1
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Maire J, Collingro A, Horn M, van Oppen MJH. Chlamydiae in corals: shared functional potential despite broad taxonomic diversity. ISME COMMUNICATIONS 2024; 4:ycae054. [PMID: 38707840 PMCID: PMC11070183 DOI: 10.1093/ismeco/ycae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/15/2024] [Accepted: 04/09/2024] [Indexed: 05/07/2024]
Abstract
Cnidarians, such as corals and sea anemones, associate with a wide range of bacteria that have essential functions, including nutrient cycling and the production of antimicrobial compounds. Within cnidarians, bacteria can colonize all microhabitats including the tissues. Among them are obligate intracellular bacteria of the phylum Chlamydiota (chlamydiae) whose impact on cnidarian hosts and holobionts, especially corals, remain unknown. Here, we conducted a meta-analysis of previously published 16S rRNA gene metabarcoding data from cnidarians (e.g. coral, jellyfish, and anemones), eight metagenome-assembled genomes (MAGs) of coral-associated chlamydiae, and one MAG of jellyfish-associated chlamydiae to decipher their diversity and functional potential. While the metabarcoding dataset showed an enormous diversity of cnidarian-associated chlamydiae, six out of nine MAGs were affiliated with the Simkaniaceae family. The other three MAGs were assigned to the Parasimkaniaceae, Rhabdochlamydiaceae, and Anoxychlamydiaceae, respectively. All MAGs lacked the genes necessary for an independent existence, lacking any nucleotide or vitamin and most amino acid biosynthesis pathways. Hallmark chlamydial genes, such as a type III secretion system, nucleotide transporters, and genes for host interaction, were encoded in all MAGs. Together these observations suggest an obligate intracellular lifestyle of coral-associated chlamydiae. No unique genes were found in coral-associated chlamydiae, suggesting a lack of host specificity. Additional studies are needed to understand how chlamydiae interact with their coral host, and other microbes in coral holobionts. This first study of the diversity and functional potential of coral-associated chlamydiae improves our understanding of both the coral microbiome and the chlamydial lifestyle and host range.
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Affiliation(s)
- Justin Maire
- School of BioSciences, The University of Melbourne, Parkville 3010, VIC, Australia
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Parkville 3010, VIC, Australia
- Australian Institute of Marine Science, PMB No 3, Townsville 4810, QLD, Australia
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2
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Giovannini M, Petroni G, Castelli M. Novel evolutionary insights on the interactions of the Holosporales (Alphaproteobacteria) with eukaryotic hosts from comparative genomics. Environ Microbiol 2024; 26:e16562. [PMID: 38173299 DOI: 10.1111/1462-2920.16562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
Holosporales are an alphaproteobacterial order engaging in obligate and complex associations with eukaryotes, in particular protists. The functional and evolutionary features of those interactions are still largely undisclosed. Here, we sequenced the genomes of two members of the species Bealeia paramacronuclearis (Holosporales, Holosporaceae) intracellularly associated with the ciliate protist Paramecium, which resulted in high correspondence. Consistent with the short-branched early-divergent phylogenetic position, Bealeia presents a larger functional repertoire than other Holosporaceae, comparable to those of other Holosporales families, particularly for energy metabolism and motility. Our analyses indicate that different Holosporales likely experienced at least partly autonomous genome reduction and adaptation to host interactions, for example regarding dependence on host biotin driven by multiple independent horizontal acquisitions of transporters. Among Alphaproteobacteria, this is reminiscent of the convergently evolved Rickettsiales, which however appear more diverse, possibly due to a probably more ancient origin. We identified in Bealeia and other Holosporales the plasmid-encoded putative genetic determinants of R-bodies, which may be involved in a killer trait towards symbiont-free hosts. While it is not clear whether these genes are ancestral or recently horizontally acquired, an intriguing and peculiar role of R-bodies is suggested in the evolution of the interactions of multiple Holosporales with their hosts.
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Affiliation(s)
| | | | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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3
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Greub G, Pillonel T, Bavoil PM, Borel N, Campbell LA, Dean D, Hefty S, Horn M, Morré SA, Ouellette SP, Pannekoek Y, Puolakkainen M, Timms P, Valdivia R, Vanrompay D. Use of gene sequences as type for naming prokaryotes: Recommendations of the international committee on the taxonomy of chlamydiae. New Microbes New Infect 2023; 54:101158. [PMID: 37416863 PMCID: PMC10320375 DOI: 10.1016/j.nmni.2023.101158] [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: 10/06/2021] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
The International Committee on Systematics of Prokaryotes (ICSP) discussed and rejected in 2020 a proposal to modify the International Code of Nomenclature of Prokaryotes to allow the use of gene sequences as type for naming prokaryotes. An alternative nomenclatural code, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), which considers genome sequences as type material for naming species, was published in 2022. Members of the ICSP subcommittee for the taxonomy of the phylum Chlamydiae (Chlamydiota) consider that the use of gene sequences as type would benefit the taxonomy of microorganisms that are difficult to culture such as the chlamydiae and other strictly intracellular bacteria. We recommend the registration of new names of uncultured prokaryotes in the SeqCode registry.
