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Bouras H, Quesnelle Y, Barozet A, Goux D, Blin JL, Savary M, Zatylny-Gaudin C, Houssin M. First isolation of Francisella halioticida strains from blue mussel (Mytilus edulis) in Normandy, France. J Invertebr Pathol 2023; 200:107950. [PMID: 37301277 DOI: 10.1016/j.jip.2023.107950] [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: 11/25/2022] [Revised: 04/26/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
Mass mortality events affecting the blue mussels Mytilus edulis have been observed in France since 2014. The DNA of the bacterium Francisella halioticida, reported as pathogen of giant abalone (Haliotis gigantea) and Yesso scallop (Mizuhopecten yessoensis) has been detected recently in mussels from areas suffering mortalities. Isolation of this bacterium was attempted from individuals collected during mortality events. Identification was performed by 16S rRNA gene sequencing, real-time specific PCR and MALDI-ToF using spectra produced from the strain 8472-13A isolated from diseased Yesso scallop in Canada. Five isolates were identified as F. halioticida by real-time specific PCR and 16S rRNA sequencing. MALDI-ToF allowed the direct identification of four isolates (FR22a,b,c,d) which had 100% identity on the 16S rRNA gene with the known strains. On the other hand, one isolate (FR21) was not recognized by MALDI-ToF and had 99.9% identity on the 16S rRNA gene. The FR22 isolates showed difficult growth and required media optimization, which was not the case with the FR21 isolate. For these reasons, it was hypothesized that two type strains are present on French coasts, named FR21 and FR22. The FR21 isolate was selected for phenotypic analysis (growth curve, biochemical characteristics, electron microscopy), phylogenetic analysis and an experimental challenge. This isolate showed distinct differences compared to published F. halioticida strains, both at phenotypic and genotypic levels. Experimental infections of adult mussels led to 36% mortalities in 23 days following intramuscular injection with 3 × 107 CFU while a lower dose (3 × 103 CFU) did not lead to significant mortalities. In the context of this study, the strain FR21 was not virulent towards adult mussels.
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Affiliation(s)
- Hélène Bouras
- Université de Caen-Normandie, Sorbonne Université, MNHN, UA, CNRS, IRD, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Esplanade de la Paix, 14032 Caen, France; LABÉO, Research department; 1 Route de Rosel, 14053 Caen Cedex 4, France.
| | - Yann Quesnelle
- LABÉO, Research department; 1 Route de Rosel, 14053 Caen Cedex 4, France
| | - Alix Barozet
- LABÉO, Research department; 1 Route de Rosel, 14053 Caen Cedex 4, France
| | - Didier Goux
- Normandie Université, UNICAEN, CMAbio3 (Centre de Microscopie Appliquée à la Biologie), SF EMerode, Esplanade de la Paix, 14032 Caen, France; Normandie Université, ENSICAEN, UNICAEN, CNRS, UMR 6508 CRISMAT, 6 boulevard du Maréchal Juin, 14000 Caen, France
| | - Jean-Louis Blin
- Synergie Mer et Littoral (SMEL), Zone Conchylicole, Blainville-sur-mer, France
| | - Manuel Savary
- Comité Régional de Conchyliculture (CRC) Normandie-Mer du Nord, 35 rue du littoral, 50560 Gouville-sur-Mer, France
| | - Céline Zatylny-Gaudin
- Université de Caen-Normandie, Sorbonne Université, MNHN, UA, CNRS, IRD, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Esplanade de la Paix, 14032 Caen, France
| | - Maryline Houssin
- Université de Caen-Normandie, Sorbonne Université, MNHN, UA, CNRS, IRD, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Esplanade de la Paix, 14032 Caen, France; LABÉO, Research department; 1 Route de Rosel, 14053 Caen Cedex 4, France
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2
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Manassero V, Vannini C. Protists' microbiome: A fine-scale, snap-shot field study on the ciliate Euplotes. Eur J Protistol 2023; 87:125952. [PMID: 36610375 DOI: 10.1016/j.ejop.2022.125952] [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: 09/13/2022] [Revised: 11/29/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023]
Abstract
Host-microbiome relationships play a fundamental role in the evolution and ecology of any living being. As unicellular organisms, protists represent a unique eukaryotic model to investigate selection mechanisms of the prokaryotic microbiome at the cellular level. Field investigations are central to disentangle relative importance of selective drivers in nature. Here we performed an analysis on data from a snap-shot field study reported previously on bacterial microbiomes associated to natural populations of protist ciliates of the genus Euplotes to detect at a fine scale any influence of habitat and/or host identity in microbiome selection. Comparative analyses revealed environment at a relatively large scale (sampling area) as the main driving factor in shaping prokaryotic communities' structures. No evidence of habitat as key-factor emerged when a smaller spatial scale was considered (pond/channel or site). When only microbiomes of ciliates from the same site were compared, a clear assessment on the influence of host identity at the species level was not achieved, probably due to the small and unbalanced number of individuals for the two considered host species. Starting from this point, wider sampling campaigns will contribute in the future to depict a general view of the drivers influencing the prokaryotic microbiomes of natural protist populations.
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Affiliation(s)
| | - Claudia Vannini
- Department of Biology, University of Pisa, 56126 Pisa, Italy.
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Boscaro V, Manassero V, Keeling PJ, Vannini C. Single-cell Microbiomics Unveils Distribution and Patterns of Microbial Symbioses in the Natural Environment. MICROBIAL ECOLOGY 2023; 85:307-316. [PMID: 35048168 DOI: 10.1007/s00248-021-01938-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
Protist-bacteria associations are extremely common. Among them, those involving ciliates of the genus Euplotes are emerging as models for symbioses between prokaryotes and eukaryotes, and a great deal of information is available from cultured representatives of this system. Even so, as for most known microbial symbioses, data on natural populations is lacking, and their ecology remains largely unexplored; how well lab cultures represent actual diversity is untested. Here, we describe a survey on natural populations of Euplotes based on a single-cell microbiomic approach, focusing on taxa that include known endosymbionts of this ciliate. The results reveal an unexpected variability in symbiotic communities, with individual hosts of the same population harboring different sets of bacterial endosymbionts. Co-occurring Euplotes individuals of the same population can even have different essential symbionts, Polynucleobacter and "Candidatus Protistobacter," which might suggest that replacement events could be more frequent in nature than previously hypothesized. Accessory symbionts are even more variable: some showed a strong affinity for one host species, some for a sampling site, and two ("Candidatus Cyrtobacter" and "Candidatus Anadelfobacter") displayed an unusual pattern of competitive exclusion. These data represent the first insight into the prevalence and patterns of bacterial symbionts in natural populations of free-living protists.
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Affiliation(s)
- Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Claudia Vannini
- Department of Biology, University of Pisa, 56126, Pisa, Italy.
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4
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Fokin SI, Serra V. Bacterial Symbiosis in Ciliates (Alveolata, Ciliophora): Roads Traveled and Those Still to be Taken. J Eukaryot Microbiol 2022; 69:e12886. [PMID: 35006645 PMCID: PMC9539572 DOI: 10.1111/jeu.12886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 11/30/2022]
Abstract
The diversity of prokaryotic symbionts in Ciliophora and other protists is fascinatingly rich; they may even include some potentially pathogenic bacteria. In this review, we summarize currently available data on biodiversity and some morphological and biological peculiarities of prokaryotic symbionts mainly within the genera Paramecium and Euplotes. Another direction of ciliate symbiology, neglected for a long time and now re‐discovered, is the study of epibionts of ciliates. This promises a variety of interesting outcomes. Last, but not least, we stress the new technologies, such as next generation sequencing and the use of genomics data, which all can clarify many new aspects of relevance. For this reason, a brief overview of achievements in genomic studies on ciliate's symbionts is provided. Summing up the results of numerous scientific contributions, we systematically update current knowledge and outline the prospects as to how symbiology of Ciliophora may develop in the near future.
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Affiliation(s)
- Sergei I Fokin
- University of Pisa, Pisa, Italy.,St. Petersburg State University, St. Petersburg, Russia
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5
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Davies FK, Fricker AD, Robins MM, Dempster TA, McGowen J, Charania M, Beliaev AS, Lindemann SR, Posewitz MC. Microbiota associated with the large-scale outdoor cultivation of the cyanobacterium Synechococcus sp. PCC 7002. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Jiang L, Zhuang W, El-Serehy HA, Al-Farraj SA, Warren A, Hu X. Taxonomy and Molecular Phylogeny of Two New Species of Prostomatean Ciliates With Establishment of Foissnerophrys gen. n. (Alveolata, Ciliophora). Front Microbiol 2021; 12:686929. [PMID: 34220776 PMCID: PMC8250431 DOI: 10.3389/fmicb.2021.686929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Prostomatean ciliates play important roles in the flow of material and energy in aquatic microbial food webs, and thus have attracted wide attention for over a century. Their taxonomy and systematics are, however, still poorly understood because of their relatively few taxonomically informative morphological characters. In this study, two new prostomateans, Lagynus binucleatus sp. n. and Foissnerophrys alveolata gen. n., sp. n., collected from a freshwater pool and the intertidal zone of a sandy beach, respectively, in Qingdao, China, are investigated using living observation, protargol staining, and SSU rRNA gene sequencing methods. The genus Lagynus is redefined, and the new species L. binucleatus sp. n. is established based on significant morphological differences with similar forms. Furthermore, a new genus, Foissnerophrys gen. n., is established based on a combination of morphological and molecular data with F. alveaolata sp. n. the type species by monotypy. The identities of intracellular prokaryotes of these two new species are discussed based on fluorescence in situ hybridization (FISH) data and newly obtained 16S rRNA gene sequences.
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Affiliation(s)
- Limin Jiang
- College of Fisheries and Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Wenbao Zhuang
- College of Fisheries and Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hamed A El-Serehy
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Al-Farraj
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Xiaozhong Hu
- College of Fisheries and Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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7
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Öhrman C, Sahl JW, Sjödin A, Uneklint I, Ballard R, Karlsson L, McDonough RF, Sundell D, Soria K, Bäckman S, Chase K, Brindefalk B, Sozhamannan S, Vallesi A, Hägglund E, Ramirez-Paredes JG, Thelaus J, Colquhoun D, Myrtennäs K, Birdsell D, Johansson A, Wagner DM, Forsman M. Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis. Microorganisms 2021; 9:146. [PMID: 33440900 PMCID: PMC7826819 DOI: 10.3390/microorganisms9010146] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/01/2021] [Accepted: 01/04/2021] [Indexed: 12/21/2022] Open
Abstract
In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters.
