Rebecca L Rubinstein
- Department of Civil and Environmental Engineering, ‡Department of Chemical and Biomolecular Engineering, §Department of Molecular and Cellular Biology, and ∥Center for Environmental Sciences and Engineering, University of Connecticut , Storrs, Connecticut 06269, United States
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Design and validation of four new primers for next-generation sequencing to target the 18S rRNA genes of gastrointestinal ciliate protozoa. Appl Environ Microbiol 2014; 80:5515-21. [PMID: 24973070 DOI: 10.1128/aem.01644-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Four new primers and one published primer were used to PCR amplify hypervariable regions within the protozoal 18S rRNA gene to determine which primer pair provided the best identification and statistical analysis. PCR amplicons of 394 to 498 bases were generated from three primer sets, sequenced using Roche 454 pyrosequencing with Titanium, and analyzed using the BLAST database (NCBI) and MOTHUR version 1.29. The protozoal diversity of rumen contents from moose in Alaska was assessed. In the present study, primer set 1, P-SSU-316F and GIC758R (amplicon of 482 bases), gave the best representation of diversity using BLAST classification, and the set amplified Entodinium simplex and Ostracodinium spp., which were not amplified by the other two primer sets. Primer set 2, GIC1080F and GIC1578R (amplicon of 498 bases), had similar BLAST results and a slightly higher percentage of sequences that were identified with a higher sequence identity. Primer sets 1 and 2 are recommended for use in ruminants. However, primer set 1 may be inadequate to determine protozoal diversity in nonruminants. The amplicons created by primer set 1 were indistinguishable for certain species within the genera Bandia, Blepharocorys, Polycosta, and Tetratoxum and between Hemiprorodon gymnoprosthium and Prorodonopsis coli, none of which are normally found in the rumen.
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Gromochytrium mamkaevae gen. & sp. nov. and two new orders: Gromochytriales and Mesochytriales (Chytridiomycetes). Persoonia - Molecular Phylogeny and Evolution of Fungi 2014; 32:115-26. [PMID: 25264386 PMCID: PMC4150072 DOI: 10.3767/003158514x680234] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 11/01/2013] [Indexed: 11/26/2022]
Abstract
During the last decade several new orders were established in the class Chytridiomycetes on the basis of zoospore ultrastructure and molecular phylogeny. Here we present the ultrastructure and molecular phylogeny of strain x-51 CALU – a parasite of the alga Tribonema gayanum, originally described as Rhizophydium sp. based on light microscopy. Detailed investigation revealed that the zoospore ultrastructure of this strain has unique characters not found in any order of Chytridiomycetes: posterior ribosomal core unbounded by the endoplasmic reticulum and detached from the nucleus or microbody-lipid complex, and kinetosome composed of microtubular doublets. An isolated phylogenetic position of x-51 is further confirmed by the analysis of 18S and 28S rRNA sequences, and motivates the description of a new genus and species Gromochytrium mamkaevae. The sister position of G. mamkaevae branch relative to Mesochytrium and a cluster of environmental sequences, as well as the ultrastructural differences between Gromochytrium and Mesochytrium zoospores prompted us to establish two new orders: Gromochytriales and Mesochytriales.
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Fernandes I, Duarte S, Cássio F, Pascoal C. Effects of riparian plant diversity loss on aquatic microbial decomposers become more pronounced with increasing time. MICROBIAL ECOLOGY 2013; 66:763-772. [PMID: 23963224 DOI: 10.1007/s00248-013-0278-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 08/05/2013] [Indexed: 06/02/2023]
Abstract
We examined the potential long-term impacts of riparian plant diversity loss on diversity and activity of aquatic microbial decomposers. Microbial assemblages were obtained in a mixed-forest stream by immersion of mesh bags containing three leaf species (alder, oak and eucalyptus), commonly found in riparian corridors of Iberian streams. Simulation of species loss was done in microcosms by including a set of all leaf species, retrieved from the stream, and non-colonized leaves of three, two or one leaf species. Leaves were renewed every month throughout six months, and microbial inoculum was ensured by a set of colonized leaves from the previous month. Microbial diversity, leaf mass loss and fungal biomass were assessed at the second and sixth months after plant species loss. Molecular diversity of fungi and bacteria, as the total number of operational taxonomic units per leaf diversity treatment, decreased with leaf diversity loss. Fungal biomass tended to decrease linearly with leaf species loss on oak and eucalyptus, suggesting more pronounced effects of leaf diversity on lower quality leaves. Decomposition of alder and eucalyptus leaves was affected by leaf species identity, mainly after longer times following diversity loss. Leaf decomposition of alder decreased when mixed with eucalyptus, while decomposition of eucalyptus decreased in mixtures with oak. Results suggest that the effects of leaf diversity on microbial decomposers depended on leaf species number and also on which species were lost from the system, especially after longer times. This may have implications for the management of riparian forests to maintain stream ecosystem functioning.
