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Collingro A, Köstlbacher S, Siegl A, Toenshoff ER, Schulz F, Mitchell SO, Weinmaier T, Rattei T, Colquhoun DJ, Horn M. The Fish Pathogen "Candidatus Clavichlamydia salmonicola"-A Missing Link in the Evolution of Chlamydial Pathogens of Humans. Genome Biol Evol 2023; 15:evad147. [PMID: 37615694 PMCID: PMC10448858 DOI: 10.1093/gbe/evad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2023] [Indexed: 08/25/2023] Open
Abstract
Chlamydiae like Chlamydia trachomatis and Chlamydia psittaci are well-known human and animal pathogens. Yet, the chlamydiae are a much larger group of evolutionary ancient obligate intracellular bacteria that includes predominantly symbionts of protists and diverse animals. This makes them ideal model organisms to study evolutionary transitions from symbionts in microbial eukaryotes to pathogens of humans. To this end, comparative genome analysis has served as an important tool. Genome sequence data for many chlamydial lineages are, however, still lacking, hampering our understanding of their evolutionary history. Here, we determined the first high-quality draft genome sequence of the fish pathogen "Candidatus Clavichlamydia salmonicola", representing a separate genus within the human and animal pathogenic Chlamydiaceae. The "Ca. Clavichlamydia salmonicola" genome harbors genes that so far have been exclusively found in Chlamydia species suggesting that basic mechanisms important for the interaction with chordate hosts have evolved stepwise in the history of chlamydiae. Thus, the genome sequence of "Ca. Clavichlamydia salmonicola" allows to constrain candidate genes to further understand the evolution of chlamydial virulence mechanisms required to infect mammals.
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Affiliation(s)
- Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Alexander Siegl
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Elena R Toenshoff
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich (ETH), Zürich, Switzerland
| | - Frederik Schulz
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- DOE Joint Genome Institute, Berkeley, California, USA
| | | | - Thomas Weinmaier
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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Toenshoff ER, Fields PD, Bourgeois YX, Ebert D. The End of a 60-year Riddle: Identification and Genomic Characterization of an Iridovirus, the Causative Agent of White Fat Cell Disease in Zooplankton. G3 (Bethesda) 2018; 8:1259-1272. [PMID: 29487186 PMCID: PMC5873915 DOI: 10.1534/g3.117.300429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/08/2018] [Indexed: 12/11/2022]
Abstract
The planktonic freshwater crustacean of the genus Daphnia are a model system for biomedical research and, in particular, invertebrate-parasite interactions. Up until now, no virus has been characterized for this system. Here we report the discovery of an iridovirus as the causative agent of White Fat Cell Disease (WFCD) in Daphnia WFCD is a highly virulent disease of Daphnia that can easily be cultured under laboratory conditions. Although it has been studied from sites across Eurasia for more than 60 years, its causative agent had not been described, nor had an iridovirus been connected to WFCD before now. Here we find that an iridovirus-the Daphnia iridescent virus 1 (DIV-1)-is the causative agent of WFCD. DIV-1 has a genome sequence of about 288 kbp, with 39% G+C content and encodes 367 predicted open reading frames. DIV-1 clusters together with other invertebrate iridoviruses but has by far the largest genome among all sequenced iridoviruses. Comparative genomics reveal that DIV-1 has apparently recently lost a substantial number of unique genes but has also gained genes by horizontal gene transfer from its crustacean host. DIV-1 represents the first invertebrate iridovirus that encodes proteins to purportedly cap RNA, and it contains unique genes for a DnaJ-like protein, a membrane glycoprotein and protein of the immunoglobulin superfamily, which may mediate host-pathogen interactions and pathogenicity. Our findings end a 60-year search for the causative agent of WFCD and add to our knowledge of iridovirus genomics and invertebrate-virus interactions.