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Affiliation(s)
- Caroline Öhrman
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Jason W. Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (J.W.S.); (R.B.); (R.F.M.); (K.S.); (D.B.); (D.M.W.)
| | - Andreas Sjödin
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Ingrid Uneklint
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Rebecca Ballard
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (J.W.S.); (R.B.); (R.F.M.); (K.S.); (D.B.); (D.M.W.)
| | - Linda Karlsson
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Ryelan F. McDonough
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (J.W.S.); (R.B.); (R.F.M.); (K.S.); (D.B.); (D.M.W.)
| | - David Sundell
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Kathleen Soria
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (J.W.S.); (R.B.); (R.F.M.); (K.S.); (D.B.); (D.M.W.)
| | - Stina Bäckman
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Kitty Chase
- US Army Medical Research Institute, Fort Detrick, MD 21702, USA;
| | - Björn Brindefalk
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Shanmuga Sozhamannan
- Logistics Management Institute supporting Defense Biological Product Assurance Office (DBPAO) Joint Project Lead, CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD 21702, USA;
| | - Adriana Vallesi
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy;
| | - Emil Hägglund
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Jose Gustavo Ramirez-Paredes
- Ridgeway Biologicals Limited a Ceva Santé Animale Company, Units 1-3 Old Station Business Park, Compton, Berkshire, England RG20 6NE, UK;
| | - Johanna Thelaus
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Duncan Colquhoun
- Fish Health Research Group, Norwegian Veterinary Institute, Oslo, Pb 750 Sentrum, 23 N-0106 Oslo, Norway;
| | - Kerstin Myrtennäs
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Dawn Birdsell
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (J.W.S.); (R.B.); (R.F.M.); (K.S.); (D.B.); (D.M.W.)
| | - Anders Johansson
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 85 Umeå, Sweden;
| | - David M. Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (J.W.S.); (R.B.); (R.F.M.); (K.S.); (D.B.); (D.M.W.)
| | - Mats Forsman
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
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8
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Zheng Q, Lin W, Wang Y, Xu D, Liu Y, Jiao N. Top-down controls on nutrient cycling and population dynamics in a model estuarine photoautotroph-heterotroph co-culture system. Mol Ecol 2020; 30:592-607. [PMID: 33226689 DOI: 10.1111/mec.15750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/05/2020] [Accepted: 11/19/2020] [Indexed: 11/29/2022]
Abstract
Viral lysis and protistan grazing are thought to be the major processes leading to microbial mortality in aquatic environments and thus regulate community diversity and biogeochemical cycling characteristics. Here, we studied nutrient cycling and bacterial responses to cyanophage-mediated photoautotroph lysis and ciliate predation in a model Synechococcus-heterotroph co-culture system. Both viral lysis and Euplotes grazing facilitated the transformation of organic carbon from biomass to dissolved organic matter with convention efficiencies of 20%-26%. The accumulation of ammonium after the addition of phages and ciliates suggested the importance of recycled NH4 + occurred in the interactions between Synechococcus growth and heterotrophic bacterial metabolism of photosynthate. The slower efficiency of P mineralization compared to N (primarily ammonium) indicated that P-containing organic matter was primarily integrated into bacterial biomass rather than being remineralized into inorganic phosphate under C-rich conditions. In the cyanophage addition treatment, both Fluviicola and Alteromonas exhibited rapid positive responses to Synechococcus lysing, while Marivita exhibited an apparent negative response. Further, the addition of Euplotes altered the incubation system from a Synechococcus-driven phycosphere to a ciliate-remodelled zoosphere that primarily constituted grazing-resistant bacteria and Euplotes symbionts. Top-down controls increased co-culture system diversity and resulted in a preference for free-living lifestyles of dominant populations, which was accompanied by the transfer of matter and energy. Our results indicate top-down control was particularly important for organic matter redistribution and inorganic nutrient regeneration between photoautotrophs and heterotrophs, and altered bacterial lifestyles. This study consequently sheds light on marine biogeochemical cycling and the interaction networks within these dynamic ecosystems.
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Affiliation(s)
- Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Wenxin Lin
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Dapeng Xu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Yanting Liu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
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9
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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: 26] [Impact Index Per Article: 6.5] [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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10
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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11
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John MS, Nagoth JA, Ramasamy KP, Ballarini P, Mozzicafreddo M, Mancini A, Telatin A, Liò P, Giuli G, Natalello A, Miceli C, Pucciarelli S. Horizontal gene transfer and silver nanoparticles production in a new Marinomonas strain isolated from the Antarctic psychrophilic ciliate Euplotes focardii. Sci Rep 2020; 10:10218. [PMID: 32576860 PMCID: PMC7311414 DOI: 10.1038/s41598-020-66878-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 05/23/2020] [Indexed: 01/23/2023] Open
Abstract
We isolated a novel bacterial strain from a prokaryotic consortium associated to the psychrophilic marine ciliate Euplotes focardii, endemic of the Antarctic coastal seawater. The 16S rDNA sequencing and the phylogenetic analysis revealed the close evolutionary relationship to the Antarctic marine bacterium Marinomonas sp. BSw10506 and the sub antarctic Marinomonas polaris. We named this new strain Marinomonas sp. ef1. The optimal growth temperature in LB medium was 22 °C. Whole genome sequencing and analysis showed a reduced gene loss limited to regions encoding for transposases. Additionally, five genomic islands, e.g. DNA fragments that facilitate horizontal gene transfer phenomena, were identified. Two open reading frames predicted from the genomic islands coded for enzymes belonging to the Nitro-FMN-reductase superfamily. One of these, the putative NAD(P)H nitroreductase YfkO, has been reported to be involved in the bioreduction of silver (Ag) ions and the production of silver nanoparticles (AgNPs). After the Marinomonas sp. ef1 biomass incubation with 1 mM of AgNO3 at 22 °C, we obtained AgNPs within 24 h. The AgNPs were relatively small in size (50 nm) and had a strong antimicrobial activity against twelve common nosocomial pathogenic microorganisms including Staphylococcus aureus and two Candida strains. To our knowledge, this is the first report of AgNPs biosynthesis by a Marinomonas strain. This biosynthesis may play a dual role in detoxification from silver nitrate and protection from pathogens for the bacterium and potentially for the associated ciliate. Biosynthetic AgNPs also represent a promising alternative to conventional antibiotics against common pathogens.
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Affiliation(s)
- Maria Sindhura John
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino, Italy
| | - Joseph Amruthraj Nagoth
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino, Italy
| | - Kesava Priyan Ramasamy
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino, Italy
| | - Patrizia Ballarini
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino, Italy
| | - Matteo Mozzicafreddo
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino, Italy
| | - Alessio Mancini
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino, Italy
| | - Andrea Telatin
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Program, Norwich Research Park, Norwich, UK
| | - Pietro Liò
- Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge, UK
| | - Gabriele Giuli
- School of Science and Technology, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milano, Italy
| | - Cristina Miceli
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino, Italy
| | - Sandra Pucciarelli
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino, Italy.
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12
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Ramirez-Paredes JG, Larsson P, Thompson KD, Penman DJ, Busse HJ, Öhrman C, Sjödin A, Soto E, Richards RH, Adams A, Colquhoun DJ. Reclassification of Francisella noatunensis subsp. orientalis Ottem et al. 2009 as Francisella orientalis sp. nov., Francisella noatunensis subsp. chilensis subsp. nov. and emended description of Francisella noatunensis. Int J Syst Evol Microbiol 2020; 70:2034-2048. [PMID: 32160147 DOI: 10.1099/ijsem.0.004009] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Francisella noatunensis is a fastidious facultative intracellular bacterial pathogen that causes 'piscine francisellosis', a serious disease affecting both marine and fresh water farmed and wild fish worldwide. Currently two F. noatunensis subspecies are recognized, i.e. F. noatunensis subsp. noatunensis and F. noatunensis subsp. orientalis. In the present study, the taxonomy of F. noatunensis was revisited using a polyphasic approach, including whole genome derived parameters such as digital DNA-DNA hybridization, whole genome average nucleotide identity (wg-ANIm), whole genome phylogenetic analysis, whole genome G+C content, metabolic fingerprinting and chemotaxonomic analyses. The results indicated that isolates belonging to F. noatunensis subsp. orientalis represent a phenotypically and genetically homogenous taxon, clearly distinguishable from F. noatunensis subsp. noatunensis that fulfils requirements for separate species status. We propose, therefore, elevation of F. noatunensis subsp. orientalis to the species rank as Francisella orientalis sp. nov. with the type strain remaining as Ehime-1T (DSM 21254T=LMG 24544T). Furthermore, we identified sufficient phenotypic and genetic differences between F. noatunensis subsp. noatunensis recovered from diseased farmed Atlantic salmon in Chile and those isolated from wild and farmed Atlantic cod in Northern Europe to warrant proposal of the Chilean as a novel F. noatunensis subspecies, i.e. Francisella noatunensis subsp. chilensis subsp. nov. with strain PQ1106T (CECT 9798T=NCTC14375T) as the type strain. Finally, we emend the description of F. noatunensis by including further metabolic information and the description of atypical strains.