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Affiliation(s)
- Gilbert Greub
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011, Lausanne, Switzerland
| | - Trestan Pillonel
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011, Lausanne, Switzerland
| | - Patrik M. Bavoil
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Nicole Borel
- Department of Pathobiology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, CH-8057, Zurich, Switzerland
| | - Lee Ann Campbell
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Deborah Dean
- Departments of Medicine and Pediatrics, University of California San Francisco School of Medicine, Oakland, CA, USA
| | - Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090, Vienna, Austria
| | - Servaas A. Morré
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
- Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research School GROW (School for Oncology & Developmental Biology), Faculty of Health, Medicine & Life Sciences, University of Maastricht, Maastricht, the Netherlands
- Dutch Chlamydia Trachomatis Reference Laboratory, Department of Medical Microbiology & Infection Control, VU University Medical Centre, Amsterdam, the Netherlands
| | - Scot P. Ouellette
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yvonne Pannekoek
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Mirja Puolakkainen
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Peter Timms
- Genecology Research Center, University of Sunshine Coast, Queensland, Australia
| | - Raphael Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27710, USA
| | - Daisy Vanrompay
- Department of Animal Science and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
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4
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Dharamshi JE, Köstlbacher S, Schön ME, Collingro A, Ettema TJG, Horn M. Gene gain facilitated endosymbiotic evolution of Chlamydiae. Nat Microbiol 2023; 8:40-54. [PMID: 36604515 PMCID: PMC9816063 DOI: 10.1038/s41564-022-01284-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 11/07/2022] [Indexed: 01/07/2023]
Abstract
Chlamydiae is a bacterial phylum composed of obligate animal and protist endosymbionts. However, other members of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum are primarily free living. How Chlamydiae transitioned to an endosymbiotic lifestyle is still largely unresolved. Here we reconstructed Planctomycetes-Verrucomicrobia-Chlamydiae species relationships and modelled superphylum genome evolution. Gene content reconstruction from 11,996 gene families suggests a motile and facultatively anaerobic last common Chlamydiae ancestor that had already gained characteristic endosymbiont genes. Counter to expectations for genome streamlining in strict endosymbionts, we detected substantial gene gain within Chlamydiae. We found that divergence in energy metabolism and aerobiosis observed in extant lineages emerged later during chlamydial evolution. In particular, metabolic and aerobic genes characteristic of the more metabolically versatile protist-infecting chlamydiae were gained, such as respiratory chain complexes. Our results show that metabolic complexity can increase during endosymbiont evolution, adding an additional perspective for understanding symbiont evolutionary trajectories across the tree of life.
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Affiliation(s)
- Jennah E Dharamshi
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stephan Köstlbacher
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Max E Schön
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Astrid Collingro
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| | - Matthias Horn
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria.
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5
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Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae. THE ISME JOURNAL 2022; 16:2725-2740. [PMID: 36042324 PMCID: PMC9666466 DOI: 10.1038/s41396-022-01305-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 07/24/2022] [Accepted: 08/02/2022] [Indexed: 12/15/2022]
Abstract
Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host interactions thus far remain unexplored. Here, we sequenced the microbiomes of three sponge species and found high, though variable, Chlamydiae relative abundances of up to 18.7% of bacteria. Using genome-resolved metagenomics 18 high-quality sponge-associated chlamydial genomes were reconstructed, covering four chlamydial families. Among these, Candidatus Sororchlamydiaceae shares a common ancestor with Chlamydiaceae animal pathogens, suggesting long-term co-evolution with animals. Based on gene content, sponge-associated chlamydiae resemble members from the same family more than sponge-associated chlamydiae of other families, and have greater metabolic versatility than known chlamydial animal pathogens. Sponge-associated chlamydiae are also enriched in genes for degrading diverse compounds found in sponges. Unexpectedly, we identified widespread genetic potential for secondary metabolite biosynthesis across Chlamydiae, which may represent an unexplored source of novel natural products. This finding suggests that Chlamydiae members may partake in defensive symbioses and that secondary metabolites play a wider role in mediating intracellular interactions. Furthermore, sponge-associated chlamydiae relatives were found in other marine invertebrates, pointing towards wider impacts of the Chlamydiae phylum on marine ecosystems.