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Affiliation(s)
- Isabel Fernandes
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Coyne KJ, Countway PD, Pilditch CA, Lee CK, Caron DA, Cary SC. Diversity and Distributional Patterns of Ciliates in Guaymas Basin Hydrothermal Vent Sediments. J Eukaryot Microbiol 2013; 60:433-47. [DOI: 10.1111/jeu.12051] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 03/18/2013] [Accepted: 03/18/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Kathryn J. Coyne
- College of Earth, Ocean, and Environment; University of Delaware; 700 Pilottown Road Lewes Delaware 19958 USA
| | - Peter D. Countway
- Department of Biological Sciences; University of Southern California; Los Angeles California 90089-0371 USA
| | - Conrad A. Pilditch
- Department of Biological Sciences; University of Waikato; Private Bag 3105 Hamilton 3240 New Zealand
| | - Charles K. Lee
- Department of Biological Sciences; University of Waikato; Private Bag 3105 Hamilton 3240 New Zealand
| | - David A. Caron
- Department of Biological Sciences; University of Southern California; Los Angeles California 90089-0371 USA
| | - Stephen C. Cary
- College of Earth, Ocean, and Environment; University of Delaware; 700 Pilottown Road Lewes Delaware 19958 USA
- Department of Biological Sciences; University of Waikato; Private Bag 3105 Hamilton 3240 New Zealand
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Gouba N, Raoult D, Drancourt M. Plant and fungal diversity in gut microbiota as revealed by molecular and culture investigations. PLoS One 2013; 8:e59474. [PMID: 23555039 PMCID: PMC3598745 DOI: 10.1371/journal.pone.0059474] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 02/18/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Few studies describing eukaryotic communities in the human gut microbiota have been published. The objective of this study was to investigate comprehensively the repertoire of plant and fungal species in the gut microbiota of an obese patient. METHODOLOGY/PRINCIPAL FINDINGS A stool specimen was collected from a 27-year-old Caucasian woman with a body mass index of 48.9 who was living in Marseille, France. Plant and fungal species were identified using a PCR-based method incorporating 25 primer pairs specific for each eukaryotic phylum and universal eukaryotic primers targeting 18S rRNA, internal transcribed spacer (ITS) and a chloroplast gene. The PCR products amplified using these primers were cloned and sequenced. Three different culture media were used to isolate fungi, and these cultured fungi were further identified by ITS sequencing. A total of 37 eukaryotic species were identified, including a Diatoms (Blastocystis sp.) species, 18 plant species from the Streptophyta phylum and 18 fungal species from the Ascomycota, Basidiomycota and Chytridiocomycota phyla. Cultures yielded 16 fungal species, while PCR-sequencing identified 7 fungal species. Of these 7 species of fungi, 5 were also identified by culture. Twenty-one eukaryotic species were discovered for the first time in human gut microbiota, including 8 fungi (Aspergillus flavipes, Beauveria bassiana, Isaria farinosa, Penicillium brevicompactum, Penicillium dipodomyicola, Penicillium camemberti, Climacocystis sp. and Malassezia restricta). Many fungal species apparently originated from food, as did 11 plant species. However, four plant species (Atractylodes japonica, Fibraurea tinctoria, Angelica anomala, Mitella nuda) are used as medicinal plants. CONCLUSIONS/SIGNIFICANCE Investigating the eukaryotic components of gut microbiota may help us to understand their role in human health.