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Affiliation(s)
- Jose Gustavo Ramirez-Paredes
- Ridgeway Biologicals Ltd. a Ceva Santé Animale Company, Units 1-3 Old Station Business Park, Compton, Berkshire, England, RG20 6NE, UK
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
- Present address: Ridgeway Biologicals Ltd. a Ceva Santé Animale Company, Units 1-3 Old Station Business Park, Compton, Berkshire, England, RG20 6NE, UK
| | - Pär Larsson
- Swedish Defence Research Agency (FOI), CBRN Defence and Security, Umeå, Sweden
- Department of Medical Biosciences, Umea University, Umeå, Sweden
| | - Kim D Thompson
- Aquaculture Research Group, Moredun Research Institute, Edinburgh, Scotland, EH26 0PZ, UK
| | - David J Penman
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Hans-Jürgen Busse
- Institute of Microbiology, Veterinary University, Vienna, A-1160 Wien, Austria
| | - Caroline Öhrman
- Swedish Defence Research Agency (FOI), CBRN Defence and Security, Umeå, Sweden
| | - Andreas Sjödin
- Swedish Defence Research Agency (FOI), CBRN Defence and Security, Umeå, Sweden
| | - Esteban Soto
- Department of Medicine and Epidemiology, University of California Davis, School of Veterinary Medicine, Davis, California, 95616, USA
| | - Randolph H Richards
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Alexandra Adams
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Duncan J Colquhoun
- Fish Health Research Group, Norwegian Veterinary Institute, Oslo, Pb 750 Sentrum, N-0106 Oslo, Norway
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13
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Zhao W, Li M, Xiong F, Zhang D, Wu S, Zou H, Li W, Wang G. Identification of Intracellular Bacteria in the Ciliate
Balantidium ctenopharyngodoni
(Ciliophora, Litostomatea). J Eukaryot Microbiol 2020; 67:417-426. [DOI: 10.1111/jeu.12791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/09/2020] [Accepted: 02/06/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Weishan Zhao
- Key Laboratory of Aquaculture Disease Control Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China
| | - Fan Xiong
- Key Laboratory of Aquaculture Disease Control Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China
| | - Dong Zhang
- Key Laboratory of Aquaculture Disease Control Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Shangong Wu
- Key Laboratory of Aquaculture Disease Control Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China
| | - Wenxiang Li
- Key Laboratory of Aquaculture Disease Control Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China
| | - Guitang Wang
- Key Laboratory of Aquaculture Disease Control Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China
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14
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Lanzoni O, Plotnikov A, Khlopko Y, Munz G, Petroni G, Potekhin A. The core microbiome of sessile ciliate Stentor coeruleus is not shaped by the environment. Sci Rep 2019; 9:11356. [PMID: 31388025 PMCID: PMC6684585 DOI: 10.1038/s41598-019-47701-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/22/2019] [Indexed: 12/29/2022] Open
Abstract
Microbiomes of multicellular organisms are one of the hottest topics in microbiology and physiology, while only few studies addressed bacterial communities associated with protists. Protists are widespread in all environments and can be colonized by plethora of different bacteria, including also human pathogens. The aim of this study was to characterize the prokaryotic community associated with the sessile ciliate Stentor coeruleus. 16S rRNA gene metabarcoding was performed on single cells of S. coeruleus and on their environment, water from the sewage stream. Our results showed that the prokaryotic community composition differed significantly between Stentor cells and their environment. The core microbiome common for all ciliate specimens analyzed could be defined, and it was composed mainly by representatives of bacterial genera which include also potential human pathogens and commensals, such as Neisseria, Streptococcus, Capnocytophaga, Porphyromonas. Numerous 16S rRNA gene contigs belonged to endosymbiont “Candidatus Megaira polyxenophila”. Our data suggest that each ciliate cell can be considered as an ecological microniche harboring diverse prokaryotic organisms. Possible benefits for persistence and transmission in nature for bacteria associated with protists are discussed. Our results support the hypothesis that ciliates attract potentially pathogenic bacteria and play the role of natural reservoirs for them.
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Affiliation(s)
| | - Andrey Plotnikov
- Center of Shared Scientific Equipment, Institute for Cellular and Intracellular Symbiosis, Ural Division of RAS, Orenburg, Russia
| | - Yuri Khlopko
- Center of Shared Scientific Equipment, Institute for Cellular and Intracellular Symbiosis, Ural Division of RAS, Orenburg, Russia
| | - Giulio Munz
- Department of Civil and Environmental Engineering, University of Florence, Florence, Italy
| | | | - Alexey Potekhin
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia.
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15
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Boscaro V, Husnik F, Vannini C, Keeling PJ. Symbionts of the ciliate Euplotes: diversity, patterns and potential as models for bacteria-eukaryote endosymbioses. Proc Biol Sci 2019; 286:20190693. [PMID: 31311477 DOI: 10.1098/rspb.2019.0693] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Endosymbioses between bacteria and eukaryotes are enormously important in ecology and evolution, and as such are intensely studied. Despite this, the range of investigated hosts is narrow in the context of the whole eukaryotic tree of life: most of the information pertains to animal hosts, while most of the diversity is found in unicellular protists. A prominent case study is the ciliate Euplotes, which has repeatedly taken up the bacterium Polynucleobacter from the environment, triggering its transformation into obligate endosymbiont. This multiple origin makes the relationship an excellent model to understand recent symbioses, but Euplotes may host bacteria other than Polynucleobacter, and a more detailed knowledge of these additional interactions is needed in order to correctly interpret the system. Here, we present the first systematic survey of Euplotes endosymbionts, adopting a classical as well as a metagenomic approach, and review the state of knowledge. The emerging picture is indeed quite complex, with some Euplotes harbouring rich, stable prokaryotic communities not unlike those of multicellular animals. We provide insights into the distribution, evolution and diversity of these symbionts (including the establishment of six novel bacterial taxa), and outline differences and similarities with the most well-understood group of eukaryotic hosts: insects.
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Affiliation(s)
- Vittorio Boscaro
- Department of Botany, University of British Columbia, British Columbia, Canada
| | - Filip Husnik
- Department of Botany, University of British Columbia, British Columbia, Canada
| | | | - Patrick J Keeling
- Department of Botany, University of British Columbia, British Columbia, Canada
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16
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Rossi A, Bellone A, Fokin SI, Boscaro V, Vannini C. Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study. MICROBIAL ECOLOGY 2019; 78:232-242. [PMID: 30411190 DOI: 10.1007/s00248-018-1279-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.
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Affiliation(s)
- Alessia Rossi
- Department of Biology, University of Pisa, Pisa, Italy
| | | | - Sergei I Fokin
- Department of Biology, University of Pisa, Pisa, Italy
- Department of Invertebrate Zoology, St.-Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch of the S.I. Vavilov Institute of History of Science and Technology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Vittorio Boscaro
- Department of Biology, University of Pisa, Pisa, Italy
- Department of Botany, University of British Columbia, Vancouver, Canada
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17
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Vallesi A, Sjödin A, Petrelli D, Luporini P, Taddei AR, Thelaus J, Öhrman C, Nilsson E, Di Giuseppe G, Gutiérrez G, Villalobo E. A New Species of the γ-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species. MICROBIAL ECOLOGY 2019; 77:587-596. [PMID: 30187088 DOI: 10.1007/s00248-018-1256-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
The study of the draft genome of an Antarctic marine ciliate, Euplotes petzi, revealed foreign sequences of bacterial origin belonging to the γ-proteobacterium Francisella that includes pathogenic and environmental species. TEM and FISH analyses confirmed the presence of a Francisella endocytobiont in E. petzi. This endocytobiont was isolated and found to be a new species, named F. adeliensis sp. nov.. F. adeliensis grows well at wide ranges of temperature, salinity, and carbon dioxide concentrations implying that it may colonize new organisms living in deeply diversified habitats. The F. adeliensis genome includes the igl and pdp gene sets (pdpC and pdpE excepted) of the Francisella pathogenicity island needed for intracellular growth. Consistently with an F. adeliensis ancient symbiotic lifestyle, it also contains a single insertion-sequence element. Instead, it lacks genes for the biosynthesis of essential amino acids such as cysteine, lysine, methionine, and tyrosine. In a genome-based phylogenetic tree, F. adeliensis forms a new early branching clade, basal to the evolution of pathogenic species. The correlations of this clade with the other clades raise doubts about a genuine free-living nature of the environmental Francisella species isolated from natural and man-made environments, and suggest to look at F. adeliensis as a pioneer in the Francisella colonization of eukaryotic organisms.
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Affiliation(s)
- Adriana Vallesi
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy.
| | - Andreas Sjödin
- Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
- Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden
| | - Dezemona Petrelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Pierangelo Luporini
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Anna Rita Taddei
- Center of Large Equipment-section of Electron Microscopy, University of Tuscia, Largo dell'Università, snc, Viterbo, Italy
| | - Johanna Thelaus
- Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden
| | - Caroline Öhrman
- Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden
| | - Elin Nilsson
- Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden
| | | | - Gabriel Gutiérrez
- Departamento de Genética, Universidad de Sevilla, Av Reina Mercedes 6, 41012, Seville, Spain
| | - Eduardo Villalobo
- Departamento de Microbiología, Universidad de Sevilla, Av Reina Mercedes 6, 41012, Seville, Spain.
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18
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Zhao Y, Yi Z, Warren A, Song W. Species delimitation for the molecular taxonomy and ecology of the widely distributed microbial eukaryote genus Euplotes (Alveolata, Ciliophora). Proc Biol Sci 2019; 285:rspb.2017.2159. [PMID: 29367393 DOI: 10.1098/rspb.2017.2159] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/03/2018] [Indexed: 11/12/2022] Open
Abstract
Recent advances in high-throughput sequencing and metabarcoding technologies are revolutionizing our understanding of the diversity and ecology of microbial eukaryotes (protists). The interpretation of protist diversity and the elucidation of their ecosystem function are, however, impeded by problems with species delimitation, especially as it applies to molecular taxonomy. Here, using the ciliate Euplotes as an example, we describe approaches for species delimitation based on integrative taxonomy by using evolutionary and ecological perspectives and selecting the most appropriate metabarcoding gene markers as proxies for species units. Our analyses show that: Euplotes (sensu lato) comprises six distinct clades, mainly as result of ecological speciation; the validity of the genera Euplotes (sensu stricto), Euplotoides, Euplotopsis and Moneuplotes are not supported; the vannus-type group, which includes species without distinct morphological differences, seems to be undergoing incipient speciation and contains cryptic species; the hypervariable V4 region of the small subunit rDNA and D1-D2 region of the large subunit rDNA are the promising candidates for general species delimitation in Euplotes.