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6
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Characterization of a Pseudokeronopsis Strain (Ciliophora, Urostylida) and Its Bacterial Endosymbiont “Candidatus Trichorickettsia” (Alphaproteobacteria, Rickettsiales). DIVERSITY 2022. [DOI: 10.3390/d14121032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Symbiotic associations between bacteria and ciliate protists are rather common. In particular, several cases were reported involving bacteria of the alphaproteobacterial lineage Rickettsiales, but the diversity, features, and interactions in these associations are still poorly understood. In this work, we characterized a novel ciliate protist strain originating from Brazil and its associated Rickettsiales endosymbiont by means of live and ultrastructural observations, as well as molecular phylogeny. Though with few morphological peculiarities, the ciliate was found to be phylogenetically affiliated with Pseudokeronopsis erythrina, a euryhaline species, which is consistent with its origin from a lagoon with significant spatial and seasonal salinity variations. The bacterial symbiont was assigned to “Candidatus Trichorickettsia mobilis subsp. hyperinfectiva”, being the first documented case of a Rickettsiales associated with urostylid ciliates. It resided in the host cytoplasm and bore flagella, similarly to many, but not all, conspecifics in other host species. These findings highlight the ability of “Candidatus Trichorickettsia” to infect multiple distinct host species and underline the importance of further studies on this system, in particular on flagella and their regulation, from a functional and also an evolutionary perspective, considering the phylogenetic proximity with the well-studied and non-flagellated Rickettsia.
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7
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Halter T, Köstlbacher S, Collingro A, Sixt BS, Tönshoff ER, Hendrickx F, Kostanjšek R, Horn M. Ecology and evolution of chlamydial symbionts of arthropods. ISME COMMUNICATIONS 2022; 2:45. [PMID: 37938728 PMCID: PMC9723776 DOI: 10.1038/s43705-022-00124-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 05/08/2023]
Abstract
The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae, which is predicted to be the largest and most diverse chlamydial family, with the few described members known to infect arthropod hosts. Using published 16 S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we used a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we added novel complete genome sequences of Rhabdochlamydia porcellionis infecting the woodlouse Porcellio scaber, and of 'Candidatus R. oedothoracis' associated with the linyphiid dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested distinct niches for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia, pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. This type of genome reduction has never been described before for any member of the phylum Chlamydiae. This study provides new insights into the molecular ecology, genomic diversity, and evolution of representatives of one of the most divergent chlamydial families.
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Affiliation(s)
- Tamara Halter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental 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
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Barbara S Sixt
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Elena R Tönshoff
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich (ETH), Zurich, Switzerland
| | | | - Rok Kostanjšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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8
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Dagleish MP, Flockhart AF, Baily JL, Hall AJ, Simpson TI, Longbottom D. Presence of DNA from Chlamydia-like organisms in the nasal cavities of grey seal pups (Halichoerus grypus) and three different substrates present in a breeding colony. BMC Vet Res 2021; 17:328. [PMID: 34645426 PMCID: PMC8515689 DOI: 10.1186/s12917-021-03032-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/27/2021] [Indexed: 12/03/2022] Open
Abstract
Background Chlamydia-like organisms (CLO) have been found to be present in many environmental niches, including human sewage and agricultural run-off, as well as in a number of aquatic species worldwide. Therefore, monitoring their presence in sentinel wildlife species may be useful in assessing the wider health of marine food webs in response to habitat loss, pollution and disease. We used nasal swabs from live (n = 42) and dead (n = 50) pre-weaned grey seal pups and samples of differing natal substrates (n = 8) from an off-shore island devoid of livestock and permanent human habitation to determine if CLO DNA is present in these mammals and to identify possible sources. Results We recovered CLO DNA from 32/92 (34.7%) nasal swabs from both live (n = 17) and dead (n = 15) seal pups that clustered most closely with currently recognised species belonging to three chlamydial families: Parachlamydiaceae (n = 22), Rhabdochlamydiaceae (n = 6), and Simkaniaceae (n = 3). All DNA positive sediment samples (n = 7) clustered with the Rhabdochlamydiaceae. No difference was found in rates of recovery of CLO DNA in live versus dead pups suggesting the organisms are commensal but their potential as opportunistic secondary pathogens could not be determined. Conclusion This is the first report of CLO DNA being found in marine mammals. This identification warrants further investigation in other seal populations around the coast of the UK and in other areas of the world to determine if this finding is unique or more common than shown by this data. Further investigation would also be warranted to determine if they are present as purely commensal organisms or whether they could also be opportunistic pathogens in seals, as well as to investigate possible sources of origin, including whether they originated as a result of anthropogenic impacts, including human waste and agricultural run-off.
