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van de Merwe C, Simpson DJ, Qiao N, Otto SJG, Kovacevic J, Gänzle MG, McMullen LM. Is the persistence of Listeria monocytogenes in food processing facilities and its resistance to pathogen intervention linked to its phylogeny? Appl Environ Microbiol 2024; 90:e0086124. [PMID: 38809044 PMCID: PMC11218633 DOI: 10.1128/aem.00861-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/30/2024] Open
Abstract
The foodborne pathogen Listeria monocytogenes is differentiated into four distinct lineages which differ in their virulence. It remains unknown, however, whether the four lineages also differ with respect to their ability to persist in food processing facilities, their resistance to high pressure, a preservation method that is used commercially for Listeria control on ready-to-eat meats, and their ability to form biofilms. This study aimed to determine differences in the pressure resistance and biofilm formation of 59 isolates of L. monocytogenes representing lineages I and II. Furthermore, the genetic similarity of 9 isolates of L. monocytogenes that were obtained from a meat processing facility over a period of 1 year and of 20 isolates of L. monocytogenes from food processing facilities was analyzed to assess whether the ability of the lineages of L. monocytogenes to persist in these facilities differs. Analysis of 386 genomes with respect to the source of isolation revealed that genomes of lineage II are over-represented in meat isolates when compared with clinical isolates. Of the 38 strains of Lm. monocytogenes that persisted in food processing facilities (this study or published studies), 31 were assigned to lineage II. Isolates of lineage I were more resistant to treatments at 400 to 600 MPa. The thickness of biofilms did not differ between lineages. In conclusion, strains of lineage II are more likely to persist in food processing facilities while strains of lineage I are more resistant to high pressure.IMPORTANCEListeria monocytogenes substantially contributes to the mortality of foodborne disease in developed countries. The virulence of strains of four lineages of L. monocytogenes differs, indicating that risks associated with the presence of L. monocytogenes are lineage specific. Our study extends the current knowledge by documentation that the lineage-level phylogeny of L. monocytogenes plays a role in the source of isolation, in the persistence in food processing facilities, and in the resistance to pathogen intervention technologies. In short, the control of risks associated with the presence of L. monocytogenes in food is also lineage specific. Understanding the route of contamination L. monocytogenes is an important factor to consider when designing improved control measures.
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Affiliation(s)
- Chandré van de Merwe
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - David J. Simpson
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Nanzhen Qiao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Simon J. G. Otto
- Human-Environment-Animal Transdisciplinary Antimicrobial Resistance (HEAT-AMR) Research Group, University of Alberta School of Public Health, Edmonton, Alberta, Canada
| | - Jovana Kovacevic
- Food Innovation Center, Oregon State University, Portland, Oregon, USA
| | - Michael G. Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Lynn M. McMullen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
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2
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Sheinman M, Arndt PF, Massip F. Modeling the mosaic structure of bacterial genomes to infer their evolutionary history. Proc Natl Acad Sci U S A 2024; 121:e2313367121. [PMID: 38517978 PMCID: PMC10990148 DOI: 10.1073/pnas.2313367121] [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: 08/03/2023] [Accepted: 01/30/2024] [Indexed: 03/24/2024] Open
Abstract
The chronology and phylogeny of bacterial evolution are difficult to reconstruct due to a scarce fossil record. The analysis of bacterial genomes remains challenging because of large sequence divergence, the plasticity of bacterial genomes due to frequent gene loss, horizontal gene transfer, and differences in selective pressure from one locus to another. Therefore, taking advantage of the rich and rapidly accumulating genomic data requires accurate modeling of genome evolution. An important technical consideration is that loci with high effective mutation rates may diverge beyond the detection limit of the alignment algorithms used, biasing the genome-wide divergence estimates toward smaller divergences. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genome comparisons. We find that the length distribution of sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers, and by the aligner sensitivity. Based on these inputs, we build a model and show that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Our method allows to distinguish segments of vertical and horizontal origins and to estimate the time divergence and exchange rate between any pair of taxa from genome-wide alignments. Based on the estimated time divergences, we construct a time-calibrated phylogenetic tree to demonstrate the accuracy of the method.