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Affiliation(s)
- Yan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China .,Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, People's Republic of China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Weibo Song
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, People's Republic of China
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19
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Gignoux-Wolfsohn SA, Aronson FM, Vollmer SV. Complex interactions between potentially pathogenic, opportunistic, and resident bacteria emerge during infection on a reef-building coral. FEMS Microbiol Ecol 2017. [PMID: 28637338 DOI: 10.1093/femsec/fix080] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Increased bacterial diversity on diseased corals can obscure disease etiology and complicate our understanding of pathogenesis. To untangle microbes that may cause white band disease signs from microbes responding to disease, we inoculated healthy Acropora cervicornis corals with an infectious dose from visibly diseased corals. We sampled these dosed corals and healthy controls over time for sequencing of the bacterial 16S region. Endozoicomonas were associated with healthy fragments from 4/10 colonies, dominating microbiomes before dosing and decreasing over time only in corals that displayed disease signs, suggesting a role in disease resistance. We grouped disease-associated bacteria by when they increased in abundance (primary vs secondary) and whether they originated in the dose (colonizers) or the previously healthy corals (responders). We found that all primary responders increased in all dosed corals regardless of final disease state and are therefore unlikely to cause disease signs. In contrast, primary colonizers in the families Pasteurellaceae and Francisellaceae increased solely in dosed corals that ultimately displayed disease signs, and may be infectious foreign bacteria involved in the development of disease signs. Moving away from a static comparison of diseased and healthy bacterial communities, we provide a framework to identify key players in other coral diseases.
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Affiliation(s)
- Sarah A Gignoux-Wolfsohn
- Department of Ecology, Evolution, & Natural Resources School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8525, USA
| | - Felicia M Aronson
- Marine Science Center, Northeastern University, Nahant, MA 01908, USA
| | - Steven V Vollmer
- Marine Science Center, Northeastern University, Nahant, MA 01908, USA
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20
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Boscaro V, Fokin SI, Petroni G, Verni F, Keeling PJ, Vannini C. Symbiont replacement between bacteria of different classes reveals additional layers of complexity in the evolution of symbiosis in the ciliate Euplotes. Protist 2017; 169:43-52. [PMID: 29414319 DOI: 10.1016/j.protis.2017.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 12/08/2017] [Accepted: 12/12/2017] [Indexed: 11/25/2022]
Abstract
Symbiosis is a diverse and complex phenomenon requiring diverse model systems. The obligate relationship between a monophyletic group of Euplotes species ("clade B") and the betaproteobacteria Polynucleobacter and "Candidatus Protistobacter" is among the best-studied in ciliates, and provides a framework to investigate symbiont replacements. Several other Euplotes-bacteria relationships exist but are less understood, such as the co-dependent symbiosis between Euplotes magnicirratus (which belongs to "clade A") and the alphaproteobacterium "Candidatus Devosia euplotis". Here we describe a new Devosia inhabiting the cytoplasm of a strain of Euplotes harpa, a clade B species that usually depends on Polynucleobacter for survival. The novel bacterial species, "Candidatus Devosia symbiotica", is closely related to the symbiont of E. magnicirratus, casting a different light on the history of bacteria colonizing ciliates of this genus. The two Devosia species may have become symbionts independently or as the result of a symbiont exchange between hosts, in either case replacing a previous essential bacterium in E. harpa. Alternatively, both may be remnants of an ancient symbiotic relationship between Euplotes and Devosia, in which case Polynucleobacter and "Ca. Protistobacter" are recent invaders. Either way, symbiont replacement between bacteria belonging to different classes must be evoked to explain this fascinating system.
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Affiliation(s)
- Vittorio Boscaro
- University of Pisa, Department of Biology, Italy; University of British Columbia, Department of Botany, Canada
| | - Sergei I Fokin
- University of Pisa, Department of Biology, Italy; St.-Petersburg State University, Department of Invertebrate Zoology, Russia
| | | | - Franco Verni
- University of Pisa, Department of Biology, Italy
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21
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Sabaneyeva E, Castelli M, Szokoli F, Benken K, Lebedeva N, Salvetti A, Schweikert M, Fokin S, Petroni G. Host and symbiont intraspecific variability: The case of Paramecium calkinsi and "Candidatus Trichorickettsia mobilis". Eur J Protistol 2017; 62:79-94. [PMID: 29287245 DOI: 10.1016/j.ejop.2017.12.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 10/17/2017] [Accepted: 12/04/2017] [Indexed: 01/08/2023]
Abstract
Newly isolated strains of the ciliate Paramecium calkinsi and their cytoplasmic bacterial endosymbionts were characterized by a multidisciplinary approach, including live observation, ultrastructural investigation, and molecular analysis. Despite morphological resemblance, the characterized P. calkinsi strains showed a significant molecular divergence compared to conspecifics, possibly hinting for a cryptic speciation. The endosymbionts were clearly found to be affiliated to the species "Candidatus Trichorickettsia mobilis" (Rickettsiales, Rickettsiaceae), currently encompassing only bacteria retrieved in an obligate intracellular association with other ciliates. However, a relatively high degree of intraspecific divergence was observed as well, thus it was possible to split "Candidatus Trichorickettsia" into three subspecies, one of which represented so far only by the newly characterized endosymbionts of P. calkinsi. Other features distinguished the members of each different subspecies. In particular, the endosymbionts of P. calkinsi resided in the cytoplasm and possessed numerous peritrichous flagella, although no motility was evidenced, whereas their conspecifics in other hosts were either cytoplasmic and devoid of flagella, or macronuclear, displaying flagellar-driven motility. Moreover, contrarily to previously analyzed "Candidatus Trichorickettsia" hosts, infected P. calkinsi cells frequently became amicronucleate and demonstrated abnormal cell division, eventually leading to decline of the laboratory culture.
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Affiliation(s)
- E Sabaneyeva
- Department of Cytology and Histology, St. Petersburg State University, Russian Federation.
| | - M Castelli
- Department of Veterinary Medicine, University of Milan, Italy; Department of Biosciences, University of Milan, Italy
| | - F Szokoli
- Dipartimento di Biologia, Università di Pisa, Italy; Institut für Hydrobiologie, Technische Universität Dresden, Germany
| | - K Benken
- Core Facility Center for Microscopy and Microanalysis, St. Petersburg State University, Russian Federation
| | - N Lebedeva
- Core Facility Center for Cultivation of Microorganisms, St. Petersburg State University, Russian Federation
| | - A Salvetti
- Dipartimento di Medicina Clinica e Sperimentale, Università di Pisa, Italy
| | - M Schweikert
- Institut of Biomaterials and Biomolecular Systems, Stuttgart University, Germany
| | - S Fokin
- Dipartimento di Biologia, Università di Pisa, Italy; Department of Invertebrate Zoology, St. Petersburg State University, Russian Federation
| | - G Petroni
- Dipartimento di Biologia, Università di Pisa, Italy.
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22
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Ricci F, Lauro FM, Grzymski JJ, Read R, Bakiu R, Santovito G, Luporini P, Vallesi A. The Anti-Oxidant Defense System of the Marine Polar Ciliate Euplotes nobilii: Characterization of the MsrB Gene Family. BIOLOGY 2017; 6:biology6010004. [PMID: 28106766 PMCID: PMC5371997 DOI: 10.3390/biology6010004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/04/2017] [Accepted: 01/07/2017] [Indexed: 01/16/2023]
Abstract
Organisms living in polar waters must cope with an extremely stressful environment dominated by freezing temperatures, high oxygen concentrations and UV radiation. To shed light on the genetic mechanisms on which the polar marine ciliate, Euplotes nobilii, relies to effectively cope with the oxidative stress, attention was focused on methionine sulfoxide reductases which repair proteins with oxidized methionines. A family of four structurally distinct MsrB genes, encoding enzymes specific for the reduction of the methionine-sulfoxide R-forms, were identified from a draft of the E. nobilii transcriptionally active (macronuclear) genome. The En-MsrB genes are constitutively expressed to synthesize proteins markedly different in amino acid sequence, number of CXXC motifs for zinc-ion binding, and presence/absence of a cysteine residue specific for the mechanism of enzyme regeneration. The En-MsrB proteins take different localizations in the nucleus, mitochondria, cytosol and endoplasmic reticulum, ensuring a pervasive protection of all the major subcellular compartments from the oxidative damage. These observations have suggested to regard the En-MsrB gene activity as playing a central role in the genetic mechanism that enables E. nobilii and ciliates in general to live in the polar environment.
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Affiliation(s)
- Francesca Ricci
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy.
| | - Federico M Lauro
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore 637551, Singapore.
| | - Joseph J Grzymski
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV 89512, USA.
| | - Robert Read
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV 89512, USA.
| | - Rigers Bakiu
- Department of Aquaculture and Fisheries, Agricultural University of Tirana, Tirana 1019, Albania.
| | - Gianfranco Santovito
- Department of Biology, University of Padova, via U. Bassi 58/B, Padua 35100, Italy.
| | - Pierangelo Luporini
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy.
| | - Adriana Vallesi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy.
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Serra V, Fokin SI, Castelli M, Basuri CK, Nitla V, Verni F, Sandeep BV, Kalavati C, Petroni G. " Candidatus Gortzia shahrazadis", a Novel Endosymbiont of Paramecium multimicronucleatum and a Revision of the Biogeographical Distribution of Holospora-Like Bacteria. Front Microbiol 2016; 7:1704. [PMID: 27867371 PMCID: PMC5095128 DOI: 10.3389/fmicb.2016.01704] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 10/12/2016] [Indexed: 11/13/2022] Open
Abstract
Holospora spp. and "Candidatus Gortzia infectiva", known as Holospora-like bacteria (HLB), are commonly found as nuclear endosymbionts of ciliates, especially the Paramecium genus. HLB are related by phylogenetic relationships, morphological features, and life-cycles, which involve two alternating morphotypes: reproductive and infectious forms (RF, IF). In this paper we describe a novel species belonging to the "Ca. Gortzia" genus, detected in P. multimicronucleatum, a ciliate for which infection by an HLB has not been reported, discovered in India. This novel endosymbiont shows unusual and surprising features with respect to other HLB, such as large variations in IF morphology and the occasional ability to reproduce in the host cytoplasm. We propose the name of "Candidatus Gortzia shahrazadis" for this novel HLB. Moreover, we report two additional species of HLB from Indian Paramecium populations: "Ca. Gortzia infectiva" (from P. jenningsi), and H. obtusa (from P. caudatum); the latter is the first record of Holospora from a tropical country. Although tropical, we retrieved H. obtusa at an elevation of 706 m corresponding to a moderate climate not unlike conditions where Holospora are normally found, suggesting the genus Holospora does exist in tropical countries, but restricted to higher elevations.
