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Li R, Zhuang W, Feng X, Zhu X, Hu X. Morphology and molecular phylogeny of three Parasonderia species including a new species (Ciliophora, Plagiopylea). Eur J Protistol 2024; 94:126087. [PMID: 38761673 DOI: 10.1016/j.ejop.2024.126087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/28/2024] [Accepted: 04/30/2024] [Indexed: 05/20/2024]
Abstract
Ciliates of the class Plagiopylea play a vital role in various anaerobic environments as consumers of prokaryotes. Yet, the diversity and phylogeny of this group of ciliates, especially marine representatives, remain poorly known. In this study, three Parasonderia species, viz., Parasonderia elongata spec. nov., and the already known P. cyclostoma and P. vestita, discovered in anaerobic sediments from various intertidal zones in China, were investigated based on their living morphology, infraciliature, and small subunit ribosomal rRNA gene sequences. Parasonderia elongata can be recognized by its larger body size, elongated body shape, oval oral opening, number of oral kineties, and significantly shortened leftmost postbuccal polykineties on the cell surface. Improved diagnosis and redescription of P. cyclostoma is provided for the first time, including data on infraciliature and molecular sequence. Phylogenetic analyses revealed that the three species cluster together and with the sequence of a Chinese population of P. vestita already present in the GenBank database, forming a robust clade.
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Affiliation(s)
- Ran Li
- College of Fisheries, & Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Wenbao Zhuang
- College of Fisheries, & Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaochen Feng
- College of Fisheries, & Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaoxuan Zhu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xiaozhong Hu
- College of Fisheries, & Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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2
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Lanzoni O, Szokoli F, Schrallhammer M, Sabaneyeva E, Krenek S, Doak TG, Verni F, Berendonk TU, Castelli M, Petroni G. "Candidatus Intestinibacterium parameciiphilum"-member of the "Candidatus Paracaedibacteraceae" family (Alphaproteobacteria, Holosporales) inhabiting the ciliated protist Paramecium. Int Microbiol 2024; 27:659-671. [PMID: 37615902 PMCID: PMC11144129 DOI: 10.1007/s10123-023-00414-5] [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: 05/13/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023]
Abstract
Protists frequently host diverse bacterial symbionts, in particular those affiliated with the order Holosporales (Alphaproteobacteria). All characterised members of this bacterial lineage have been retrieved in obligate association with a wide range of eukaryotes, especially multiple protist lineages (e.g. amoebozoans, ciliates, cercozoans, euglenids, and nucleariids), as well as some metazoans (especially arthropods and related ecdysozoans). While the genus Paramecium and other ciliates have been deeply investigated for the presence of symbionts, known members of the family "Candidatus Paracaedibacteraceae" (Holosporales) are currently underrepresented in such hosts. Herein, we report the description of "Candidatus Intestinibacterium parameciiphilum" within the family "Candidatus Paracaedibacteraceae", inhabiting the cytoplasm of Paramecium biaurelia. This novel bacterium is almost twice as big as its relative "Candidatus Intestinibacterium nucleariae" from the opisthokont Nuclearia and does not present a surrounding halo. Based on phylogenetic analyses of 16S rRNA gene sequences, we identified six further potential species-level lineages within the genus. Based on the provenance of the respective samples, we investigated the environmental distribution of the representatives of "Candidatus Intestinibacterium" species. Obtained results are consistent with an obligate endosymbiotic lifestyle, with protists, in particular freshwater ones, as hosts. Thus, available data suggest that association with freshwater protists could be the ancestral condition for the members of the "Candidatus Intestinibacterium" genus.