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Affiliation(s)
- Elena R Toenshoff
- Basel University, Department of Environmental Sciences, Zoology, Vesalgasse 1, CH-4051 Basel, Switzerland
| | - Peter D Fields
- Basel University, Department of Environmental Sciences, Zoology, Vesalgasse 1, CH-4051 Basel, Switzerland
| | - Yann X Bourgeois
- Basel University, Department of Environmental Sciences, Zoology, Vesalgasse 1, CH-4051 Basel, Switzerland
| | - Dieter Ebert
- Basel University, Department of Environmental Sciences, Zoology, Vesalgasse 1, CH-4051 Basel, Switzerland
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Sixt BS, Kostanjšek R, Mustedanagic A, Toenshoff ER, Horn M. Developmental cycle and host interaction of Rhabdochlamydia porcellionis, an intracellular parasite of terrestrial isopods. Environ Microbiol 2013; 15:2980-93. [PMID: 24024954 DOI: 10.1111/1462-2920.12252] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/05/2013] [Accepted: 08/12/2013] [Indexed: 12/01/2022]
Abstract
Environmental chlamydiae are a diverse group of obligate intracellular bacteria related to well-known pathogens of humans. To date, only very little is known about chlamydial species infecting arthropods. In this study, we used cocultivation with insect cells for recovery and maintenance of Rhabdochlamydia porcellionis, a parasite of the crustacean host Porcellio scaber. In vitro, the infection cycle of R. porcellionis was completed within 7 days, resulting in the release of infectious particles by host cell lysis. Lack of apoptosis induction during the entire course of infection, combined with a reduced sensitivity of infected cultures to experimentally induced programmed cell death, indicates that R. porcellionis like its human pathogenic relatives counteracts this host defence mechanism. Interestingly, the rod-shaped variant of R. porcellionis, proposed to represent their mature infective stage, was not detected in cell culture, suggesting that its development may require prolonged maturation or may be triggered by specific conditions encountered only in the animal host. This first cell culture-based system for the cultivation and investigation of an arthropod-associated chlamydial species will help to better understand the biology of a so far neglected group of chlamydiae and its recently suggested potential to cause disease in humans.
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Affiliation(s)
- Barbara S Sixt
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Rok Kostanjšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Azra Mustedanagic
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Elena R Toenshoff
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Matthias Horn
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
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Mitchell SO, Steinum TM, Toenshoff ER, Kvellestad A, Falk K, Horn M, Colquhoun DJ. 'Candidatus Branchiomonas cysticola' is a common agent of epitheliocysts in seawater-farmed Atlantic salmon Salmo salar in Norway and Ireland. Dis Aquat Organ 2013; 103:35-43. [PMID: 23482383 DOI: 10.3354/dao02563] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The prevalence and geographical distribution of the recently described endosymbiont 'Candidatus Branchiomonas cysticola' in Atlantic salmon Salmo salar gill epithelial cell cysts was investigated in seawater-farmed fish suffering proliferative gill inflammation (PGI). To this end, we developed a specific and sensitive real-time PCR assay for detection of the bacterium. 'Ca. B. cysticola' was found to be highly prevalent in Atlantic salmon gills sampled over 7 yr and from 17 geographically distant seawater locations in Norway and Ireland. 'Ca. B. cysticola' was found in significantly greater quantities in fish with large numbers of epitheliocysts, and fluorescence in situ hybridization confirmed its localisation within cysts. 'Ca. Piscichlamydia salmonis', a bacterium previously linked to epitheliocysts, was identified at relatively low levels of infection, apparently independent of epitheliocyst prevalence. These results suggest that 'Ca. B. cysticola' is the main cyst-forming bacterium in seawater-farmed Atlantic salmon in the studied countries. Our results also suggest a relationship between load of 'Ca. B. cysticola' and extent of pathological changes. Taken together with a previously described association between epitheliocyst load and severity of PGI in Norwegian salmon, the results could indicate a role for 'Ca. B. cysticola' in gill diseases such as PGI.
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Affiliation(s)
- Susan O Mitchell
- Norwegian Veterinary Institute, Ullevålsveien 68, 0454 Oslo, Norway
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Toenshoff ER, Gruber D, Horn M. Co-evolution and symbiont replacement shaped the symbiosis between adelgids (Hemiptera: Adelgidae) and their bacterial symbionts. Environ Microbiol 2012; 14:1284-95. [DOI: 10.1111/j.1462-2920.2012.02712.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Schimak MP, Toenshoff ER, Bright M. Simultaneous 16S and 18S rRNA fluorescence in situ hybridization (FISH) on LR White sections demonstrated in Vestimentifera (Siboglinidae) tubeworms. Acta Histochem 2012; 114:122-30. [PMID: 21507466 PMCID: PMC3278570 DOI: 10.1016/j.acthis.2011.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 03/18/2011] [Accepted: 03/20/2011] [Indexed: 12/01/2022]
Abstract
Traditional morphological identification of invertebrate marine species is limited in early life history stages for many taxa. In this study, we demonstrate, by example of Vestimentiferan tubeworms (Siboglinidae, Polychaeta), that the simultaneous fluorescence in situ hybridization (FISH) of both eukaryotic host and bacterial symbiont cells is possible on a single semi-thin (1 μm) section. This allows the identification of host specimens to species level as well as offering visualization of bacteria distributed within the host tissue. Previously published 18S rRNA host-specific oligonucleotide probes for Riftia pachyptila, Tevnia jerichonana and a newly designed Oasisia alvinae probe, as well as a 16S rRNA probe targeting symbionts found in all host species, were applied. A number of standard fixation and hybridization parameters were tested and optimized for the best possible signal intensity and cellular resolution. Ethanol conserved samples embedded in LR White low viscosity resin yielded the best results with regard to both signal intensity and resolution. We show that extended storage times of specimens does not affect the quality of signals attained by FISH and use our protocol to identify morphologically unidentifiable tubeworm individuals from a small data set, conforming to previous findings in succession studies of the Siboglinidae family.