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Affiliation(s)
- Mark P Dagleish
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK
| | - Allen F Flockhart
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK.,Present address: School of Applied Sciences, Edinburgh Napier University, Sighthill Campus, Edinburgh, UK
| | - Johanna L Baily
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK.,Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews, UK.,Present address: Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Ailsa J Hall
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews, UK
| | - T Ian Simpson
- Biomathematics and Statistics Scotland, JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, UK.,Present address: School of Informatics, University of Edinburgh, Crichton Street, Edinburgh, UK
| | - David Longbottom
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK.
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9
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Köstlbacher S, Collingro A, Halter T, Schulz F, Jungbluth SP, Horn M. Pangenomics reveals alternative environmental lifestyles among chlamydiae. Nat Commun 2021; 12:4021. [PMID: 34188040 PMCID: PMC8242063 DOI: 10.1038/s41467-021-24294-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the "Genomes from Earth's Microbiomes" initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.
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Affiliation(s)
- Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Tamara Halter
- 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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10
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Matzke NJ, Lin A, Stone M, Baker MAB. Flagellar export apparatus and ATP synthetase: Homology evidenced by synteny predating the Last Universal Common Ancestor. Bioessays 2021; 43:e2100004. [PMID: 33998015 DOI: 10.1002/bies.202100004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 11/07/2022]
Abstract
We report evidence further supporting homology between proteins in the F1 FO -ATP synthetase and the bacterial flagellar motor (BFM). BFM proteins FliH, FliI, and FliJ have been hypothesized to be homologous to FO -b + F1 -δ, F1 -α/β, and F1 -γ, with similar structure and interactions. We conduct a further test by constructing a gene order dataset, examining the order of fliH, fliI, and fliJ genes across the phylogenetic breadth of flagellar and nonflagellar type 3 secretion systems, and comparing this to published surveys of gene order in the F1 FO -ATP synthetase, its N-ATPase relatives, and the bacterial/archaeal V- and A-type ATPases. Strikingly, the fliHIJ gene order was deeply conserved, with the few exceptions appearing derived, and exactly matching the widely conserved F-ATPase gene order atpFHAG, coding for subunits b-δ-α-γ. The V/A-type ATPases have a similar conserved gene order. Our results confirm homology between these systems, and suggest a rare case of synteny conserved over billions of years, predating the Last Universal Common Ancestor (LUCA).
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Affiliation(s)
- Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Micaella Stone
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew A B Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, Australia
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11
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Abstract
This paper provides an overview of the current knowledge of chlamydiae. These intracellular microorganisms belonging to the Chlamydiaceae family are widely distributed throughout the world. Constant development of culture-independent approaches for characterisation of microbial genomes enables new discoveries in the field of Chlamydia. The number of new taxa is continuously increasing as well as the range of hosts. New species and genotypes are constantly being discovered, particularly new avian and reptilian agents, which are discussed in this article. Interestingly, wild animals are the main hosts for new Chlamydia species including different species of bird, turtle and snake. The availability of next-generation sequencing opens up a new prospect for research and leads to deeper knowledge of these interesting microorganisms about which much is still to discover.
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12
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Microbial Evolution: Chlamydial Creatures from the Deep. Curr Biol 2020; 30:R267-R269. [PMID: 32208150 DOI: 10.1016/j.cub.2020.01.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A metagenomic study of marine sediments from a hydrothermal vent field in the Arctic Mid-Ocean Ridge revealed wider diversity amongst members of the phylum Chlamydiae than was previously known. Unlike known chlamydiae, some of the newly described marine-sediment species may be potentially free-living.
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13
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Collingro A, Köstlbacher S, Horn M. Chlamydiae in the Environment. Trends Microbiol 2020; 28:877-888. [PMID: 32591108 DOI: 10.1016/j.tim.2020.05.020] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022]
Abstract
Chlamydiae have been known for more than a century as major pathogens of humans. Yet they are also found ubiquitously in the environment where they thrive within protists and in an unmatched wide range of animals. This review summarizes recent advances in understanding chlamydial diversity and distribution in nature. Studying these environmental chlamydiae provides a novel perspective on basic chlamydial biology and evolution. A picture is beginning to emerge with chlamydiae representing one of the evolutionarily most ancient and successful groups of obligate intracellular bacteria.