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Affiliation(s)
| | - Sergei I Fokin
- Department of Biology, University of PisaPisa, Italy; Department of Invertebrate Zoology, Saint Petersburg State UniversitySaint Petersburg, Russia
| | - Michele Castelli
- Department of Biology, University of PisaPisa, Italy; Department of Veterinary Medicine, University of MilanMilan, Italy
| | - Charan K Basuri
- Department of Zoology, Andhra University Visakhapatnam, India
| | | | - Franco Verni
- Department of Biology, University of Pisa Pisa, Italy
| | - Bhagavatula V Sandeep
- Department of Zoology, Andhra UniversityVisakhapatnam, India; Department of Biotechnology, Andhra UniversityVisakhapatnam, India
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Castelli M, Lanzoni O, Rossi L, Potekhin A, Schrallhammer M, Petroni G. Evaluation of Enrichment Protocols for Bacterial Endosymbionts of Ciliates by Real-Time PCR. Curr Microbiol 2016; 72:723-32. [PMID: 26894821 DOI: 10.1007/s00284-016-1006-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/03/2016] [Indexed: 11/30/2022]
Abstract
Large-scale studies on obligate bacterial endosymbionts may frequently require preliminary purification and enrichment protocols, which are often elaborate to set up and to evaluate, especially if the host organism is a protist. The purpose of this study was to develop a real-time PCR-based strategy and employ it for assessing two of such enrichment protocols for Holospora caryophila, hosted by the ciliate Paramecium. Four SSU rRNA gene-targeted real-time PCR assays were designed, which allowed to compare the amount of H. caryophila to other organisms, namely the host, its food bacterium (Raoultella planticola), and free-living bacteria present in the culture medium. By the use of the real-time PCR assays in combination, it was possible to conclude that the "cell fractionation" protocol was quite successful in the enrichment of the symbiont, while the "Percoll gradient" protocol will need further refinements to be fully repeatable. The proposed approach has the potential to facilitate and encourage future studies on the yet underexplored field of bacterial endosymbionts of ciliates and other protists. It can also find valuable applications for experimental questions other than those tested, such as fast and precise assessment of symbiont abundance in natural populations and comparison among multiple coexisting symbionts.
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Affiliation(s)
| | - Olivia Lanzoni
- Department of Biology, University of Pisa, 56126, Pisa, Italy
| | - Leonardo Rossi
- Department of Clinical and Experimental Medicine, University of Pisa, 56126, Pisa, Italy
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, St. Petersburg State University, Saint Petersburg, Russia, 199034
| | - Martina Schrallhammer
- Microbiology, Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany
| | - Giulio Petroni
- Department of Biology, University of Pisa, 56126, Pisa, Italy.
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25
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Senra MVX, Dias RJP, Castelli M, Silva-Neto ID, Verni F, Soares CAG, Petroni G. A House for Two--Double Bacterial Infection in Euplotes woodruffi Sq1 (Ciliophora, Euplotia) Sampled in Southeastern Brazil. MICROBIAL ECOLOGY 2016; 71:505-517. [PMID: 26381539 DOI: 10.1007/s00248-015-0668-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 08/28/2015] [Indexed: 06/05/2023]
Abstract
Several ciliated protists form symbiotic associations with a diversity of microorganisms, leading to drastic impact on their ecology and evolution. In this work, two Euplotes spp. sampled in Rio de Janeiro, Brazil, were identified based on morphological and molecular features as Euplotes woodruffi strain Sq1 and E. encysticus strain Sq2 and investigated for the presence of endosymbionts. While E. woodruffi Sq1 stably hosts two bacterial populations, namely Polynucleobacter necessarius (Betaproteobacteria) and a new member of the family "Candidatus Midichloriaceae" (Alphaproteobacteria, Rickettsiales), here described as "Candidatus Bandiella woodruffii," branching with a broad host range bacterial group found in association with cnidarians, sponges, euglenoids, and some arthropods; in E. encysticus Sq2 no symbiotic bacterium could be detected. The dispersion ability of this novel bacterium was tested by co-incubating E. woodruffi Sq1 with three different ciliate species. Among the tested strains "Ca. B. woodruffii" could only be detected in association with E. encysticus Sq2 with a prevalence of 20 % after 1 week and 40 % after 2 weeks, maintaining this level for up to 6 months. Nevertheless, this apparent in vitro association was abolished when E. woodruffi Sq1 donor was removed from the microcosm, suggesting that this bacterium has the capacity for at least a short-term survival outside its natural host and the aptitude to ephemerally interact with other organisms. Together, these findings strongly suggest the need for more detailed investigations to evaluate the host range for "Ca. B. woodruffii" and any possible pathogenic effect of this bacterium on other organisms including humans.
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Affiliation(s)
- Marcus V X Senra
- Departamento de Genética, Universidade Federal do Rio de Janeiro, UFRJ, Av. Carlos Chagas Filho 373 - CCS A2-120, Rio de Janeiro, 21.944-970, Brazil
- Departamento de Zoologia, Universidade Federal de Juiz de Fora, UFJF, Rio de Janeiro, Brazil
| | - Roberto J P Dias
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
- Departamento de Zoologia, Universidade Federal de Juiz de Fora, UFJF, Rio de Janeiro, Brazil
| | - Michele Castelli
- Department of Biology, University of Pisa, via A. Volta 4/6, Pisa, 56126, Italy
| | - Inácio D Silva-Neto
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
| | - Franco Verni
- Department of Biology, University of Pisa, via A. Volta 4/6, Pisa, 56126, Italy
| | - Carlos A G Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, UFRJ, Av. Carlos Chagas Filho 373 - CCS A2-120, Rio de Janeiro, 21.944-970, Brazil.
| | - Giulio Petroni
- Department of Biology, University of Pisa, via A. Volta 4/6, Pisa, 56126, Italy.
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Szokoli F, Sabaneyeva E, Castelli M, Krenek S, Schrallhammer M, Soares CAG, da Silva-Neto ID, Berendonk TU, Petroni G. "Candidatus Fokinia solitaria", a Novel "Stand-Alone" Symbiotic Lineage of Midichloriaceae (Rickettsiales). PLoS One 2016; 11:e0145743. [PMID: 26731731 PMCID: PMC4701390 DOI: 10.1371/journal.pone.0145743] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/08/2015] [Indexed: 12/26/2022] Open
Abstract
Recently, the family Midichloriaceae has been described within the bacterial order Rickettsiales. It includes a variety of bacterial endosymbionts detected in different metazoan host species belonging to Placozoa, Cnidaria, Arthropoda and Vertebrata. Representatives of Midichloriaceae are also considered possible etiological agents of certain animal diseases. Midichloriaceae have been found also in protists like ciliates and amoebae. The present work describes a new bacterial endosymbiont, "Candidatus Fokinia solitaria", retrieved from three different strains of a novel Paramecium species isolated from a wastewater treatment plant in Rio de Janeiro (Brazil). Symbionts were characterized through the full-cycle rRNA approach: SSU rRNA gene sequencing and fluorescence in situ hybridization (FISH) with three species-specific oligonucleotide probes. In electron micrographs, the tiny rod-shaped endosymbionts (1.2 x 0.25-0.35 μm in size) were not surrounded by a symbiontophorous vacuole and were located in the peripheral host cytoplasm, stratified in the host cortex in between the trichocysts or just below them. Frequently, they occurred inside autolysosomes. Phylogenetic analyses of Midichloriaceae apparently show different evolutionary pathways within the family. Some genera, such as "Ca. Midichloria" and "Ca. Lariskella", have been retrieved frequently and independently in different hosts and environmental surveys. On the contrary, others, such as Lyticum, "Ca. Anadelfobacter", "Ca. Defluviella" and the presently described "Ca. Fokinia solitaria", have been found only occasionally and associated to specific host species. These last are the only representatives in their own branches thus far. Present data do not allow to infer whether these genera, which we named "stand-alone lineages", are an indication of poorly sampled organisms, thus underrepresented in GenBank, or represent fast evolving, highly adapted evolutionary lineages.
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Affiliation(s)
- Franziska Szokoli
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Elena Sabaneyeva
- Department of Cytology and Histology, St. Petersburg State University, St. Petersburg, Russia
| | | | - Sascha Krenek
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Martina Schrallhammer
- Mikrobiologie, Biologisches Institut II, Albert-Ludwigs Universität Freiburg, Freiburg, Germany
| | - Carlos A. G. Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Thomas U. Berendonk
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Giulio Petroni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
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Pucciarelli S, Devaraj RR, Mancini A, Ballarini P, Castelli M, Schrallhammer M, Petroni G, Miceli C. Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences. MICROBIAL ECOLOGY 2015; 70:484-97. [PMID: 25704316 PMCID: PMC4494151 DOI: 10.1007/s00248-015-0568-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 01/08/2015] [Indexed: 05/23/2023]
Abstract
We report the characterization of the bacterial consortium associated to Euplotes focardii, a strictly psychrophilic marine ciliate that was maintained in laboratory cultures at 4 °C after its first isolation from Terra Nova Bay, in Antarctica. By Illumina genome analyser, we obtained 11,179 contigs of potential prokaryotic origin and classified them according to the NCBI's prokaryotic attributes table. The majority of these sequences correspond to either Bacteroidetes (16 %) or Proteobacteria (78 %). The latter were dominated by gamma- (39 %, including sequences related to the pathogenic genus Francisella), and alpha-proteobacterial (30 %) sequences. Analysis of the Pfam domain family and Gene Ontology term variation revealed that the most frequent terms that appear unique to this consortium correspond to proteins involved in "transmembrane transporter activity" and "oxidoreductase activity". Furthermore, we identified genes that encode for enzymes involved in the catabolism of complex substance for energy reserves. We also characterized members of the transposase and integrase superfamilies, whose role in bacterial evolution is well documented, as well as putative antifreeze proteins. Antibiotic treatments of E. focardii cultures delayed the cell division of the ciliate. To conclude, our results indicate that this consortium is largely represented by bacteria derived from the original Antarctic sample and may contribute to the survival of E. focardii in laboratory condition. Furthermore, our results suggest that these bacteria may have a more general role in E. focardii survival in its natural cold and oxidative environment.