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Affiliation(s)
| | - Franziska Szokoli
- Department of Biology, University of Pisa, Pisa, Italy
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Martina Schrallhammer
- Mikrobiologie, Institut für Biologie II, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Elena Sabaneyeva
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Sascha Krenek
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | | | - Franco Verni
- Department of Biology, University of Pisa, Pisa, Italy
| | - Thomas U Berendonk
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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3
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Li R, Zhuang W, Feng X, Hines HN, Hu X. First redescription and molecular phylogeny of Trimyema claviforme Kahl, 1933 with the description of a Chinese population of Plagiopyla nasuta Stein, 1860 (Ciliophora, Plagiopylea). Eur J Protistol 2023; 90:126003. [PMID: 37453202 DOI: 10.1016/j.ejop.2023.126003] [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: 01/11/2023] [Revised: 06/14/2023] [Accepted: 06/17/2023] [Indexed: 07/18/2023]
Abstract
Ciliates belonging to the class Plagiopylea are obligate anaerobes that are often neglected due to their cryptic lifestyles, difficulty of observation, and overall under-sampling. Here, we investigate two species, namely Trimyema claviforme Kahl, 1933 and Plagiopyla nasuta Stein, 1860, collected in China from marine and freshwater anaerobic sediments, respectively. A complete morphological dataset, together with SSU rRNA gene sequence data were obtained and used to diagnose the species. No molecular sequencing had ever been performed on Trimyema claviforme, with its ciliature also previously unknown. Based on these novel data presented here, the ciliate is characterized by a claviform cell shape, with a size of 35-45 × 10-20 μm in vivo, 28-39 longitudinal somatic ciliary rows forming five ciliary girdles (four complete girdles and a shorter one), two dikinetids left to anterior end of oral kinety 1, and an epaulet. A Chinese population of the well-known ciliate P. nasuta was investigated, and morphological comparisons revealed phenotypic stability of the species. The phylogenetic analyses supported previous findings about the monophyly of the families Trimyemidae and Plagiopylidae, with Trimyema claviforme branching off early in the genus Trimyema. The Chinese population of P. nasuta clusters together with two other populations with full support corroborating their conspecificity.
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Affiliation(s)
- Ran Li
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Wenbao Zhuang
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaochen Feng
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Hunter N Hines
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida 34946, USA
| | - Xiaozhong Hu
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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4
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Li R, Zhuang W, Feng X, Al-Farraj SA, Warren A, Hu X. Phylogeny of the anaerobic ciliate genus Sonderia (Protista: Ciliophora: Plagiopylea), including the description of three novel species and a brief revision of the genus. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:493-512. [PMID: 37078079 PMCID: PMC10077210 DOI: 10.1007/s42995-022-00142-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/06/2022] [Indexed: 05/03/2023]
Abstract
Anaerobic protists in general, and ciliates in particular, are important components of anoxic or hypoxic environments, however, their diversity remains underestimated. Sonderia is a poorly studied genus that is distributed worldwide and is commonly found in anaerobic environments. In the present study, the taxonomy and phylogeny of three new species, namely Sonderia aposinuata sp. nov., Sonderia paramacrochilus sp. nov. and Sonderia steini sp. nov., collected from China, were investigated based on microscopic observations and SSU rRNA gene sequencing methods. Sonderia aposinuata sp. nov. is diagnosed mainly by having a relatively large body size, a crescent-shaped oral opening, numerous slender extrusomes, one suture on the ventral side and two on the dorsal side, and a buccal cavity that occupies the anterior third of the cell. Sonderia paramacrochilus sp. nov. closely resembles S. macrochilus but differs mainly by its oral opening being located closer to the anterior cell margin and its spindle-shaped extrusomes. Sonderia steini sp. nov. is a freshwater species that can be recognized by its shallow buccal cavity, sparsely distributed rod-shaped extrusomes, and having 68-79 monokinetidal somatic kineties that form sutures on both sides of the body. Phylogenetic analyses based on small subunit ribosomal RNA (SSU rRNA) gene sequence data support the monophyly of the family Sonderiidae, however, Sonderia is paraphyletic. The genus Sonderia is briefly revised and a key to the identification of species belonging to this genus is supplied.
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Affiliation(s)
- Ran Li
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Wenbao Zhuang
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Xiaochen Feng
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Saleh A. Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, 11451 Saudi Arabia
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK
| | - Xiaozhong Hu
- College of Fisheries, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
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5
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Rotterová J, Edgcomb VP, Čepička I, Beinart R. Anaerobic Ciliates as a Model Group for Studying Symbioses in Oxygen-depleted Environments. J Eukaryot Microbiol 2022; 69:e12912. [PMID: 35325496 DOI: 10.1111/jeu.12912] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anaerobiosis has independently evolved in multiple lineages of ciliates, allowing them to colonize a variety of anoxic and oxygen-depleted habitats. Anaerobic ciliates commonly form symbiotic relationships with various prokaryotes, including methanogenic archaea and members of several bacterial groups. The hypothesized functions of these ecto- and endosymbionts include the symbiont utilizing the ciliate's fermentative end-products to increase host's anaerobic metabolic efficiency, or the symbiont directly providing the host with energy by denitrification or photosynthesis. The host, in turn, may protect the symbiont from competition, the environment, and predation. Despite rapid advances in sampling, molecular, and microscopy methods, as well as the associated broadening of the known diversity of anaerobic ciliates, many aspects of these ciliate symbioses, including host-specificity and co-evolution, remain largely unexplored. Nevertheless, with the number of comparative genomic and transcriptomic analyses targeting anaerobic ciliates and their symbionts on the rise, insights into the nature of these symbioses and the evolution of the ciliate transition to obligate anaerobiosis continue to deepen. This review summarizes the current body of knowledge regarding the complex nature of symbioses in anaerobic ciliates, the diversity of these symbionts, their role in the evolution of ciliate anaerobiosis and their significance in ecosystem-level processes.