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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
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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14
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Huang Z, Petersen JM, Martijn J, Ettema TJG, Shao Z. A novel alphaproteobacterium with a small genome identified from the digestive gland of multiple species of abalone. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:387-395. [PMID: 32307920 DOI: 10.1111/1758-2229.12845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/01/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
We identified an alphaproteobacterium in the digestive gland of the abalone species Haliotis discus hannai. This phylotype dominated our 16S rRNA clone libraries from the digestive gland of H. discus hannai. Diversity surveys revealed that this phylotype was associated with H. discus hannai and also in another host species, H. gigantea. Whole genome phylogenies placed this bacterium as a new member affiliated with the family Rhodospirillaceae in Alphaproteobacteria. Gene annotation revealed a nearly complete glycolysis pathway but no TCA cycle, but the presence of anaerobic ribonucleoside-triphosphate reductase and oxygen-insensitive NAD(P)H-dependent nitroreductase, which show the genomic potential for anaerobic metabolism. A large cluster of genes encoding ankyrin repeat proteins (ANK) of eukaryotic-like repeat domains and a large gene set for the flagellar system were also detected. Alginate-binding periplasmic proteins and key genes responsible for alginate assimilation were found in the genome, which could potentially contribute to the breakdown of the host's alginate-rich macroalgal diet. These results raise the possibility that this novel alphaproteobacterium is a widespread member of the abalone microbiome that may use polysaccharides derived from its host's macroalgal diet.
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Affiliation(s)
- Zhaobin Huang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
| | - Jillian M Petersen
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Joran Martijn
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, the Netherlands
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
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Diversity of sediment associated Planctomycetes and its related phyla with special reference to anammox bacterial community in a high Arctic fjord. World J Microbiol Biotechnol 2020; 36:107. [PMID: 32638161 DOI: 10.1007/s11274-020-02886-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/02/2020] [Indexed: 10/23/2022]
Abstract
The fjords of west Spitsbergen Svalbard, Arctic Norway, are undergoing a transformation as the impact of nutrient rich warmer Atlantic water is significantly altering the primary production and subsequently the carbon pool. Members of the phylum Planctomycetes are ubiquitous in marine systems and are important in the mineralization of organic matter. Hence, the phylogenetic diversity and distribution pattern of Planctomycetes in the surface sediments of a high Arctic fjord, the Kongsfjorden were studied. Further, considering the release of ammonium as a part of mineralization, the diversity of bacterial community involved in anaerobic ammonium oxidation (anammox) was also evaluated. The highly diverse Planctomycetes community, which consisted mainly of uncultivated and uncharacterized Planctomycetes, was observed in the study area with a total of 162 OTUs. The major genera observed were Blastopirellula (13.3%), Gimesia (13%), Rhodopirellula (10%), Planctomicrobium (2%) and Thermogutta (1.6%). Functional prediction revealed the dominance of carbohydrate metabolism genes and the presence of gene clusters for production of secondary metabolites and xenobiotic degradation. Anammox bacterial sequences were detected from all the samples with a total of 52 OTUs. Most of the OTUs belonged to the genus Candidatus Scalindua and three distinct clusters were observed in the phylogenetic tree, (a) Ca. Scalindua brodae (49%), (b) Ca. Scalindua wagneri (31%) and (c) Ca. Scalindua marina (12%) based on their phylogenic distance. Our findings suggest the existence of highly diverse Planctomycetes and anammox bacterial community with regional variants in the sediments of Kongsfjorden.
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Dharamshi JE, Tamarit D, Eme L, Stairs CW, Martijn J, Homa F, Jørgensen SL, Spang A, Ettema TJG. Marine Sediments Illuminate Chlamydiae Diversity and Evolution. Curr Biol 2020; 30:1032-1048.e7. [PMID: 32142706 DOI: 10.1016/j.cub.2020.02.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/22/2019] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
Abstract
The bacterial phylum Chlamydiae is so far composed of obligate symbionts of eukaryotic hosts. Well known for Chlamydiaceae, pathogens of humans and other animals, Chlamydiae also include so-called environmental lineages that primarily infect microbial eukaryotes. Environmental surveys indicate that Chlamydiae are found in a wider range of environments than anticipated previously. However, the vast majority of this chlamydial diversity has been underexplored, biasing our current understanding of their biology, ecological importance, and evolution. Here, we report that previously undetected and active chlamydial lineages dominate microbial communities in deep anoxic marine sediments taken from the Arctic Mid-Ocean Ridge. Reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic units, these Chlamydiae represent important community members. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, expanding by over a third the known genomic diversity in this phylum. Phylogenomic analyses revealed several novel clades across the phylum, including a previously unknown sister lineage of the Chlamydiaceae, providing new insights into the origin of pathogenicity in this family. We were unable to identify putative eukaryotic hosts for these marine sediment chlamydiae, despite identifying genomic features that may be indicative of host-association. The high abundance and genomic diversity of Chlamydiae in these anoxic marine sediments indicate that some members could play an important, and thus far overlooked, ecological role in such environments and may indicate alternate lifestyle strategies.