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Affiliation(s)
- Mario P Schimak
- University of Vienna, Department of Marine Biology, Austria.
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Haider S, Wagner M, Schmid MC, Sixt BS, Christian JG, Häcker G, Pichler P, Mechtler K, Müller A, Baranyi C, Toenshoff ER, Montanaro J, Horn M. Raman microspectroscopy reveals long-term extracellular activity of Chlamydiae. Mol Microbiol 2010; 77:687-700. [PMID: 20545842 DOI: 10.1111/j.1365-2958.2010.07241.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The phylum Chlamydiae consists exclusively of obligate intracellular bacteria. Some of them are formidable pathogens of humans, while others occur as symbionts of amoebae. These genetically intractable bacteria possess a developmental cycle consisting of replicative reticulate bodies and infectious elementary bodies, which are believed to be physiologically inactive. Confocal Raman microspectroscopy was applied to differentiate between reticulate bodies and elementary bodies of Protochlamydia amoebophila and to demonstrate in situ the labelling of this amoeba symbiont after addition of isotope-labelled phenylalanine. Unexpectedly, uptake of this amino acid was also observed for both developmental stages for up to 3 weeks, if incubated extracellularly with labelled phenylalanine, and P. amoebophila remained infective during this period. Furthermore, P. amoebophila energizes its membrane and performs protein synthesis outside of its host. Importantly, amino acid uptake and protein synthesis after extended extracellular incubation could also be demonstrated for the human pathogen Chlamydia trachomatis, which synthesizes stress-related proteins under these conditions as shown by 2-D gel electrophoresis and MALDI-TOF/TOF mass spectrometry. These findings change our perception of chlamydial biology and reveal that host-free analyses possess a previously not recognized potential for direct experimental access to these elusive microorganisms.
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Affiliation(s)
- Susanne Haider
- Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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Schmitz-Esser S, Toenshoff ER, Haider S, Heinz E, Hoenninger VM, Wagner M, Horn M. Diversity of bacterial endosymbionts of environmental acanthamoeba isolates. Appl Environ Microbiol 2008; 74:5822-31. [PMID: 18641160 PMCID: PMC2547052 DOI: 10.1128/aem.01093-08] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 07/11/2008] [Indexed: 11/20/2022] Open
Abstract
Free-living amoebae are frequent hosts for bacterial endosymbionts. In this study, the symbionts of eight novel environmental Acanthamoeba strains isolated from different locations worldwide were characterized. Phylogenetic analysis revealed that they were related to one of four evolutionary lineages of amoeba symbionts recognized previously. This study provides evidence for the existence of only a small number of phylogenetically well-separated groups of obligate intracellular endosymbionts of acanthamoebae with global distribution.
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MESH Headings
- Acanthamoeba/genetics
- Acanthamoeba/microbiology
- Animals
- Bacteria/classification
- Bacteria/genetics
- Biodiversity
- DNA, Bacterial/genetics
- DNA, Protozoan/genetics
- Genes, Bacterial
- Genes, Protozoan
- Genes, rRNA
- Geologic Sediments/microbiology
- Molecular Sequence Data
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/genetics
- Sequence Analysis, DNA
- Soil Microbiology
- Symbiosis
- Water Microbiology
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Affiliation(s)
- Stephan Schmitz-Esser
- Department of Microbial Ecology, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
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Abstract
Acanthamoebae are ubiquitous free-living amoebae and important predators of microbial communities. They frequently contain obligate intracellular bacterial symbionts, which show a worldwide distribution. All Acanthamoeba spp. described so far harboured no or only a single specific endosymbiont phylotype, and in some cases evidence for coevolution between the symbiotic bacteria and the amoeba host has been reported. In this study we have isolated and characterized an Acanthamoeba sp. (strain OEW1) showing a stable symbiotic relationship with two morphologically different endosymbionts. 16S rRNA sequence analysis assigned these symbionts to the candidate genus Procabacter (Betaproteobacteria) and the genus Parachlamydia (Chlamydiae) respectively. Fluorescence in situ hybridization and transmission electron microscopy confirmed the affiliation of the endosymbionts and showed their co-occurrence in the amoeba host cells and their intracellular location within separate compartments enclosed by host-derived membranes. Further analysis of this stable relationship should provide novel insights into the complex interactions of intracellular multiple-partner associations.