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Affiliation(s)
- Johana Rotterová
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Roxanne Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
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Li R, Zhuang W, Wang C, El-Serehy H, Al-Farraj SA, Warren A, Hu X. Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea). Int J Syst Evol Microbiol 2021; 71. [PMID: 34427553 DOI: 10.1099/ijsem.0.004936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.
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Affiliation(s)
- Ran Li
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, PR China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, PR China
| | - Wenbao Zhuang
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, PR China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, PR China
| | - Congcong Wang
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, PR China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, PR China
| | - Hamed El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK
| | - Xiaozhong Hu
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, PR China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, PR China
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7
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Multidisciplinary integrated characterization of a native Chlorella-like microalgal strain isolated from a municipal landfill leachate. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Serra V, Gammuto L, Nitla V, Castelli M, Lanzoni O, Sassera D, Bandi C, Sandeep BV, Verni F, Modeo L, Petroni G. Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont "Candidatus Pinguicoccus supinus" sp. nov. Sci Rep 2020; 10:20311. [PMID: 33219271 PMCID: PMC7679464 DOI: 10.1038/s41598-020-76348-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/30/2020] [Indexed: 01/30/2023] Open
Abstract
Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics and, more recently, on evolutionary relationships. With the birth of novel genomics/bioinformatics techniques and the increasing interest in microbiome studies, a further advance of taxonomic discipline appears not only possible but highly desirable. The present work proposes a new approach to modern taxonomy, consisting in the inclusion of novel descriptors in the organism characterization: (1) the presence of associated microorganisms (e.g.: symbionts, microbiome), (2) the mitochondrial genome of the host, (3) the symbiont genome. This approach aims to provide a deeper comprehension of the evolutionary/ecological dimensions of organisms since their very first description. Particularly interesting, are those complexes formed by the host plus associated microorganisms, that in the present study we refer to as "holobionts". We illustrate this approach through the description of the ciliate Euplotes vanleeuwenhoeki sp. nov. and its bacterial endosymbiont "Candidatus Pinguicoccus supinus" gen. nov., sp. nov. The endosymbiont possesses an extremely reduced genome (~ 163 kbp); intriguingly, this suggests a high integration between host and symbiont.
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Affiliation(s)
- Valentina Serra
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Leandro Gammuto
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Venkatamahesh Nitla
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Michele Castelli
- Department of Biosciences, Romeo and Enrica Invernizzi Pediatric Research Center, University of Milan, Milan, Italy
- Department of Biology and Biotechnology "Lazzaro Spallanzani", Pavia University, Pavia, Italy
| | - Olivia Lanzoni
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Davide Sassera
- Department of Biology and Biotechnology "Lazzaro Spallanzani", Pavia University, Pavia, Italy
| | - Claudio Bandi
- Department of Biosciences, Romeo and Enrica Invernizzi Pediatric Research Center, University of Milan, Milan, Italy
| | | | - Franco Verni
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Letizia Modeo
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy.
- CIME, Centro Interdipartimentale di Microscopia Elettronica, Università di Pisa, Pisa, Italy.
- CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Pisa, India.
| | - Giulio Petroni
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy.
- CIME, Centro Interdipartimentale di Microscopia Elettronica, Università di Pisa, Pisa, Italy.
- CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Pisa, India.