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Affiliation(s)
- Jennah E Dharamshi
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Daniel Tamarit
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Orsay 91400, France
| | - Courtney W Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Joran Martijn
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Felix Homa
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Steffen L Jørgensen
- Department of Earth Science, Centre for Deep Sea Research, University of Bergen, Bergen 5020, Norway
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg 1790 AB, the Netherlands
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, the Netherlands.
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Taylor-Brown A, Pillonel T, Greub G, Vaughan L, Nowak B, Polkinghorne A. Metagenomic Analysis of Fish-Associated Ca. Parilichlamydiaceae Reveals Striking Metabolic Similarities to the Terrestrial Chlamydiaceae. Genome Biol Evol 2018; 10:2587-2595. [PMID: 30202970 PMCID: PMC6171736 DOI: 10.1093/gbe/evy195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chlamydiae are an example of obligate intracellular bacteria that possess highly reduced, compact genomes (1.0-3.5 Mbp), reflective of their abilities to sequester many essential nutrients from the host that they no longer need to synthesize themselves. The Chlamydiae is a phylum with a very wide host range spanning mammals, birds, fish, invertebrates, and unicellular protists. This ecological and phylogenetic diversity offers ongoing opportunities to study intracellular survival and metabolic pathways and adaptations. Of particular evolutionary significance are Chlamydiae from the recently proposed Ca. Parilichlamydiaceae, the earliest diverging clade in this phylum, species of which are found only in aquatic vertebrates. Gill extracts from three Chlamydiales-positive Australian aquaculture species (Yellowtail kingfish, Striped trumpeter, and Barramundi) were subject to DNA preparation to deplete host DNA and enrich microbial DNA, prior to metagenome sequencing. We assembled chlamydial genomes corresponding to three Ca. Parilichlamydiaceae species from gill metagenomes, and conducted functional genomics comparisons with diverse members of the phylum. This revealed highly reduced genomes more similar in size to the terrestrial Chlamydiaceae, standing in contrast to members of the Chlamydiae with a demonstrated cosmopolitan host range. We describe a reduction in genes encoding synthesis of nucleotides and amino acids, among other nutrients, and an enrichment of predicted transport proteins. Ca. Parilichlamydiaceae share 342 orthologs with other chlamydial families. We hypothesize that the genome reduction exhibited by Ca. Parilichlamydiaceae and Chlamydiaceae is an example of within-phylum convergent evolution. The factors driving these events remain to be elucidated.
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Affiliation(s)
- Alyce Taylor-Brown
- USC Animal Research Centre, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Trestan Pillonel
- Institute of Microbiology, University of Lausanne and University Hospital Center, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, Switzerland
| | - Lloyd Vaughan
- Institute of Veterinary Pathology, University of Zurich, Switzerland.,Pathovet AG, Tagelswangen, Switzerland
| | - Barbara Nowak
- Institute of Marine and Antarctic Studies, University of Tasmania, Newnham, Tasmania, Australia
| | - Adam Polkinghorne
- USC Animal Research Centre, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
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Jarett JK, Nayfach S, Podar M, Inskeep W, Ivanova NN, Munson-McGee J, Schulz F, Young M, Jay ZJ, Beam JP, Kyrpides NC, Malmstrom RR, Stepanauskas R, Woyke T. Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis. MICROBIOME 2018; 6:161. [PMID: 30223889 PMCID: PMC6142677 DOI: 10.1186/s40168-018-0539-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/26/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. While Nanoarchaeota diversity has been detected in a variety of habitats using 16S rRNA gene surveys, genome sequences have been available for only three Nanoarchaeota and their hosts. The host range and adaptation of Nanoarchaeota to a wide range of environmental conditions has thus largely remained elusive. Single-cell genomics is an ideal approach to address these questions as Nanoarchaeota can be isolated while still attached to putative hosts, enabling the exploration of cell-cell interactions and fine-scale genomic diversity. RESULTS From 22 single amplified genomes (SAGs) from three hot springs in Yellowstone National Park, we derived a genome-based phylogeny of the phylum Nanoarchaeota, linking it to global 16S rRNA gene diversity. By exploiting sequencing of co-sorted tightly attached cells, we associated Nanoarchaeota with 6 novel putative hosts, 2 of which were found in multiple SAGs, and showed that the same host species may associate with multiple species of Nanoarchaeota. Comparison of single nucleotide polymorphisms (SNPs) within a population of Nanoarchaeota SAGs indicated that Nanoarchaeota attached to a single host cell in situ are likely clonal. In addition to an overall pattern of purifying selection, we found significantly higher densities of non-synonymous SNPs in hypothetical cell surface proteins, as compared to other functional categories. Genes implicated in interactions in other obligate microbe-microbe symbioses, including those encoding a cytochrome bd-I ubiquinol oxidase and a FlaJ/TadC homologue possibly involved in type IV pili production, also had relatively high densities of non-synonymous SNPs. CONCLUSIONS This population genetics study of Nanoarchaeota greatly expands the known potential host range of the phylum and hints at what genes may be involved in adaptation to diverse environments or different hosts. We provide the first evidence that Nanoarchaeota cells attached to the same host cell are clonal and propose a hypothesis for how clonality may occur despite diverse symbiont populations.