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Affiliation(s)
- Michael Sheinman
- Institute for Advanced Studies, Sevastopol State University, Sevastopol299053, Crimea
| | - Peter F. Arndt
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin12163, Germany
| | - Florian Massip
- Department U900, Centre for Computational Biology, Mines Paris, PSL University, Paris75006, France
- Department U900, Institut Curie, Université Paris Sciences et Lettres, Paris75005, France
- INSERM, U900, Paris75005, France
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3
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Stanojković A, Skoupý S, Johannesson H, Dvořák P. The global speciation continuum of the cyanobacterium Microcoleus. Nat Commun 2024; 15:2122. [PMID: 38459017 PMCID: PMC10923798 DOI: 10.1038/s41467-024-46459-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/27/2024] [Indexed: 03/10/2024] Open
Abstract
Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium Microcoleus. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that Microcoleus represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.
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Affiliation(s)
- Aleksandar Stanojković
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic
| | - Svatopluk Skoupý
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic
| | - Hanna Johannesson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Petr Dvořák
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic.
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4
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Hoetzinger M, Hahn MW, Andersson LY, Buckley N, Ramsin C, Buck M, Nuy JK, Garcia SL, Puente-Sánchez F, Bertilsson S. Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria. THE ISME JOURNAL 2024; 18:wrae113. [PMID: 38959851 PMCID: PMC11283720 DOI: 10.1093/ismejo/wrae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 06/09/2024] [Indexed: 07/05/2024]
Abstract
Implications of geographic separation and temporal dynamics on the evolution of free-living bacterial species are widely unclear. However, the vast amount of metagenome sequencing data generated during the last decades from various habitats around the world provides an unprecedented opportunity for such investigations. Here, we exploited publicly available and new freshwater metagenomes in combination with the genomes of abundant freshwater bacteria to reveal geographic and temporal population structure. We focused on species that were detected across broad geographic ranges at high enough sequence coverage for meaningful population genomic analyses, associated with the predominant freshwater taxa acI, LD12, Polynucleobacter, and Candidatus Methylopumilus. Despite the broad geographic ranges, each species appeared as a sequence-discrete cluster, in contrast to abundant marine taxa, for which continuous diversity structures were reported on a global scale. Population differentiation increased significantly with spatial distance in all species, but notable dispersal barriers (e.g. oceanic) were not apparent. Yet, the different species showed contrasting rates of geographic divergence and strikingly different intra-population dynamics in time series within individual habitats. The change in an LD12 population over 7 years was minor (FST = 0.04) compared to differentiation between lakes, whereas a Polynucleobacter population displayed strong changes within merely 2 months (FST up to 0.54), similar in scale to differentiation between populations separated by thousands of kilometers. The slowly and steadily evolving LD12 population showed high strain diversity, whereas the dynamic Polynucleobacter population exhibited alternating clonal expansions of mostly two strains only. Based on the contrasting population structures, we propose distinct models of speciation.
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Affiliation(s)
- Matthias Hoetzinger
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, 5310 Mondsee, Austria
| | - Linnéa Y Andersson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Nathaniel Buckley
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Chelsea Ramsin
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Julia K Nuy
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 104 05 Stockholm, Sweden
- Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Germany
| | - Sarahi L Garcia
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 104 05 Stockholm, Sweden
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg, Germany
| | - Fernando Puente-Sánchez
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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5
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Zein-Eddine R, Hak F, Le Meur A, Genestet C, Dumitrescu O, Guyeux C, Senelle G, Sola C, Refrégier G. The paradoxes of Mycobacterium tuberculosis molecular evolution and consequences for the inference of tuberculosis emergence date. Tuberculosis (Edinb) 2023; 143S:102378. [PMID: 38012921 DOI: 10.1016/j.tube.2023.102378] [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: 01/25/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 11/29/2023]
Abstract
The date of Mycobacterium tuberculosis complex emergence has been the subject of long debates. New studies joining archaeological efforts with sequencing methods raise high hopes for solving whether this emergence is closer to 70,000 or to 6000 years before present. Inferring the date of emergence of this pathogen based on sequence data requires a molecular clock. Several clocks inferred from different types of loci and/or different samples, using both sound reasoning and reliable data, are actually very different, which we refer to as the paradoxes of M. tuberculosis molecular evolution. After having presented these paradoxes, we will remind the limits of the molecular clocks used in the different studies such as the assumption of homogeneous substitution rate. We will then review recent results that shed new light on the characteristics of M. tuberculosis molecular evolution: traces of diverse selection pressures, the impact of host dynamics, etc. We provide some ideas on what to do next to get nearer to a reliable dating of Mycobacterium tuberculosis complex emergence. Among them, the collection of additional remains from ancient tuberculosis seems still essential.