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Modeo L, Salvetti A, Rossi L, Castelli M, Szokoli F, Krenek S, Serra V, Sabaneyeva E, Di Giuseppe G, Fokin SI, Verni F, Petroni G. "Candidatus Trichorickettsia mobilis", a Rickettsiales bacterium, can be transiently transferred from the unicellular eukaryote Paramecium to the planarian Dugesia japonica. PeerJ 2020; 8:e8977. [PMID: 32351785 PMCID: PMC7183750 DOI: 10.7717/peerj.8977] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 03/24/2020] [Indexed: 01/10/2023] Open
Abstract
Most of the microorganisms responsible for vector-borne diseases (VBD) have hematophagous arthropods as vector/reservoir. Recently, many new species of microorganisms phylogenetically related to agents of VBD were found in a variety of aquatic eukaryotic hosts; in particular, numerous new bacterial species related to the genus Rickettsia (Alphaproteobacteria, Rickettsiales) were discovered in protist ciliates and other unicellular eukaryotes. Although their pathogenicity for humans and terrestrial animals is not known, several indirect indications exist that these bacteria might act as etiological agents of possible VBD of aquatic organisms, with protists as vectors. In the present study, a novel strain of the Rickettsia-Like Organism (RLO) endosymbiont "Candidatus (Ca.) Trichorickettsia mobilis" was identified in the macronucleus of the ciliate Paramecium multimicronucleatum. We performed transfection experiments of this RLO to planarians (Dugesia japonica) per os. Indeed, the latter is a widely used model system for studying bacteria pathogenic to humans and other Metazoa. In transfection experiments, homogenized paramecia were added to food of antibiotic-treated planarians. Treated and non-treated (i.e. control) planarians were investigated at day 1, 3, and 7 after feeding for endosymbiont presence by means of PCR and ultrastructural analyses. Obtained results were fully concordant and suggest that this RLO endosymbiont can be transiently transferred from ciliates to metazoans, being detected up to day 7 in treated planarians' enterocytes. Our findings might offer insights into the potential role of ciliates or other protists as putative vectors for diseases caused by Rickettsiales or other RLOs and occurring in fish farms or in the wild.
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Affiliation(s)
- Letizia Modeo
- Department of Biology, University of Pisa, Pisa, Italy.,CIME, Centro Interdipartimentale di Microscopia Elettronica, University of Pisa, Pisa, Italy.,CISUP, Centro per l'Integrazione della Strumentazione, University of Pisa, Pisa, Italy
| | - Alessandra Salvetti
- CIME, Centro Interdipartimentale di Microscopia Elettronica, University of Pisa, Pisa, Italy.,CISUP, Centro per l'Integrazione della Strumentazione, University of Pisa, Pisa, Italy.,Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Leonardo Rossi
- CIME, Centro Interdipartimentale di Microscopia Elettronica, University of Pisa, Pisa, Italy.,CISUP, Centro per l'Integrazione della Strumentazione, University of Pisa, Pisa, Italy.,Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Michele Castelli
- Centro Romeo ed Enrica Invernizzi Ricerca Pediatrica, Department of Biosciences, University of Milan, Milan, Italy
| | - Franziska Szokoli
- Institute of Hydrobiology, Dresden University of Technology, Dresden, Germany
| | - Sascha Krenek
- Institute of Hydrobiology, Dresden University of Technology, Dresden, Germany.,Department of River Ecology, Helmholtz Center for Environmental Research-UFZ, Magdeburg, Germany
| | | | - Elena Sabaneyeva
- Department of Cytology and Histology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Sergei I Fokin
- Department of Biology, University of Pisa, Pisa, Italy.,CIME, Centro Interdipartimentale di Microscopia Elettronica, University of Pisa, Pisa, Italy.,Department of Invertebrate Zoology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Franco Verni
- Department of Biology, University of Pisa, Pisa, Italy.,CIME, Centro Interdipartimentale di Microscopia Elettronica, University of Pisa, Pisa, Italy.,CISUP, Centro per l'Integrazione della Strumentazione, University of Pisa, Pisa, Italy
| | - Giulio Petroni
- Department of Biology, University of Pisa, Pisa, Italy.,CIME, Centro Interdipartimentale di Microscopia Elettronica, University of Pisa, Pisa, Italy.,CISUP, Centro per l'Integrazione della Strumentazione, University of Pisa, Pisa, Italy
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10
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Sigona C, Bardi A, Modeo L, Mori G, Potekhin A, Verni F, Munz G, Petroni G. Role of bacterivorous organisms on fungal-based systems for natural tannin degradation. Heliyon 2020; 6:e03604. [PMID: 32258507 PMCID: PMC7118291 DOI: 10.1016/j.heliyon.2020.e03604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 08/04/2019] [Accepted: 03/11/2020] [Indexed: 11/29/2022] Open
Abstract