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Affiliation(s)
| | | | - Mircea Podar
- Oak Ridge National Laboratory, Oak Ridge, TN USA
- Department of Microbiology, University of Tennessee, Knoxville, TN USA
| | - William Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT USA
| | | | - Jacob Munson-McGee
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT USA
| | | | - Mark Young
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT USA
| | - Zackary J. Jay
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT USA
| | - Jacob P. Beam
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME USA
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
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19
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St John E, Liu Y, Podar M, Stott MB, Meneghin J, Chen Z, Lagutin K, Mitchell K, Reysenbach AL. A new symbiotic nanoarchaeote (Candidatus Nanoclepta minutus) and its host (Zestosphaera tikiterensis gen. nov., sp. nov.) from a New Zealand hot spring. Syst Appl Microbiol 2018; 42:94-106. [PMID: 30195930 DOI: 10.1016/j.syapm.2018.08.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/08/2018] [Accepted: 08/08/2018] [Indexed: 01/22/2023]
Abstract
Three thermophilic Nanoarchaeota-Crenarchaeota symbiotic systems have been described. We obtained another stable anaerobic enrichment culture at 80°C, pH 6.0 from a New Zealand hot spring. The nanoarchaeote (Ncl-1) and its host (NZ3T) were isolated in co-culture and their genomes assembled. The small (∼200nm) flagellated cocci were often attached to larger cocci. Based on 16S rRNA gene similarity (88.4%) and average amino acid identity (52%), Ncl-1 is closely related to Candidatus Nanopusillus acidilobi. Their genomes both encode for archaeal flagella and partial glycolysis and gluconeogenesis pathways, but lack ATP synthase genes. Like Nanoarchaeum equitans, Ncl-1 has a CRISPR-Cas system. Ncl-1 also relies on its crenarchaeotal host for most of its biosynthetic needs. The host NZ3T was isolated and grows on proteinaceous substrates but not on sugars, alcohols, or fatty acids. NZ3T requires thiosulfate and grows best at 82°C, pH 6.0. NZ3T is most closely related to the Desulfurococcaceae, Ignisphaera aggregans (∼92% 16S rRNA gene sequence similarity, 45% AAI). Based on phylogenetic, physiological and genomic data, Ncl-1 and NZ3T represent novel genera in the Nanoarchaeota and the Desulfurococcaceae, respectively, with the proposed names Candidatus Nanoclepta minutus and Zestosphaera tikiterensis gen. nov., sp. nov., type strain NZ3T (=DSMZ 107634T=OCM 1213T).
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Affiliation(s)
- Emily St John
- Biology Department, Portland State University, Portland, OR 97201, USA
| | - Yitai Liu
- Biology Department, Portland State University, Portland, OR 97201, USA
| | - Mircea Podar
- Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jennifer Meneghin
- Biology Department, Portland State University, Portland, OR 97201, USA
| | - Zhiqiang Chen
- Center for Electron Microscopy and Nanofabrication, Portland State University, Portland, OR 97201, USA
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Pillonel T, Bertelli C, Greub G. Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle. Front Microbiol 2018. [PMID: 29515524 PMCID: PMC5826181 DOI: 10.3389/fmicb.2018.00079] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Chlamydiae phylum exclusively encompasses bacteria sharing a similar obligate intracellular life cycle. Existing 16S rDNA data support a high diversity within the phylum, however genomic data remain scarce owing to the difficulty in isolating strains using culture systems with eukaryotic cells. Yet, Chlamydiae genome data extracted from large scale metagenomic studies might help fill this gap. This work compares 33 cultured and 27 environmental, uncultured chlamydial genomes, in order to clarify the phylogenetic relatedness of the new chlamydial clades and to investigate the genetic diversity of the Chlamydiae phylum. The analysis of published chlamydial genomes from metagenomics bins and single cell sequencing allowed the identification of seven new deeply branching chlamydial clades sharing genetic hallmarks of parasitic Chlamydiae. Comparative genomics suggests important biological differences between those clades, including loss of many proteins involved in cell division in the genus Similichlamydia, and loss of respiratory chain and tricarboxylic acid cycle in several species. Comparative analyses of chlamydial genomes with two proteobacterial orders, the Rhizobiales and the Rickettsiales showed that genomes of different Rhizobiales families are much more similar than genomes of different Rickettsiales families. On the other hand, the chlamydial 16S rRNAs exhibit a higher sequence conservation than their Rickettsiales counterparts, while chlamydial proteins exhibit increased sequence divergence. Studying the diversity and genome plasticity of the entire Chlamydiae phylum is of major interest to better understand the emergence and evolution of this ubiquitous and ancient clade of obligate intracellular bacteria.