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Affiliation(s)
- Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, 62032, Italy,
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28
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Gavelis GS, White RA, Suttle CA, Keeling PJ, Leander BS. Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates. BMC Genomics 2015; 16:528. [PMID: 26183220 PMCID: PMC4504456 DOI: 10.1186/s12864-015-1636-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/18/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most microbial eukaryotes are uncultivated and thus poorly suited to standard genomic techniques. This is the case for Polykrikos lebouriae, a dinoflagellate with ultrastructurally aberrant plastids. It has been suggested that these plastids stem from a novel symbiosis with either a diatom or haptophyte, but this hypothesis has been difficult to test as P. lebouriae dwells in marine sand rife with potential genetic contaminants. RESULTS We applied spliced-leader targeted PCR (SLPCR) to obtain dinoflagellate-specific transcriptomes on single-cell isolates of P. lebouriae from marine sediments. Polykrikos lebouriae expressed nuclear-encoded photosynthetic genes that were characteristic of the peridinin-plastids of dinoflagellates, rather than those from a diatom of haptophyte. We confirmed these findings at the genomic level using multiple displacement amplification (MDA) to obtain a partial plastome of P. lebouriae. CONCLUSION From these data, we infer that P. lebouriae has retained the peridinin plastids ancestral for dinoflagellates as a whole, while its closest relatives have lost photosynthesis multiple times independently. We discuss these losses with reference to mixotrophy in polykrikoid dinoflagellates. Our findings demonstrate new levels of variation associated with the peridinin plastids of dinoflagellates and the usefulness of SLPCR approaches on single cell isolates. Unlike other transcriptomic methods, SLPCR has taxonomic specificity, and can in principle be adapted to different splice-leader bearing groups.
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Affiliation(s)
- Gregory S Gavelis
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
| | - Richard A White
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
| | - Curtis A Suttle
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
- Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
- Department of Earth, Ocean and Atmospheric Sciences, Vancouver, BC, V6T1Z4, Canada.
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
| | - Brian S Leander
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
- Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
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Castelli M, Lanzoni O, Fokin SI, Schrallhammer M, Petroni G. Response of the bacterial symbiont Holospora caryophila to different growth conditions of its host. Eur J Protistol 2014; 51:98-108. [PMID: 25635695 DOI: 10.1016/j.ejop.2014.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 11/12/2014] [Accepted: 11/17/2014] [Indexed: 11/17/2022]
Abstract
Previous studies on bacterial symbionts of ciliates have shown that some symbionts can be maintained relatively well under standard laboratory conditions whereas others are frequently lost, especially when the host is cultivated at a high division rate. In this study, the variation in infection level by the endosymbiont Holospora caryophila within its host population Paramecium octaurelia was investigated in response to three alimentary treatments and a subsequent starvation phase. The response of the ciliates was determined as a nearly exponential growth rate with different slopes in each treatment, proportional to the amount of food received. The initial infection level was higher than 90%. After 24 days of exponential host's growth, the prevalence remained stable at approximately 90% in all treatments, even after a subsequent starvation phase of 20 days. However, at intermediate time-points in both the feeding and the starvation phase, fluctuations in the presence of the intracellular bacteria were observed. These results show that H. caryophila is able to maintain its infection under the tested range of host growth conditions, also due to the possibility of an effective re-infection in case of partial loss.
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Affiliation(s)
- Michele Castelli
- Protistology-Zoology Unit, Department of Biology, University of Pisa, 56126 Pisa, Italy
| | - Olivia Lanzoni
- Protistology-Zoology Unit, Department of Biology, University of Pisa, 56126 Pisa, Italy
| | - Sergei I Fokin
- Protistology-Zoology Unit, Department of Biology, University of Pisa, 56126 Pisa, Italy; Department of Invertebrate Zoology, St Petersburg State University, 199034 St. Petersburg, Russia
| | - Martina Schrallhammer
- Institute of Hydrobiology, Technische Universität Dresden, 01217 Dresden, Germany; Microbiology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
| | - Giulio Petroni
- Protistology-Zoology Unit, Department of Biology, University of Pisa, 56126 Pisa, Italy.
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Complete Genome Sequence of Francisella endociliophora Strain FSC1006, Isolated from a Laboratory Culture of the Marine Ciliate Euplotes raikovi. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01227-14. [PMID: 25428973 PMCID: PMC4246165 DOI: 10.1128/genomea.01227-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A strain of Francisella endociliophora was isolated from a laboratory culture of the marine ciliate Euplotes raikovi. Here, we report the complete genome sequence of the bacterial strain FSC1006 (Francisella Strain Collection, Swedish Defence Research Agency, Umeå, Sweden).
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Dobri N, Candelori A, Ricci F, Luporini P, Vallesi A. Evidence for methionine-sulfoxide-reductase gene transfer from Alphaproteobacteria to the transcriptionally active (macro)nucleus of the ciliate, Euplotes raikovi. BMC Microbiol 2014; 14:288. [PMID: 25420622 PMCID: PMC4247871 DOI: 10.1186/s12866-014-0288-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 11/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deleterious phenomena of protein oxidation affect every aerobic organism and methionine residues are their elective targets. The reduction of methionine sulfoxides back to methionines is catalyzed by methionine-sulfoxide reductases (Msrs), enzymes which are particularly active in microorganisms because of their unique nature of individual cells directly exposed to environmental oxidation. RESULTS From the transcriptionally active somatic genome of a common free-living marine protist ciliate, Euplotes raikovi, we cloned multiple gene isoforms encoding Msr of type A (MsrA) committed to repair methionine-S-sulfoxides. One of these isoforms, in addition to including a MsrA-specific nucleotide sequence, included also a sequence specific for a Msr of type B (MsrB) committed to repair methionine-R-sulfoxides. Analyzed for its structural relationships with MsrA and MsrB coding sequences of other organisms, the coding region of this gene (named msrAB) showed much more significant relationships with Msr gene coding sequences of Rhodobacterales and Rhizobiales (Alphaproteobacteria), than of other eukaryotic organisms. CONCLUSIONS Based on the fact that the msrAB gene is delimited by Euplotes-specific regulatory 5' and 3' regions and telomeric C4A4/G4T4 repeats, it was concluded that E. raikovi inherited the coding region of this gene through a phenomenon of horizontal gene transfer from species of Alphaproteobacteria with which it coexists in nature and on which it likely feeds.
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Fokin SI, Schrallhammer M, Chiellini C, Verni F, Petroni G. Free-living ciliates as potential reservoirs for eukaryotic parasites: occurrence of a trypanosomatid in the macronucleus of Euplotes encysticus. Parasit Vectors 2014; 7:203. [PMID: 24774858 PMCID: PMC4022238 DOI: 10.1186/1756-3305-7-203] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 04/13/2014] [Indexed: 12/27/2022] Open
Abstract
Background Flagellates of the family Trypanosomatidae are obligate endoparasites, which can be found in various hosts. Several genera infect insects and occur as monoxenous parasites especially in representatives of Diptera and Hemiptera. These trypanosomatid flagellates probably share the worldwide distribution of their hosts, which are often infested by large numbers of endoparasites. Traditionally, their taxonomy was based on morphology, host origin, and life cycle. Here we report the characterization of a trypanosomatid infection detected in a protozoan, a ciliate collected from a polluted freshwater pond in a suburb of New Delhi (India). Methods Live observations and morphological studies applying light, fluorescence and transmission electron microscopy were conducted. Molecular analyses of host and parasite were performed and used for phylogenetic reconstructions and species (host) or genus level (parasite) identification. Results Although the morphological characteristics were not revealing, a high similarity of the trypanosomatids 18S rRNA gene sequence to Herpetomonas ztiplika and Herpetomonas trimorpha (Kinetoplastida, Trypanosomatidae), both parasites of biting midges (Culicoides kibunensis and Culicoides truncorum, respectively) allowed the assignment to this genus. The majority of the host population displayed a heavy infection that significantly affected the shape of the host macronucleus, which was the main site of parasite localization. In addition, the growth rate of host cultures, identified as Euplotes encysticus according to cell morphology and 18S rRNA gene sequence, was severely impacted by the infection. Conclusions The host-parasite system described here represents a recent example of free-living protists acting as environmental reservoirs for parasitic eukaryotic microorganisms.
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Affiliation(s)
| | - Martina Schrallhammer
- Microbiology, Institute of Biology II, University of Freiburg, Schänzlestraße 1, Freiburg 79104, Germany.
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Boscaro V, Schrallhammer M, Benken KA, Krenek S, Szokoli F, Berendonk TU, Schweikert M, Verni F, Sabaneyeva EV, Petroni G. Rediscovering the genus Lyticum, multiflagellated symbionts of the order Rickettsiales. Sci Rep 2013; 3:3305. [PMID: 24264310 PMCID: PMC3837311 DOI: 10.1038/srep03305] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/21/2013] [Indexed: 11/09/2022] Open
Abstract
Among the bacterial symbionts harbored by the model organism Paramecium, many still lack a recent investigation that includes a molecular characterization. The genus Lyticum consists of two species of large-sized bacteria displaying numerous flagella, despite their inability to move inside their hosts' cytoplasm. We present a multidisciplinary redescription of both species, using the deposited type strains as well as newly collected material. On the basis of 16S rRNA gene sequences, we assigned Lyticum to the order Rickettsiales, that is intensely studied because of its pathogenic representatives and its position as the extant group most closely related to the mitochondrial ancestor. We provide conclusive proofs that at least some Rickettsiales possess actual flagella, a feature that has been recently predicted from genomic data but never confirmed. We give support to the hypothesis that the mitochondrial ancestor could have been flagellated, and provide the basis for further studies on these ciliate endosymbionts.
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Gong J, Qing Y, Guo X, Warren A. "Candidatus Sonnebornia yantaiensis", a member of candidate division OD1, as intracellular bacteria of the ciliated protist Paramecium bursaria (Ciliophora, Oligohymenophorea). Syst Appl Microbiol 2013; 37:35-41. [PMID: 24231291 DOI: 10.1016/j.syapm.2013.08.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 10/26/2022]
Abstract
An intracellular bacterium was discovered in an isolate of Paramecium bursaria from a freshwater pond in Yantai, China. The bacteria were abundant and exclusively found in the cytoplasm of the host which, along with the green alga Chlorella, formed a three-partner consortium that could survive in pure water for at least one week. Cloning, sequencing and phylogenetic analysis of the bacterial 16S rRNA gene showed that the bacterium belonged to the uncultured candidate division OD1, which usually forms part of the rare biosphere. Transmission electron microscopy and fluorescence in situ hybridization (FISH) with specific probes showed that the bacteria were usually located close to the perialgal membranes of endosymbiotic Chlorella cells, and occasionally irregularly distributed throughout the host cytoplasm. The name "Candidatus Sonnebornia yantaiensis" gen. nov., sp. nov. is proposed for the new bacterium. A strongly supported monophyletic subclade, OD1-p, which included the new species, was recognized and this study highlights that protists can be important hosts for rare bacterial taxa.