Tannery wastewater presents high concentrations of organic load and pollutant recalcitrant molecules (e.g. tannins), which reduce the efficiency of biological treatment processes. Recent studies showed that several fungal species and strains are effective in the degradation of tannins. However, high bacterial load can negatively affect fungal growth, reducing system stability and degradation performances. The aim of the present study was to evaluate the effects of the introduction of bacterivorous grazers (ciliates and/or rotifers) in batch scale experiments using fungi to remove Tara tannin, i.e. to check the potential synergistic effect between fungi and bacterivorous grazers in the degradation of recalcitrant compounds. In this context, the ciliated grazers Paramecium calkinsi, Tetrahymena sp., Pseudovorticella sp., and the rotifer Lecane inermis, preliminary selected according to their ability to grow in a solution prepared with Tara tannin, were separately tested. Activated sludge, including a complex mixture of native grazers, was used as experimental control. The following parameters were monitored: bacterial load, number of grazers/mL and Soluble Chemical Oxygen Demand (SCOD). Colony Forming Unit (CFU)/grazers ratio was also calculated. Particular attention was paid to: i) bacterial load reduction and ii) enhancement of recalcitrant compounds degradation, and we observed that in all experimental conditions where grazers occurred bacterial load was significantly reduced and the system achieved a higher SCOD removal in a shorter time. Our findings provide useful insights for the stabilization of fungal-based systems in non-sterile conditions.
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Affiliation(s)
- Cristiana Sigona
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain
| | - Alessandra Bardi
- Department of Civil and Environmental Engineering, University of Florence, Via Santa Marta 3, 50139, Florence, Italy
| | - Letizia Modeo
- Department of Biology, University of Pisa, Via Alessandro Volta 4, 56126, Pisa, Italy.,CIME, Centro Interdipartimentale di Microscopia Elettronica, Univerisità di Pisa, via A. Volta 4, 56126, Pisa, Italy.,CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Lungarno Pacinotti 43, Pisa, Italy
| | - Gualtiero Mori
- CER2CO (Centro Ricerca Reflui Conciari), Via Arginale Ovest 81, 56028, San Romano-San Miniato, Pisa, Italy
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint-Petersburg State University, 7/9 University Embankment, 199034, Saint Petersburg, Russia
| | - Franco Verni
- Department of Biology, University of Pisa, Via Alessandro Volta 4, 56126, Pisa, Italy.,CIME, Centro Interdipartimentale di Microscopia Elettronica, Univerisità di Pisa, via A. Volta 4, 56126, Pisa, Italy.,CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Lungarno Pacinotti 43, Pisa, Italy
| | - Giulio Munz
- Department of Civil and Environmental Engineering, University of Florence, Via Santa Marta 3, 50139, Florence, Italy
| | - Giulio Petroni
- Department of Biology, University of Pisa, Via Alessandro Volta 4, 56126, Pisa, Italy.,CIME, Centro Interdipartimentale di Microscopia Elettronica, Univerisità di Pisa, via A. Volta 4, 56126, Pisa, Italy.,CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Lungarno Pacinotti 43, Pisa, Italy
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11
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Campello-Nunes PH, Fernandes NM, Szokoli F, Fokin SI, Serra V, Modeo L, Petroni G, Soares CA, Paiva TDS, Silva-Neto IDD. Parablepharisma (Ciliophora) is not a Heterotrich: A Phylogenetic and Morphological Study with the Proposal of New Taxa. Protist 2020; 171:125716. [DOI: 10.1016/j.protis.2020.125716] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/30/2020] [Accepted: 02/02/2020] [Indexed: 12/13/2022]
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12
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Castelli M, Sabaneyeva E, Lanzoni O, Lebedeva N, Floriano AM, Gaiarsa S, Benken K, Modeo L, Bandi C, Potekhin A, Sassera D, Petroni G. Deianiraea, an extracellular bacterium associated with the ciliate Paramecium, suggests an alternative scenario for the evolution of Rickettsiales. THE ISME JOURNAL 2019; 13:2280-2294. [PMID: 31073215 PMCID: PMC6776064 DOI: 10.1038/s41396-019-0433-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/19/2019] [Accepted: 04/10/2019] [Indexed: 12/28/2022]
Abstract
Rickettsiales are a lineage of obligate intracellular Alphaproteobacteria, encompassing important human pathogens, manipulators of host reproduction, and mutualists. Here we report the discovery of a novel Rickettsiales bacterium associated with Paramecium, displaying a unique extracellular lifestyle, including the ability to replicate outside host cells. Genomic analyses show that the bacterium possesses a higher capability to synthesise amino acids, compared to all investigated Rickettsiales. Considering these observations, phylogenetic and phylogenomic reconstructions, and re-evaluating the different means of interaction of Rickettsiales bacteria with eukaryotic cells, we propose an alternative scenario for the evolution of intracellularity in Rickettsiales. According to our reconstruction, the Rickettsiales ancestor would have been an extracellular and metabolically versatile bacterium, while obligate intracellularity would have evolved later, in parallel and independently, in different sub-lineages. The proposed new scenario could impact on the open debate on the lifestyle of the last common ancestor of mitochondria within Alphaproteobacteria.