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Affiliation(s)
- Nina Gouba
- Aix Marseille Université, URMITE, UMR63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
| | - Didier Raoult
- Aix Marseille Université, URMITE, UMR63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
- * E-mail:
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Gomaa F, Mitchell EAD, Lara E. Amphitremida (poche, 1913) is a new major, ubiquitous labyrinthulomycete clade. PLoS One 2013; 8:e53046. [PMID: 23341921 PMCID: PMC3544814 DOI: 10.1371/journal.pone.0053046] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 11/23/2012] [Indexed: 11/18/2022] Open
Abstract
Micro-eukaryotic diversity is poorly documented at all taxonomic levels and the phylogenetic affiliation of many taxa – including many well-known and common organisms - remains unknown. Among these incertae sedis taxa are Archerella flavum (Loeblich and Tappan, 1961) and Amphitrema wrightianum (Archer, 1869) (Amphitremidae), two filose testate amoebae commonly found in Sphagnum peatlands. To clarify their phylogenetic position, we amplified and sequenced the SSU rRNA gene obtained from four independent DNA extractions of A. flavum and three independent DNA extractions of A. wrightianum. Our molecular data demonstrate that genera Archerella and Amphitrema form a fully supported deep-branching clade within the Labyrinthulomycetes (Stramenopiles), together with Diplophrys sp. (ATCC50360) and several environmental clones obtained from a wide range of environments. This newly described clade we named Amphitremida is diverse genetically, ecologically and physiologically. Our phylogenetic analysis suggests that osmotrophic species evolved most likely from phagotrophic ancestors and that the bothrosome, an organelle that produces cytoplasmic networks used for attachment to the substratum and to absorb nutrients from the environments, appeared lately in labyrithulomycete evolution.
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Affiliation(s)
- Fatma Gomaa
- Laboratory of Soil Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Zoology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
- * E-mail: (FG); (EL)
| | | | - Enrique Lara
- Laboratory of Soil Biology, University of Neuchâtel, Neuchâtel, Switzerland
- * E-mail: (FG); (EL)
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Liu X, Gong J. Revealing the diversity and quantity of peritrich ciliates in environmental samples using specific primer-based PCR and quantitative PCR. Microbes Environ 2012; 27:497-503. [PMID: 23100023 PMCID: PMC4103560 DOI: 10.1264/jsme2.me12056] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Peritrichs are a diverse, ecologically important ciliate group usually with a complex life cycle. To date, the community of the peritrichs has been investigated by using morphology-based methods such as living observation and silver staining. Here we show a molecular approach for characterizing the diversity and quantity of free-living peritrichs in environmental samples. We newly designed four peritrich-specific primers targeting 18S rRNA genes that allow clone library construction, screening and analysis. A quantitative real-time PCR (qPCR) assay was developed to quantify peritrichs in environmental samples by using rDNA copy number as an indicator. DNA extracted from four water samples of contrasting environmental gradients was analysed. The results showed that the peritrich community was differentiated among these samples, and that the diversity decreased with the increase of water salinity. The qPCR results are consistent with the library sequence analysis in terms of quantity variations from sample to sample. The development of peritrich-specific primers, for the first time, for conventional PCR and qPCR assays, provides useful molecular tools for revealing the diversity and quantity of peritrich ciliates in environmental samples. Also, our study illustrates the potential of these molecular tools to ecological studies of other ciliate groups in diverse environments.
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Affiliation(s)
- Xihan Liu
- Laboratory of Environmental Microbiology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
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Jung JH, Kim S, Ryu S, Kim MS, Baek YS, Kim SJ, Choi JK, Park JK, Min GS. Development of single-nucleotide polymorphism-based phylum-specific PCR amplification technique: application to the community analysis using ciliates as a reference organism. Mol Cells 2012; 34:383-91. [PMID: 22965748 PMCID: PMC3887769 DOI: 10.1007/s10059-012-0169-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 12/13/2022] Open
Abstract
Despite recent advance in mass sequencing technologies such as pyrosequencing, assessment of culture-independent microbial eukaryote community structures using universal primers remains very difficult due to the tremendous richness and complexity of organisms in these communities. Use of a specific PCR marker targeting a particular group would provide enhanced sensitivity and more in-depth evaluation of microbial eukaryote communities compared to what can be achieved with universal primers. We discovered that many phylum- or group-specific single-nucleotide polymorphisms (SNPs) exist in small subunit ribosomal RNA (SSU rRNA) genes from diverse eukaryote groups. By applying this discovery to a known simple allele-discriminating (SAP) PCR method, we developed a technique that enables the identification of organisms belonging to a specific higher taxonomic group (or phylum) among diverse types of eukaryotes. We performed an assay using two complementary methods, pyrosequencing and clone library screening. In doing this, specificities for the group (ciliates) targeted in this study in bulked environmental samples were 94.6% for the clone library and 99.2% for pyrosequencing, respectively. In particular, our novel technique showed high selectivity for rare species, a feature that may be more important than the ability to identify quantitatively predominant species in community structure analyses. Additionally, our data revealed that a target-specific library (or ciliate-specific one for the present study) can better explain the ecological features of a sampling locality than a universal library.