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Affiliation(s)
- Jun Gong
- Microbial Ecology Group, Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; College of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Yao Qing
- Microbial Ecology Group, Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaohong Guo
- Microbial Ecology Group, Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom
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Abstract
A 69-year-old patient presented with a tender, thickly crusted skin lesion of 1 week's duration. A bacterial culture swab taken from the underlying granular tissue yielded a pure isolate of a Gram-negative coccobacillus, presumptively identified as a novel Francisella species via 16S rRNA and multilocus gene sequence analysis.
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Boscaro V, Petroni G, Ristori A, Verni F, Vannini C. "Candidatus Defluviella procrastinata" and "Candidatus Cyrtobacter zanobii", two novel ciliate endosymbionts belonging to the "Midichloria clade". MICROBIAL ECOLOGY 2013; 65:302-310. [PMID: 23296446 DOI: 10.1007/s00248-012-0170-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 12/17/2012] [Indexed: 06/01/2023]
Abstract
The "Midichloria clade" is a recently discovered but well-established evolutionary lineage clustering inside the order Rickettsiales (Alphaproteobacteria). Not much is known about the biology of these organisms. The best characterized ones are endocellular symbionts of very different eukaryotic hosts, ranging from arthropods to protists. "Candidatus Midichloria mitochondrii", the most studied organism of the group, is an interesting object of study because of its unique capability to infect metazoans' mitochondria and the presence of flagellar genes in its genome. With this work, we aim at increasing the knowledge on the biodiversity and phylogeny of the "Midichloria group". We characterized according to the "full cycle rRNA approach" two novel endosymbionts of ciliated protozoa, i.e. Paramecium nephridiatum and Euplotes aediculatus. According to the nomenclatural rules for uncultivated prokaryotes, we established the novel taxa "Candidatus Defluviella procrastinata" and "Candidatus Cyrtobacter zanobii" for the two bacterial symbionts. Our phylogenetic analysis based on 16S rRNA gene sequences confirms that the evolutionary histories of "Midichloria clade" representatives and of their hosts are very different. This suggests that the symbiotic processes arose many times independently, perhaps through ways of transmission still not described in Rickettsiales.
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Affiliation(s)
- Vittorio Boscaro
- Biology Department, Protistology-Zoology Unit, University of Pisa, Pisa, Italy
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Boscaro V, Fokin SI, Schrallhammer M, Schweikert M, Petroni G. Revised systematics of Holospora-like bacteria and characterization of "Candidatus Gortzia infectiva", a novel macronuclear symbiont of Paramecium jenningsi. MICROBIAL ECOLOGY 2013; 65:255-267. [PMID: 22940732 DOI: 10.1007/s00248-012-0110-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 08/07/2012] [Indexed: 06/01/2023]
Abstract
The genus Holospora (Rickettsiales) includes highly infectious nuclear symbionts of the ciliate Paramecium with unique morphology and life cycle. To date, nine species have been described, but a molecular characterization is lacking for most of them. In this study, we have characterized a novel Holospora-like bacterium (HLB) living in the macronuclei of a Paramecium jenningsi population. This bacterium was morphologically and ultrastructurally investigated in detail, and its life cycle and infection capabilities were described. We also obtained its 16S rRNA gene sequence and developed a specific probe for fluorescence in situ hybridization experiments. A new taxon, "Candidatus Gortzia infectiva", was established for this HLB according to its unique characteristics and the relatively low DNA sequence similarities shared with other bacteria. The phylogeny of the order Rickettsiales based on 16S rRNA gene sequences has been inferred, adding to the available data the sequence of the novel bacterium and those of two Holospora species (Holospora obtusa and Holospora undulata) characterized for the purpose. Our phylogenetic analysis provided molecular support for the monophyly of HLBs and showed a possible pattern of evolution for some of their features. We suggested to classify inside the family Holosporaceae only HLBs, excluding other more distantly related and phenotypically different Paramecium endosymbionts.
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Affiliation(s)
- Vittorio Boscaro
- Biology Department, Protistology-Zoology Unit, University of Pisa, Via A. Volta 4, 56126 Pisa, Italy
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Boscaro V, Vannini C, Fokin SI, Verni F, Petroni G. Characterization of “Candidatus Nebulobacter yamunensis” from the cytoplasm of Euplotes aediculatus (Ciliophora, Spirotrichea) and emended description of the family Francisellaceae. Syst Appl Microbiol 2012; 35:432-40. [DOI: 10.1016/j.syapm.2012.07.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 07/02/2012] [Accepted: 07/26/2012] [Indexed: 12/31/2022]
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Siddaramappa S, Challacombe JF, Petersen JM, Pillai S, Kuske CR. Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources. BMC Genomics 2012; 13:422. [PMID: 22920915 PMCID: PMC3479022 DOI: 10.1186/1471-2164-13-422] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 08/14/2012] [Indexed: 12/14/2022] Open
Abstract
Background Francisella tularensis is an intracellular pathogen that causes tularemia in humans and the public health importance of this bacterium has been well documented in recent history. Francisella philomiragia, a distant relative of F. tularensis, is thought to constitute an environmental lineage along with Francisella novicida. Nevertheless, both F. philomiragia and F. novicida have been associated with human disease, primarily in immune-compromised individuals. To understand the genetic relationships and evolutionary contexts among different lineages within the genus Francisella, the genome of Francisella spp. strain TX07-7308 was sequenced and compared to the genomes of F. philomiragia strains ATCC 25017 and 25015, F. novicida strain U112, and F. tularensis strain Schu S4. Results The size of strain ATCC 25017 chromosome was 2,045,775 bp and contained 1,983 protein-coding genes. The size of strain TX07-7308 chromosome was 2,035,931 bp and contained 1,980 protein-coding genes. Pairwise BLAST comparisons indicated that strains TX07-7308 and ATCC 25017 contained 1,700 protein coding genes in common. NUCmer analyses revealed that the chromosomes of strains TX07-7308 and ATCC 25017 were mostly collinear except for a few gaps, translocations, and/or inversions. Using the genome sequence data and comparative analyses with other members of the genus Francisella (e.g., F. novicida strain U112 and F. tularensis strain Schu S4), several strain-specific genes were identified. Strains TX07-7308 and ATCC 25017 contained an operon with six open reading frames encoding proteins related to enzymes involved in thiamine biosynthesis that was absent in F. novicida strain U112 and F. tularensis strain Schu S4. Strain ATCC 25017 contained an operon putatively involved in lactose metabolism that was absent in strain TX07-7308, F. novicida strain U112, and F. tularensis strain Schu S4. In contrast, strain TX07-7308 contained an operon putatively involved in glucuronate metabolism that was absent in the genomes of strain ATCC 25017, F. novicida strain U112, and F. tularensis strain Schu S4. The polymorphic nature of polysaccharide biosynthesis/modification gene clusters among different Francisella strains was also evident from genome analyses. Conclusions From genome comparisons, it appeared that genes encoding novel functions have contributed to the metabolic enrichment of the environmental lineages within the genus Francisella. The inability to acquire new genes coupled with the loss of ancestral traits and the consequent reductive evolution may be a cause for, as well as an effect of, niche selection of F. tularensis. Sequencing and comparison of the genomes of more isolates are required to obtain further insights into the ecology and evolution of different species within the genus Francisella.
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Dziallas C, Allgaier M, Monaghan MT, Grossart HP. Act together-implications of symbioses in aquatic ciliates. Front Microbiol 2012; 3:288. [PMID: 22891065 PMCID: PMC3413206 DOI: 10.3389/fmicb.2012.00288] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 07/22/2012] [Indexed: 02/01/2023] Open
Abstract
Mutual interactions in the form of symbioses can increase the fitness of organisms and provide them with the capacity to occupy new ecological niches. The formation of obligate symbioses allows for rapid evolution of new life forms including multitrophic consortia. Microbes are important components of many known endosymbioses and their short generation times and strong potential for genetic exchange may be important drivers of speciation. Hosts provide endo- and ectosymbionts with stable, nutrient-rich environments, and protection from grazers. This is of particular importance in aquatic ecosystems, which are often highly variable, harsh, and nutrient-deficient habitats. It is therefore not surprising that symbioses are widespread in both marine and freshwater environments. Symbioses in aquatic ciliates are good model systems for exploring symbiont-host interactions. Many ciliate species are globally distributed and have been intensively studied in the context of plastid evolution. Their relatively large cell size offers an ideal habitat for numerous microorganisms with different functional traits including commensalism and parasitism. Phagocytosis facilitates the formation of symbiotic relationships, particularly since some ingested microorganisms can escape the digestion. For example, photoautotrophic algae and methanogens represent endosymbionts that greatly extend the biogeochemical functions of their hosts. Consequently, symbiotic relationships between protists and prokaryotes are widespread and often result in new ecological functions of the symbiotic communities. This enables ciliates to thrive under a wide range of environmental conditions including ultraoligotrophic or anoxic habitats. We summarize the current understanding of this exciting research topic to identify the many areas in which knowledge is lacking and to stimulate future research by providing an overview on new methodologies and by formulating a number of emerging questions in this field.