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Affiliation(s)
- Michele Castelli
- Centro Romeo ed Enrica Invernizzi Ricerca Pediatrica, Dipartimento di Bioscienze, Università degli studi di Milano, Milan, Italy
| | - Elena Sabaneyeva
- Department of Cytology and Histology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Olivia Lanzoni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Natalia Lebedeva
- Centre of Core Facilities "Culture Collections of Microorganisms", Saint Petersburg State University, Saint Petersburg, Russia
| | - Anna Maria Floriano
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Stefano Gaiarsa
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Konstantin Benken
- Core Facility Center for Microscopy and Microanalysis, Saint Petersburg State University, Saint Petersburg, Russia
| | - Letizia Modeo
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Claudio Bandi
- Centro Romeo ed Enrica Invernizzi Ricerca Pediatrica, Dipartimento di Bioscienze, Università degli studi di Milano, Milan, Italy
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Davide Sassera
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy.
| | - Giulio Petroni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy.
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13
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Illa K, Shameem U, Serra V, Melai M, Mangam S, Basuri CK, Petroni G, Modeo L. Multidisciplinary investigation on the catfish parasite Hamatopeduncularia Yamaguti, 1953 (Monogenoidea: Dactylogyridae): description of two new species from India, and phylogenetic considerations. EUROPEAN ZOOLOGICAL JOURNAL 2019. [DOI: 10.1080/24750263.2019.1597931] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- K. Illa
- Department of Zoology, Andhra University, Visakhapatnam, India
| | - U. Shameem
- Department of Zoology, Andhra University, Visakhapatnam, India
| | - V. Serra
- Department of Biology, University of Pisa, Pisa, Italy
| | - M. Melai
- Department of Biology, University of Pisa, Pisa, Italy
| | - S. Mangam
- Department of Zoology, Andhra University, Visakhapatnam, India
| | - C. K. Basuri
- National Centre for Coastal Research, NIOT Campus, Ministry of Earth Science, Chennai, India
| | - G. Petroni
- Department of Biology, University of Pisa, Pisa, Italy
| | - L. Modeo
- Department of Biology, University of Pisa, Pisa, Italy
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14
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Fokin SI, Serra V, Ferrantini F, Modeo L, Petroni G. "Candidatus Hafkinia simulans" gen. nov., sp. nov., a Novel Holospora-Like Bacterium from the Macronucleus of the Rare Brackish Water Ciliate Frontonia salmastra (Oligohymenophorea, Ciliophora): Multidisciplinary Characterization of the New Endosymbiont and Its Host. MICROBIAL ECOLOGY 2019; 77:1092-1106. [PMID: 30627761 DOI: 10.1007/s00248-018-1311-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/19/2018] [Indexed: 05/09/2023]
Abstract
We characterized a novel Holospora-like bacterium (HLB) (Alphaproteobacteria, Holosporales) living in the macronucleus of the brackish water ciliate Frontonia salmastra. This bacterium was morphologically and ultrastructurally investigated, and its life cycle and infection capabilities were described. We also obtained its 16S rRNA gene sequence and performed in situ hybridization experiments with a specifically-designed probe. A new taxon, "Candidatus Hafkinia simulans", was established for this HLB. The phylogeny of the family Holosporaceae based on 16S rRNA gene sequences was inferred, adding to the already available data both the sequence of the novel bacterium and those of other Holospora and HLB species recently characterized. Our phylogenetic analysis provided molecular support for the monophyly of HLBs and placed the new endosymbiont as the sister genus of Holospora. Additionally, the host ciliate F. salmastra, recorded in Europe for the first time, was concurrently described through a multidisciplinary study. Frontonia salmastra's phylogenetic position in the subclass Peniculia and the genus Frontonia was assessed according to 18S rRNA gene sequencing. Comments on the biodiversity of this genus were added according to past and recent literature.