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Affiliation(s)
- Jae-Ho Jung
- Department of Biological Sciences, Inha University, Incheon 402-751,
Korea
| | - Sanghee Kim
- Korea Polar Research Institute (KORDI), Songdo Techno Park, Incheon 406-840,
Korea
| | - Seongho Ryu
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065,
USA
| | - Min-Seok Kim
- Department of Biological Sciences, Inha University, Incheon 402-751,
Korea
| | - Ye-Seul Baek
- Department of Biological Sciences, Inha University, Incheon 402-751,
Korea
| | - Se-Joo Kim
- Department of Biological Sciences, Inha University, Incheon 402-751,
Korea
- Present address: Deep-sea and Seabed Resources Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744,
Korea
| | - Joong- Ki Choi
- Department of Oceanography, Inha University, Incheon 402-751,
Korea
| | - Joong-Ki Park
- Department of Parasitology and Graduate Program in Cell Biology and Genetics, College of Medicine, Chungbuk National University, Cheongju 361-763,
Korea
| | - Gi-Sik Min
- Department of Biological Sciences, Inha University, Incheon 402-751,
Korea
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Zirnstein I, Arnold T, Krawczyk-Bärsch E, Jenk U, Bernhard G, Röske I. Eukaryotic life in biofilms formed in a uranium mine. Microbiologyopen 2012; 1:83-94. [PMID: 22950016 PMCID: PMC3426414 DOI: 10.1002/mbo3.17] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 01/31/2012] [Accepted: 02/06/2012] [Indexed: 11/27/2022] Open
Abstract
The underground uranium mine Königstein (Saxony, Germany), currently in the process of remediation, represents an underground acid mine drainage (AMD) environment, that is, low pH conditions and high concentrations of heavy metals including uranium, in which eye-catching biofilm formations were observed. During active uranium mining from 1984 to 1990, technical leaching with sulphuric acid was applied underground on-site resulting in a change of the underground mine environment and initiated the formation of AMD and also the growth of AMD-related copious biofilms. Biofilms grow underground in the mine galleries in a depth of 250 m (50 m above sea level) either as stalactite-like slime communities or as acid streamers in the drainage channels. The eukaryotic diversity of these biofilms was analyzed by microscopic investigations and by molecular methods, that is, 18S rDNA PCR, cloning, and sequencing. The biofilm communities of the Königstein environment showed a low eukaryotic biodiversity and consisted of a variety of groups belonging to nine major taxa: ciliates, flagellates, amoebae, heterolobosea, fungi, apicomplexa, stramenopiles, rotifers and arthropoda, and a large number of uncultured eukaryotes, denoted as acidotolerant eukaryotic cluster (AEC). In Königstein, the flagellates Bodo saltans, the stramenopiles Diplophrys archeri, and the phylum of rotifers, class Bdelloidea, were detected for the first time in an AMD environment characterized by high concentrations of uranium. This study shows that not only bacteria and archaea may live in radioactive contaminated environments, but also species of eukaryotes, clearly indicating their potential influence on carbon cycling and metal immobilization within AMD-affected environment.