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Affiliation(s)
| | | | | | | | | | - Matthias Horn
- For correspondence. E-mail ; Tel. (+43) 1 4277 54393; Fax (+43) 1 4277 54389
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Stoecker K, Bendinger B, Schöning B, Nielsen PH, Nielsen JL, Baranyi C, Toenshoff ER, Daims H, Wagner M. Cohn's Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proc Natl Acad Sci U S A 2006; 103:2363-7. [PMID: 16452171 PMCID: PMC1413686 DOI: 10.1073/pnas.0506361103] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
135 years ago Ferdinand Cohn, the founder of bacteriology, microscopically observed a conspicuous filamentous bacterium with a complex life cycle and described it as Crenothrix polyspora. This uncultured bacterium is infamous for mass developments in drinking water systems, but its phylogeny and physiology remained unknown. We show that C. polyspora is a gammaproteobacterium closely related to methanotrophs and capable of oxidizing methane. We discovered that C. polyspora encodes a phylogenetically very unusual particulate methane monooxygenase whose expression is strongly increased in the presence of methane. Our findings demonstrate a previously unrecognized complexity of the evolutionary history and cell biology of methane-oxidizing bacteria.
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Affiliation(s)
- Kilian Stoecker
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
| | - Bernd Bendinger
- Deutsche Vereinigung des Gas- und Wasserfaches-Forschungsstelle, Technische Universität Hamburg, D-21073 Hamburg, Germany; and
| | - Björn Schöning
- Deutsche Vereinigung des Gas- und Wasserfaches-Forschungsstelle, Technische Universität Hamburg, D-21073 Hamburg, Germany; and
| | - Per H. Nielsen
- Department of Life Sciences, Aalborg University, DK-9000 Aalborg, Denmark
| | - Jeppe L. Nielsen
- Department of Life Sciences, Aalborg University, DK-9000 Aalborg, Denmark
| | - Christian Baranyi
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
| | - Elena R. Toenshoff
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
| | - Holger Daims
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
| | - Michael Wagner
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
- To whom correspondence should be addressed at:
Department for Mikrobielle Ökologie, Universität Wien, Althanstrasse 14, A-1090 Wien, Austria. E-mail:
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Collingro A, Toenshoff ER, Taylor MW, Fritsche TR, Wagner M, Horn M. 'Candidatus Protochlamydia amoebophila', an endosymbiont of Acanthamoeba spp. Int J Syst Evol Microbiol 2005; 55:1863-1866. [PMID: 16166679 DOI: 10.1099/ijs.0.63572-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The obligately intracellular coccoid bacterium UWE25, a symbiont of Acanthamoeba spp., was previously identified as being related to chlamydiae based upon the presence of a chlamydia-like developmental cycle and its 16S rRNA gene sequence. Analysis of its complete genome sequence demonstrated that UWE25 shows many characteristic features of chlamydiae, including dependency on host-derived metabolites, composition of the cell envelope and the ability to thrive as an energy parasite within the cells of its eukaryotic host. Phylogenetic analysis of 44 ribosomal proteins further confirmed the affiliation of UWE25 to the 'Chlamydiae'. Within this phylum, UWE25 could be assigned to the family Parachlamydiaceae based on comparative analyses of the 16S rRNA, 23S rRNA and endoribonuclease P RNA genes. The distinct dissimilarities from its closest relative, Parachlamydia acanthamoebae Bn(9)(T) (7.1, 9.7 and 28.8%, respectively), observed in this analysis justify its classification in a new genus. Therefore, the name 'Candidatus Protochlamydia amoebophila' is proposed for the designation of the Acanthamoeba sp. symbiont UWE25 (=ATCC PRA-7).
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Affiliation(s)
- Astrid Collingro
- Department of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Elena R Toenshoff
- Department of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Michael W Taylor
- Department of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | | | - Michael Wagner
- Department of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Matthias Horn
- Department of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
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