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Affiliation(s)
- Sergei I Fokin
- Department of Biology, University of Pisa, 56126, Pisa, Italy.
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia, 199034.
- St. Petersburg Branch of the S.I. Vavilov Institute of History of Science and Technology, Russian Academy of Sciences, St. Petersburg, Russia, 199034.
| | - Valentina Serra
- Department of Biology, University of Pisa, 56126, Pisa, Italy.
| | | | - Letizia Modeo
- Department of Biology, University of Pisa, 56126, Pisa, Italy
| | - Giulio Petroni
- Department of Biology, University of Pisa, 56126, Pisa, Italy
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15
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Chiellini C, Pasqualetti C, Lanzoni O, Fagorzi C, Bazzocchi C, Fani R, Petroni G, Modeo L. Harmful Effect of Rheinheimera sp. EpRS3 ( Gammaproteobacteria) Against the Protist Euplotes aediculatus (Ciliophora, Spirotrichea): Insights Into the Ecological Role of Antimicrobial Compounds From Environmental Bacterial Strains. Front Microbiol 2019; 10:510. [PMID: 31001206 PMCID: PMC6457097 DOI: 10.3389/fmicb.2019.00510] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/27/2019] [Indexed: 01/24/2023] Open
Abstract
Rheinheimera sp. strain EpRS3, isolated from the rhizosphere of Echinacea purpurea, is already known for its ability to produce antibacterial compounds. By use of culture experiments, we verified and demonstrated its harmful effect against the ciliated protist Euplotes aediculatus (strain EASCc1), which by FISH experiments resulted to harbor in its cytoplasm the obligate bacterial endosymbiont Polynucleobacter necessarius (Betaproteobacteria) and the secondary endosymbiont "Candidatus Nebulobacter yamunensis" (Gammaproteobacteria). In culture experiments, the number of ciliates treated both with liquid broth bacteria-free (Supernatant treatment) and bacteria plus medium (Tq treatment), decreases with respect to control cells, with complete disappearance of ciliates within 6 h after Tq treatment. Results suggest that Rheinheimera sp. EpRS3 produces and releases in liquid culture one or more bioactive molecules affecting E. aediculatus survival. TEM analysis of control (not treated) ciliates allowed to morphologically characterize both kind of E. aediculatus endosymbionts. In treated ciliates, collected soon after the arising of cell suffering leading to death, TEM observations revealed some ultrastructural damages, indicating that P. necessarius endosymbionts went into degradation and vacuolization after both Supernatant and Tq treatments. Additionally, TEM investigation showed that when the ciliate culture was inoculated with Tq treatment, both a notable decrease of P. necessarius number and an increase of damaged and degraded mitochondria occur. FISH experiments performed on treated ciliates confirmed TEM results and, by means of the specific probe herein designed, disclosed the presence of Rheinheimera sp. EpRS3 both inside phagosomes and free in cytoplasm in ciliates after Tq treatment. This finding suggests a putative ability of Rheinheimera sp. EpRS3 to reintroduce itself in the environment avoiding ciliate digestion.
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Affiliation(s)
| | | | | | - Camilla Fagorzi
- Department of Biology, University of Florence, Florence, Italy
| | - Chiara Bazzocchi
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Florence, Italy
| | | | - Letizia Modeo
- Department of Biology, University of Pisa, Pisa, Italy
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16
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Lanzoni O, Sabaneyeva E, Modeo L, Castelli M, Lebedeva N, Verni F, Schrallhammer M, Potekhin A, Petroni G. Diversity and environmental distribution of the cosmopolitan endosymbiont "Candidatus Megaira". Sci Rep 2019; 9:1179. [PMID: 30718604 PMCID: PMC6362216 DOI: 10.1038/s41598-018-37629-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/11/2018] [Indexed: 02/08/2023] Open
Abstract
Members of the order Rickettsiales are often found in association with ciliated protists. An interesting case is the bacterial endosymbiont “Candidatus Megaira”, which is phylogenetically closely related to the pathogen Rickettsia. “Candidatus Megaira” was first described as an intracellular bacterium in several ciliate species. Since then it has been found in association with diverse evolutionary distantly-related hosts, among them other unicellular eukaryotes, and also algae, and metazoa, such as cnidarians. We provide the characterization of several new strains of the type species “Candidatus Megaira polyxenophila”, and the multidisciplinary description of a novel species, “Candidatus Megaira venefica”, presenting peculiar features, which highlight the diversity and variability of these widespread bacterial endosymbionts. Screening of the 16S rRNA gene short amplicon database and phylogenetic analysis of 16S rRNA gene hypervariable regions revealed the presence of further hidden lineages, and provided hints on the possibility that these bacteria may be horizontally transmitted among aquatic protists and metazoa. The phylogenetic reconstruction supports the existence of at least five different separate species-level clades of “Candidatus Megaira”, and we designed a set of specific probes allowing easy recognition of the four major clades of the genus.