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Affiliation(s)
- R Zein-Eddine
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Institut National de la Santé et de la Recherche Médicale: U1182, Centre National de la Recherche Scientifique: UMR7645, France
| | - F Hak
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France
| | - A Le Meur
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France
| | - C Genestet
- CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - O Dumitrescu
- CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - C Guyeux
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000, Besançon, France
| | - G Senelle
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000, Besançon, France
| | - C Sola
- Université de Paris, IAME, UMR1137, INSERM, Paris, France; AP-HP, GHU Nord, Service de mycobactériologie spécialisée et de référence, Paris, France; Université Paris-Saclay, Saint-Aubin, France
| | - G Refrégier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France.
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6
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Moeller AH, Sanders JG, Sprockett DD, Landers A. Assessing co-diversification in host-associated microbiomes. J Evol Biol 2023; 36:1659-1668. [PMID: 37750599 PMCID: PMC10843161 DOI: 10.1111/jeb.14221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 08/08/2023] [Accepted: 08/29/2023] [Indexed: 09/27/2023]
Abstract
When lineages of hosts and microbial symbionts engage in intimate interactions over evolutionary timescales, they can diversify in parallel (i.e., co-diversify), producing associations between the lineages' phylogenetic histories. Tests for co-diversification of individual microbial lineages and their hosts have been developed previously, and these have been applied to discover ancient symbioses in diverse branches of the tree of life. However, most host-microbe relationships are not binary but multipartite, in that a single host-associated microbiota can contain many microbial lineages, generating challenges for assessing co-diversification. Here, we review recent evidence for co-diversification in complex microbiota, highlight the limitations of prior studies, and outline a hypothesis testing approach designed to overcome some of these limitations. We advocate for the use of microbiota-wide scans for co-diversifying symbiont lineages and discuss tools developed for this purpose. Tests for co-diversification for simple host symbiont systems can be extended to entire phylogenies of microbial lineages (e.g., metagenome-assembled or isolate genomes, amplicon sequence variants) sampled from host clades, thereby providing a means for identifying co-diversifying symbionts present within complex microbiota. The relative ages of symbiont clades can corroborate co-diversification, and multi-level permutation tests can account for multiple comparisons and phylogenetic non-independence introduced by repeated sampling of host species. Discovering co-diversifying lineages will generate powerful opportunities for interrogating the molecular evolution and lineage turnover of ancestral, host-species specific symbionts within host-associated microbiota.
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Affiliation(s)
- Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Daniel D. Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Abigail Landers
- Department of Microbiology, Cornell University, Ithaca, NY 14850, USA
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7
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Tytgat B, Verleyen E, Sweetlove M, Van den Berge K, Pinseel E, Hodgson DA, Chown SL, Sabbe K, Wilmotte A, Willems A, Vyverman W. Polar lake microbiomes have distinct evolutionary histories. SCIENCE ADVANCES 2023; 9:eade7130. [PMID: 37976353 PMCID: PMC10656066 DOI: 10.1126/sciadv.ade7130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/19/2023] [Indexed: 11/19/2023]
Abstract
Toward the poles, life on land is increasingly dominated by microorganisms, yet the evolutionary origin of polar microbiomes remains poorly understood. Here, we use metabarcoding of Arctic, sub-Antarctic, and Antarctic lacustrine benthic microbial communities to test the hypothesis that high-latitude microbiomes are recruited from a globally dispersing species pool through environmental selection. We demonstrate that taxonomic overlap between the regions is limited within most phyla, even at higher-order taxonomic levels, with unique deep-branching phylogenetic clades being present in each region. We show that local and regional taxon richness and net diversification rate of regionally restricted taxa differ substantially between polar regions in both microeukaryotic and bacterial biota. This suggests that long-term evolutionary divergence resulting from low interhemispheric dispersal and diversification in isolation has been a prominent process shaping present-day polar lake microbiomes. Our findings illuminate the distinctive biogeography of polar lake ecosystems and underscore that conservation efforts should include their unique microbiota.