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Affiliation(s)
- Claudia Dziallas
- Marine Biological Section, University of CopenhagenHelsingør, Denmark
| | - Martin Allgaier
- Department of Limnology of Stratified Lakes, Leibniz-Institute of Freshwater Ecology and Inland FisheriesStechlin, Germany
- Berlin Center for Genomics in Biodiversity ResearchBerlin, Germany
| | - Michael T. Monaghan
- Department of Limnology of Shallow Lakes and Lowland Rivers, Leibniz-Institute of Freshwater Ecology and Inland FisheriesBerlin, Germany
| | - Hans-Peter Grossart
- Department of Limnology of Stratified Lakes, Leibniz-Institute of Freshwater Ecology and Inland FisheriesStechlin, Germany
- Institute for Biochemistry and Biology, Potsdam UniversityPotsdam, Germany
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Duodu S, Larsson P, Sjödin A, Forsman M, Colquhoun DJ. The distribution of Francisella-like bacteria associated with coastal waters in Norway. MICROBIAL ECOLOGY 2012; 64:370-7. [PMID: 22370877 DOI: 10.1007/s00248-012-0023-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 02/03/2012] [Indexed: 05/17/2023]
Abstract
We report the diversity and distribution of Francisella species in Norwegian coastal and fresh waters following a nationwide survey in which water and sediment samples were collected from locations spanning almost the entire Norwegian coastline. In total, samples were obtained from 149 and 64 seawater and freshwater sites, respectively. DNA extracts from these environmental samples were initially screened by polymerase chain reaction (PCR) using Francisella genus-specific 16S rDNA primers. Positive samples were then amplified with genus-specific primers targeting Francisella succinate dehydrogenase A gene and Francisella philomiragia group-specific sequences for the SAICAR synthetase/phosphoribosylamine-glycine ligase gene. Francisella-related bacteria were identified in approximately 30% of seawater sampled sites, mainly in southern Norway, although a single positive sample was identified in the far north of the country. No PCR positives were identified from the freshwater sources. Sequences related to recognised species, both pathogenic and environmental, were identified, with the majority closely associated with F. philomiragia. However, a number of identified sequences probably represent previously undescribed species. Our data provide evidence of a significant background of Francisella spp. in geographical areas associated with outbreaks of fish francisellosis in Norway.
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Affiliation(s)
- Samuel Duodu
- Section for Bacteriology, Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750, Sentrum, 0106, Oslo, Norway.
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Sjödin A, Svensson K, Öhrman C, Ahlinder J, Lindgren P, Duodu S, Johansson A, Colquhoun DJ, Larsson P, Forsman M. Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish. BMC Genomics 2012; 13:268. [PMID: 22727144 PMCID: PMC3485624 DOI: 10.1186/1471-2164-13-268] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 06/07/2012] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Prior to this study, relatively few strains of Francisella had been genome-sequenced. Previously published Francisella genome sequences were largely restricted to the zoonotic agent F. tularensis. Only limited data were available for other members of the Francisella genus, including F. philomiragia, an opportunistic pathogen of humans, F. noatunensis, a serious pathogen of farmed fish, and other less well described endosymbiotic species. RESULTS We determined the phylogenetic relationships of all known Francisella species, including some for which the phylogenetic positions were previously uncertain. The genus Francisella could be divided into two main genetic clades: one included F. tularensis, F. novicida, F. hispaniensis and Wolbachia persica, and another included F. philomiragia and F. noatunensis.Some Francisella species were found to have significant recombination frequencies. However, the fish pathogen F. noatunensis subsp. noatunensis was an exception due to it exhibiting a highly clonal population structure similar to the human pathogen F. tularensis. CONCLUSIONS The genus Francisella can be divided into two main genetic clades occupying both terrestrial and marine habitats. However, our analyses suggest that the ancestral Francisella species originated in a marine habitat. The observed genome to genome variation in gene content and IS elements of different species supports the view that similar evolutionary paths of host adaptation developed independently in F. tularensis (infecting mammals) and F. noatunensis subsp. noatunensis (infecting fish).
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Affiliation(s)
- Andreas Sjödin
- Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Umeå, Sweden
| | - Kerstin Svensson
- Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Umeå, Sweden
| | - Caroline Öhrman
- Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Umeå, Sweden
| | - Jon Ahlinder
- Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Umeå, Sweden
| | - Petter Lindgren
- Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Umeå, Sweden
| | - Samuel Duodu
- Section for Bacteriology, Norwegian Veterinary Institute, Postbox 750 sentrum, 0106, Oslo, Norway
| | - Anders Johansson
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
| | - Duncan J Colquhoun
- Section for Bacteriology, Norwegian Veterinary Institute, Postbox 750 sentrum, 0106, Oslo, Norway
| | - Pär Larsson
- Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Umeå, Sweden
| | - Mats Forsman
- Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Umeå, Sweden
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Wangen IH, Karlsbakk E, Einen ACB, Ottem KF, Nylund A, Mortensen S. Fate of Francisella noatunensis, a pathogen of Atlantic cod Gadus morhua, in blue mussels Mytilus edulis. DISEASES OF AQUATIC ORGANISMS 2012; 98:63-72. [PMID: 22422130 DOI: 10.3354/dao02427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Francisellosis, caused by the bacterium Francisella noatunensis, is one of the most severe diseases affecting farmed cod, and has caused great economic loss for the cod farming industry in Norway. We studied the fate of F. noatunensis in the marine environment, focusing on the role of blue mussels. In experimental challenges, waterborne F. noatunensis was rapidly filtered by the blue mussel and transported to the digestive diverticulae. The bacteria passed through the entire digestive system. Intraperitoneal injection of cod with suspensions prepared from faeces collected from challenged mussels resulted in the development of francisellosis in the recipients, demonstrating that some bacteria were alive and infective when shed in mussel faeces. Bacterial clearance from the mussels was relatively fast, and no evidence was found, suggesting that the bacterium is capable of persisting or multiplying in the mussel tissues. A cohabitation experiment with cod and mussels previously exposed to F. noatunensis did not lead to infection in cod. A direct transmission from contaminated mussels to cod was thus not demonstrated; however, faeces particles with infective bacteria may play a role in the transmission of the bacterium in marine food chains.
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Soto E, Revan F. Culturability and persistence of Francisella noatunensis subsp. orientalis (syn. Francisella asiatica) in sea- and freshwater microcosms. MICROBIAL ECOLOGY 2012; 63:398-404. [PMID: 21881943 DOI: 10.1007/s00248-011-9932-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 08/17/2011] [Indexed: 05/31/2023]
Abstract
Francisella noatunensis subsp. orientalis (syn. Francisella asiatica), the causative agent of franciselliosis in warm-water fish, is a Gram-negative facultative intracellular bacterium. Although it has been characterized as one of the most pathogenic bacteria in fish, the water conditions that allow for its survival and infectious capacities outside the fish host are not known. Data obtained in this project indicate that both temperature and salinity are important factors in the culturability and persistence of F. noatunensis subsp. orientalis in both sea- and freshwater microcosms. These results indicate that culturable F. noatunensis subsp. orientalis persist for longer periods of time and at higher numbers in seawater, and its persistence is inversely related to water temperature. Moreover, the pathogenic properties of the bacteria suspended in water microcosms appear to decrease after only 24 h and become non-infective after 2 days in the absence of the fish host.
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Affiliation(s)
- Esteban Soto
- Department of Pathobiology, School of Veterinary Medicine, Basseterre, Ross University School of Veterinary Medicine, West Farm, Basseterre, St. Kitts, West Indies.
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Brevik OJ, Ottem KF, Kamaishi T, Watanabe K, Nylund A. Francisella halioticida sp. nov., a pathogen of farmed giant abalone (Haliotis gigantea) in Japan. J Appl Microbiol 2011; 111:1044-56. [PMID: 21883728 DOI: 10.1111/j.1365-2672.2011.05133.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
AIMS In 2005, a Francisella sp. was isolated from diseased cultured giant abalone (Haliotis gigantea) in Japan. The aim of this study was to clarify the taxonomic status of this Francisella sp. Shimane-1 isolate in relation to the four described Francisella species. METHODS AND RESULTS The 16S rRNA gene and several housekeeping genes of the Shimane-1 were compared to isolates of the four recognized species within the Francisella genus. DNA-DNA hybridization (DDH) and biochemical profile comparison were performed with the two phylogenetically closely related species, Francisella philomiragia and Francisella noatunensis. Results show that the Shimane-1 is genetically different from all described Francisella species and differs phenotypically from F. philomiragia and F. noatunensis. The average DDH similarity of Francisella sp. Shimane-1 to F. noatunensis ssp. noatunensis (NCIMB14265(T)) and to F. philomiragia (DSM7535(T)) was 49·2 and 61%, respectably, clearly supporting the establishment of Shimane-1 as a new species within the Francisella genus. CONCLUSIONS The phenotypic and genetic results presented in this study suggest the establishment of Shimane-1 as a novel species, for which the name Francisella halioticida sp. nov. (=LMG26062(T), =DSM23729(T)) is proposed. SIGNIFICANCE AND IMPACT OF THE STUDY This study clarifies the taxonomic position and characteristics of a novel mollusc pathogenic Francisella species.
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Affiliation(s)
- O J Brevik
- Department of Biology, University of Bergen, Bergen, Norway.
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46
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Colquhoun DJ, Duodu S. Francisella infections in farmed and wild aquatic organisms. Vet Res 2011; 42:47. [PMID: 21385413 PMCID: PMC3060124 DOI: 10.1186/1297-9716-42-47] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 03/08/2011] [Indexed: 01/08/2023] Open
Abstract
Over the last 10 years or so, infections caused by bacteria belonging to a particular branch of the genus Francisella have become increasingly recognised in farmed fish and molluscs worldwide. While the increasing incidence of diagnoses may in part be due to the development and widespread availability of molecular detection techniques, the domestication of new organisms has undoubtedly instigated emergence of clinical disease in some species. Francisellosis in fish develops in a similar fashion independent of host species and is commonly characterised by the presence of multi-organ granuloma and high morbidity, with varying associated mortality levels. A number of fish species are affected including Atlantic cod, Gadus morhua; tilapia, Oreochromis sp.; Atlantic salmon, Salmo salar; hybrid striped bass, Morone chrysops × M. saxatilis and three-lined grunt, Parapristipoma trilinineatum. The disease is highly infectious and often prevalent in affected stocks. Most, if not all strains isolated from teleost fish belong to either F. noatunensis subsp. orientalis in warm water fish species or Francisella noatunensis subsp. noatunensis in coldwater fish species. The disease is quite readily diagnosed following histological examination and identification of the aetiological bacterium by culture on cysteine rich media or PCR. The available evidence may indicate a degree of host specificity for the various Francisella strains, although this area requires further study. No effective vaccine is currently available. Investigation of the virulence mechanisms and host response shows similarity to those known from Francisella tularensis infection in mammals. However, no evidence exists for zoonotic potential amongst the fish pathogenic Francisella.
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Affiliation(s)
- Duncan J Colquhoun
- Section for Fish health, National Veterinary Institute, Postbox 750 sentrum, 0106 Oslo, Norway.
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