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Affiliation(s)
| | - Elena Sabaneyeva
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Letizia Modeo
- Department of Biology, University of Pisa, Pisa, Italy
| | - Michele Castelli
- Centro Romeo ed Enrica Invernizzi Ricerca Pediatrica, Dipartimento di Bioscienze, Università degli studi di Milano, Milan, Italy
| | - Natalia Lebedeva
- Core Facilities Centre "Culture Collections of Microorganisms", Saint Petersburg State University, Saint Petersburg, Russia
| | - Franco Verni
- Department of Biology, University of Pisa, Pisa, Italy
| | | | - Alexey Potekhin
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
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17
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Nitla V, Serra V, Fokin SI, Modeo L, Verni F, Sandeep BV, Kalavati C, Petroni G. Critical revision of the family Plagiopylidae (Ciliophora: Plagiopylea), including the description of two novel species, Plagiopyla ramani and Plagiopyla narasimhamurtii, and redescription of Plagiopyla nasuta Stein, 1860 from India. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly041] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Sergei I Fokin
- Department of Biology, University of Pisa, Pisa, Italy
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
| | - Letizia Modeo
- Department of Biology, University of Pisa, Pisa, Italy
| | - Franco Verni
- Department of Biology, University of Pisa, Pisa, Italy
| | - Bhagavatula Venkata Sandeep
- Department of Zoology, Andhra University, Visakhapatnam, India
- Department of Biotechnology, Andhra University, Visakhapatnam, India
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18
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Boscaro V, Santoferrara LF, Zhang Q, Gentekaki E, Syberg-Olsen MJ, Del Campo J, Keeling PJ. EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates. Environ Microbiol 2018; 20:2218-2230. [PMID: 29727060 DOI: 10.1111/1462-2920.14264] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/13/2018] [Accepted: 04/27/2018] [Indexed: 01/01/2023]
Abstract
High-throughput sequencing (HTS) surveys, among the most common approaches currently used in environmental microbiology, require reliable reference databases to be correctly interpreted. The EukRef Initiative (eukref.org) is a community effort to manually screen available small subunit (SSU) rRNA gene sequences and produce a public, high-quality and informative framework of phylogeny-based taxonomic annotations. In the context of EukRef, we present a database for the monophyletic phylum Ciliophora, one of the most complex, diverse and ubiquitous protist groups. We retrieved more than 11 500 sequences of ciliates present in GenBank (28% from identified isolates and 72% from environmental surveys). Our approach included the inference of phylogenetic trees for every ciliate lineage and produced the largest SSU rRNA tree of the phylum Ciliophora to date. We flagged approximately 750 chimeric or low-quality sequences, improved the classification of 70% of GenBank entries and enriched environmental and literature metadata by 30%. The performance of EukRef-Ciliophora is superior to the current SILVA database in classifying HTS reads from a global marine survey. Comprehensive outputs are publicly available to make the new tool a useful guide for non-specialists and a quick reference for experts.
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Affiliation(s)
- Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Luciana F Santoferrara
- Department of Marine Sciences, University of Connecticut, Stamford, CT, USA.,Department of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, USA
| | - Qianqian Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | | | - Javier Del Campo
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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19
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Focusing on Genera to Improve Species Identification: Revised Systematics of the Ciliate Spirostomum. Protist 2014; 165:527-41. [DOI: 10.1016/j.protis.2014.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/18/2014] [Accepted: 05/21/2014] [Indexed: 11/20/2022]
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