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Affiliation(s)
- Trestan Pillonel
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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21
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Abstract
The expanding field of bacterial genomics has revolutionized our understanding of microbial diversity, biology and phylogeny. For most species, DNA extracted from culture material is used as the template for genome sequencing; however, the majority of microbes are actually uncultivable, and others, such as obligate intracellular bacteria, require laborious tissue culture to yield sufficient genomic material for sequencing. Chlamydiae are one such group of obligate intracellular microbes whose characterization has been hampered by this requirement. To circumvent these challenges, researchers have developed culture-independent sample preparation methods that can be applied to the sample directly or to genomic material extracted from the sample. These methods, which encompass both targeted [immunomagnetic separation-multiple displacement amplification (IMS-MDA) and sequence capture] and non-targeted approaches (host methylated DNA depletion-microbial DNA enrichment and cell-sorting-MDA), have been applied to a range of clinical and environmental samples to generate whole genomes of novel chlamydial species and strains. This review aims to provide an overview of the application, advantages and limitations of these targeted and non-targeted approaches in the chlamydial context. The methods discussed also have broad application to other obligate intracellular bacteria or clinical and environmental samples.
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Affiliation(s)
- Alyce Taylor-Brown
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia
| | - Danielle Madden
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia
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22
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Bacterial Flagellins: Does Size Matter? Trends Microbiol 2017; 26:575-581. [PMID: 29258714 DOI: 10.1016/j.tim.2017.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/20/2017] [Accepted: 11/29/2017] [Indexed: 01/31/2023]
Abstract
The bacterial flagellum is the principal organelle of motility in bacteria. Here, we address the question of size when applied to the chief flagellar protein flagellin and the flagellar filament. Surprisingly, nature furnishes multiple examples of 'giant flagellins' greater than a thousand amino acids in length, with large surface-exposed hypervariable domains. We review the contexts in which these giant flagellins occur, speculate as to their functions, and highlight the potential for biotechnology to build on what nature provides.
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Rivas-Marín E, Devos DP. The Paradigms They Are a-Changin': past, present and future of PVC bacteria research. Antonie van Leeuwenhoek 2017; 111:785-799. [PMID: 29058138 PMCID: PMC5945725 DOI: 10.1007/s10482-017-0962-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/10/2017] [Indexed: 11/22/2022]
Abstract
These are exciting times for PVC researchers! The PVC superphylum is composed of the bacterial phyla Planctomycetes, Verrucomicrobia, Chlamydiae (those three founders giving it its name), Lentisphaerae and Kirimatiellaeota as well as some uncultured candidate phyla, such as the Candidatus Omnitrophica (previously known as OP3). Despite early debates, most of the disagreements that surround this group of bacteria have been recently resolved. In this article, we review the history of the study of PVC bacteria, with a particular focus on the misinterpretations that emerged early in the field and their resolution. We begin with a historical perspective that describes the relevant facts of PVC research from the early times when they were not yet termed PVC. Those were controversial times and we refer to them as the “discovery age” of the field. We continue by describing new discoveries due to novel techniques and data that combined with the reinterpretations of old ones have contributed to solve most of the discordances and we refer to these times as the “illumination age” of PVC research. We follow by arguing that we are just entering the “golden age” of PVC research and that the future of this growing community is looking bright. We finish by suggesting a few of the directions that PVC researches might take in the future.
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Affiliation(s)
- Elena Rivas-Marín
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, University Pablo de Olavide, Carretera Utrera, km 1, 41013, Seville, Spain
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, University Pablo de Olavide, Carretera Utrera, km 1, 41013, Seville, Spain.
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