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Affiliation(s)
- Bjorn Tytgat
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
| | - Maxime Sweetlove
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
| | - Koen Van den Berge
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
| | - Eveline Pinseel
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Dominic A. Hodgson
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
- Department of Geography, Durham University, Durham, UK
| | - Steven L. Chown
- Securing Antarctica’s Environmental Future, School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
| | - Annick Wilmotte
- InBio-Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Ghent University, Gent, Belgium
| | | | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
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8
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Jurdzinski KT, Mehrshad M, Delgado LF, Deng Z, Bertilsson S, Andersson AF. Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity. SCIENCE ADVANCES 2023; 9:eadg2059. [PMID: 37235649 PMCID: PMC10219603 DOI: 10.1126/sciadv.adg2059] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. In contrast, distinct brackish basins cohosted numerous species, but their intraspecific population structures displayed clear signs of geographic separation. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed toward the brackish biome. Transitions were accompanied by systematic changes in amino acid composition and isoelectric point distributions of inferred proteomes, which evolved over millions of years, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content constrains the cross-biome transitions, resulting in species-level separation between aquatic biomes.
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Affiliation(s)
- Krzysztof T. Jurdzinski
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Luis Fernando Delgado
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Ziling Deng
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders F. Andersson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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9
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Li F, Li X, Cheng CC, Bujdoš D, Tollenaar S, Simpson DJ, Tasseva G, Perez-Muñoz ME, Frese S, Gänzle MG, Walter J, Zheng J. A phylogenomic analysis of Limosilactobacillus reuteri reveals ancient and stable evolutionary relationships with rodents and birds and zoonotic transmission to humans. BMC Biol 2023; 21:53. [PMID: 36907868 PMCID: PMC10010030 DOI: 10.1186/s12915-023-01541-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 02/09/2023] [Indexed: 03/14/2023] Open
Abstract
BACKGROUND Gut microbes play crucial roles in the development and health of their animal hosts. However, the evolutionary relationships of gut microbes with vertebrate hosts, and the consequences that arise for the ecology and lifestyle of the microbes are still insufficiently understood. Specifically, the mechanisms by which strain-level diversity evolved, the degree by which lineages remain stably associated with hosts, and how their evolutionary history influences their ecological performance remain a critical gap in our understanding of vertebrate-microbe symbiosis. RESULTS This study presents the characterization of an extended collection of strains of Limosilactobacillus reuteri and closely related species from a wide variety of hosts by phylogenomic and comparative genomic analyses combined with colonization experiments in mice to gain insight into the long-term evolutionary relationship of a bacterial symbiont with vertebrates. The phylogenetic analysis of L. reuteri revealed early-branching lineages that primarily consist of isolates from rodents (four lineages) and birds (one lineage), while lineages dominated by strains from herbivores, humans, pigs, and primates arose more recently and were less host specific. Strains from rodent lineages, despite their phylogenetic divergence, showed tight clustering in gene-content-based analyses. These L. reuteri strains but not those ones from non-rodent lineages efficiently colonize the forestomach epithelium of germ-free mice. The findings support a long-term evolutionary relationships of L. reuteri lineages with rodents and a stable host switch to birds. Associations of L. reuteri with other host species are likely more dynamic and transient. Interestingly, human isolates of L. reuteri cluster phylogenetically closely with strains from domesticated animals, such as chickens and herbivores, suggesting zoonotic transmissions. CONCLUSIONS Overall, this study demonstrates that the evolutionary relationship of a vertebrate gut symbiont can be stable in particular hosts over time scales that allow major adaptations and specialization, but also emphasizes the diversity of symbiont lifestyles even within a single bacterial species. For L. reuteri, symbiont lifestyles ranged from autochthonous, likely based on vertical transmission and stably aligned to rodents and birds over evolutionary time, to allochthonous possibly reliant on zoonotic transmission in humans. Such information contributes to our ability to use these microbes in microbial-based therapeutics.