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Affiliation(s)
- Isabel Zirnstein
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf e.V.P.O. Box 510119, D-01314 Germany
| | - Thuro Arnold
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf e.V.P.O. Box 510119, D-01314 Germany
| | - Evelyn Krawczyk-Bärsch
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf e.V.P.O. Box 510119, D-01314 Germany
| | - Ulf Jenk
- Wismut GmbHJagdschänkenstraße 29, D-09117 Chemnitz, Germany
| | - Gert Bernhard
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf e.V.P.O. Box 510119, D-01314 Germany
- Institute of Chemistry, Technical University DresdenD-01062 Dresden, Germany
| | - Isolde Röske
- Institute of Microbiology, Technical University DresdenZellescher Weg 20 b, D-01217 Dresden, Germany
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Sweet M, Bythell J. Ciliate and bacterial communities associated with White Syndrome and Brown Band Disease in reef-building corals. Environ Microbiol 2012; 14:2184-99. [PMID: 22507379 PMCID: PMC3465780 DOI: 10.1111/j.1462-2920.2012.02746.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
White Syndrome (WS) and Brown Band Disease (BrB) are important causes of reef coral mortality for which causal agents have not been definitively identified. Here we use culture-independent molecular techniques (DGGE and clone libraries) to characterize ciliate and bacterial communities in these diseases. Bacterial (16S rRNA gene) and ciliate (18S rRNA gene) communities were highly similar between the two diseases. Four bacterial and nine ciliate ribotypes were observed in both diseases, but absent in non-diseased specimens. Only one of the bacteria, Arcobacter sp. (JF831360) increased substantially in relative 16S rRNA gene abundance and was consistently represented in all diseased samples. Four of the eleven ciliate morphotypes detected contained coral algal symbionts, indicative of the ingestion of coral tissues. In both WS and BrB, there were two ciliate morphotypes consistently represented in all disease lesion samples. Morph1 (JN626268) was observed to burrow into and underneath the coral tissues at the lesion boundary. Morph2 (JN626269), previously identified in BrB, appears to play a secondary, less invasive role in pathogenesis, but has a higher population density in BrB, giving rise to the visible brown band. The strong similarity in bacterial and ciliate community composition of these diseases suggests that they are actually the same syndrome.
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Affiliation(s)
- Michael Sweet
- School of Biology, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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Bourland WA, Hampikian G, Vďačný P. Morphology and phylogeny of a new woodruffiid ciliate, Etoschophrya inornata sp. n. (Ciliophora, Colpodea, Platyophryida), with an account on evolution of platyophryids. ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00539.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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47
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Dasytricha dominance in Surti buffalo rumen revealed by 18S rRNA sequences and real-time PCR assay. Curr Microbiol 2011; 63:281-8. [PMID: 21744288 DOI: 10.1007/s00284-011-9975-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 06/28/2011] [Indexed: 10/18/2022]
Abstract
The genetic diversity of protozoa in Surti buffalo rumen was studied by amplified ribosomal DNA restriction analysis, 18S rDNA sequence homology and phylogenetic and Real-time PCR analysis methods. Three animals were fed diet comprised green fodder Napier bajra 21 (Pennisetum purpureum), mature pasture grass (Dicanthium annulatum) and concentrate mixture (20% crude protein, 65% total digestible nutrients). A protozoa-specific primer (P-SSU-342f) and a eukarya-specific primer (Medlin B) were used to amplify a 1,360 bp fragment of DNA encoding protozoal small subunit (SSU) ribosomal RNA from rumen fluid. A total of 91 clones were examined and identified 14 different 18S RNA sequences based on PCR-RFLP pattern. These 14 phylotypes were distributed into four genera-based 18S rDNA database sequences and identified as Dasytricha (57 clones), Isotricha (14 clones), Ostracodinium (11 clones) and Polyplastron (9 clones). Phylogenetic analyses were also used to infer the makeup of protozoa communities in the rumen of Surti buffalo. Out of 14 sequences, 8 sequences (69 clones) clustered with the Dasytricha ruminantium-like clone and 4 sequences (13 clones) were also phylogenetically placed with the Isotricha prostoma-like clone. Moreover, 2 phylotypes (9 clones) were related to Polyplastron multivesiculatum-like clone. In addition, the number of 18S rDNA gene copies of Dasytricha ruminantium (0.05% to ciliate protozoa) was higher than Entodinium sp. (2.0 × 10(5) vs. 1.3 × 10(4)) in per ml ruminal fluid.
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Preferential feeding by the ciliates Chilodonella and Tetrahymena spp. and effects of these protozoa on bacterial biofilm structure and composition. Appl Environ Microbiol 2011; 77:4564-72. [PMID: 21602372 DOI: 10.1128/aem.02421-10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Protozoa are important components of microbial food webs, but protozoan feeding preferences and their effects in the context of bacterial biofilms are not well understood. The feeding interactions of two contrasting ciliates, the free-swimming filter feeder Tetrahymena sp. and the surface-associated predator Chilodonella sp., were investigated using biofilm-forming bacteria genetically modified to express fluorescent proteins. According to microscopy, both ciliates readily consumed cells from both Pseudomonas costantinii and Serratia plymuthica biofilms. When offered a choice between spatially separated biofilms, each ciliate showed a preference for P. costantinii biofilms. Experiments with bacterial cell extracts indicated that both ciliates used dissolved chemical cues to locate biofilms. Chilodonella sp. evidently used bacterial chemical cues as a basis for preferential feeding decisions, but it was unclear whether Tetrahymena sp. did also. Confocal microscopy of live biofilms revealed that Tetrahymena sp. had a major impact on biofilm morphology, forming holes and channels throughout S. plymuthica biofilms and reducing P. costantinii biofilms to isolated, grazing-resistant microcolonies. Grazing by Chilodonella sp. resulted in the development of less-defined trails through S. plymuthica biofilms and caused P. costantinii biofilms to become homogeneous scatterings of cells. It was not clear whether the observed feeding preferences for spatially separated P. costantinii biofilms over S. plymuthica biofilms resulted in selective targeting of P. costantinii cells in mixed biofilms. Grazing of mixed biofilms resulted in the depletion of both types of bacteria, with Tetrahymena sp. having a larger impact than Chilodonella sp., and effects similar to those seen in grazed single-species biofilms.
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Ntougias S, Tanasidis S, Melidis P. Microfaunal indicators, Ciliophora phylogeny and protozoan population shifts in an intermittently aerated and fed bioreactor. JOURNAL OF HAZARDOUS MATERIALS 2011; 186:1862-1869. [PMID: 21237559 DOI: 10.1016/j.jhazmat.2010.12.099] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 12/17/2010] [Indexed: 05/30/2023]
Abstract
Microfauna community structure was examined in the mixed liquor of a bench-scale bioreactor equipped with an intermittent aeration and feeding system. The reactor was operated under an intermittent aeration of 25 min in every 1 h and varying feeding conditions (0.264, 0.403 and 0.773 kg BOD(5)/m(3) d). A total of 14 protozoan and metazoan taxa were identified by microscopic examination. Sessile ciliates, followed by crawling ciliates, were the major protozoan groups under 0.403 kg BOD(5)/m(3) d organic loading conditions, while sessile ciliate population was remarkably increased under an organic loading of 0.773 kg BOD(5)/m(3) d. Principal Component Analysis and Pearson correlation coefficient tests were performed in order to reveal relationships between microfauna community and operational parameters. Ciliophora specific-18S rRNA gene clone library was constructed to identify ciliate diversity under 0.773 kg BOD(5)/m(3) d organic loading conditions. Ciliophora diversity consisted of members of Aspidiscidae, Epistylidae, Opisthonectidae and Vorticellidae, with the majority of the clones being associated with the species Vorticella fusca. At least one novel phylogenetic linkage among Ciliophora was identified. Comparisons made after molecular characterization and microscopic examination of Ciliophora community showed that the estimation of broad ciliate groups is useful for ecological considerations and evaluation of the operational conditions in wastewater treatment plants.
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MESH Headings
- Animals
- Biomarkers
- Bioreactors/microbiology
- Ciliophora/physiology
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- Phylogeny
- Population
- RNA, Ribosomal/chemistry
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/isolation & purification
- Reverse Transcriptase Polymerase Chain Reaction
- Sewage/chemistry
- Sewage/microbiology
- Waste Disposal, Fluid/methods
- Water Microbiology
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Affiliation(s)
- Spyridon Ntougias
- Democritus University of Thrace, Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Vas. Sofias 12, 67100 Xanthi, Greece.
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BOURLAND WILLIAMA, VĎAČNÝ PETER, DAVIS MICHAELC, HAMPIKIAN GREG. Morphology, Morphometrics, and Molecular Characterization of Bryophrya gemmea n. sp. (Ciliophora, Colpodea): Implications for the Phylogeny and Evolutionary Scenario for the Formation of Oral Ciliature in the Order Colpodida. J Eukaryot Microbiol 2010; 58:22-36. [DOI: 10.1111/j.1550-7408.2010.00522.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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