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Affiliation(s)
- Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Xudong Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Christopher C Cheng
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Dalimil Bujdoš
- School of Microbiology, and Department of Medicine, APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Stephanie Tollenaar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - David J Simpson
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Guergana Tasseva
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Maria Elisa Perez-Muñoz
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Steven Frese
- Department of Nutrition, University of Nevada, Reno, NV, 89557, USA
| | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2E1, Canada. .,Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E1, Canada. .,School of Microbiology, and Department of Medicine, APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China.
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10
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Garavaglia M, Muzlera A, Valverde C. Comparative genomics and informational content analysis uncovered internal regions of the core genes rpoD, pepN and gltX for an MLSA with genome-level resolving power within the genus Pseudomonas. Mol Phylogenet Evol 2023; 179:107663. [PMID: 36372354 DOI: 10.1016/j.ympev.2022.107663] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 08/31/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
In the field of prokaryotic taxonomy, there has been a recent transition towards phylogenomics as the gold standard approach. However, genome-based phylogenetics is still restrictive for its cost when managing large amounts of isolates. Fast, cheap, and taxonomically competent alternatives, like multilocus sequence analysis (MLSA) are thus recommendable. Nevertheless, the criteria for selecting the conserved genes for MLSA have not been explicit for different bacterial taxa, including the broadly diverse Pseudomonas genus. Here, we have carried out an unbiased and rational workflow to select internal sequence regions of Pseudomonas core genes (CG) for a MLSA with the best phylogenetic power, and with a resolution comparable to the genome-based ANI approach. A computational workflow was established to inspect 126 complete genomes of representatives from over 60 Pseudomonas species and subspecies, in order to identify the most informative CG internal regions and determine which combinations in sets of three partial CG sequences have comparable phylogenetic resolution to that of the current ANI standard. We found that the rpoD346-1196-pepN1711-2571-gltX86-909 concatenated sequences were the best performing in terms of phylogenetic robustness and resulted highly sensitive and specific when contrasted with ANI. The rpoD-pepN-gltX MLSA was validated in silico and in vitro. Altogether, the results presented here supports the proposal of the rpoD-pepN-gltX MLSA as a fast, affordable, and robust phylogenetic tool for members of the Pseudomonas genus.
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Affiliation(s)
- Matías Garavaglia
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Andrés Muzlera
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina.
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11
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Convergent Community Assembly among Globally Separated Acidic Cave Biofilms. Appl Environ Microbiol 2023; 89:e0157522. [PMID: 36602326 PMCID: PMC9888236 DOI: 10.1128/aem.01575-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Acidophilic bacteria and archaea inhabit extreme geochemical "islands" that can tell us when and how geographic barriers affect the biogeography of microorganisms. Here, we describe microbial communities from extremely acidic (pH 0 to 1) biofilms, known as snottites, from hydrogen sulfide-rich caves. Given the extreme acidity and subsurface location of these biofilms, and in light of earlier work showing strong geographic patterns among snottite Acidithiobacillus populations, we investigated their structure and diversity in order to understand how geography might impact community assembly. We used 16S rRNA gene cloning and fluorescence in situ hybridization (FISH) to investigate 26 snottite samples from four sulfidic caves in Italy and Mexico. All samples had very low biodiversity and were dominated by sulfur-oxidizing bacteria in the genus Acidithiobacillus. Ferroplasma and other archaea in the Thermoplasmatales ranged from 0 to 50% of total cells, and relatives of the bacterial genera Acidimicrobium and Ferrimicrobium were up to 15% of total cells. Rare phylotypes included Sulfobacillus spp. and members of the phyla "Candidatus Dependentiae" and "Candidatus Saccharibacteria" (formerly TM6 and TM7). Although the same genera of acidophiles occurred in snottites on separate continents, most members of those genera represent substantially divergent populations, with 16S rRNA genes that are only 95 to 98% similar. Our findings are consistent with a model of community assembly where sulfidic caves are stochastically colonized by microorganisms from local sources, which are strongly filtered through environmental selection for extreme acid tolerance, and these different colonization histories are maintained by dispersal restrictions within and among caves. IMPORTANCE Microorganisms that are adapted to extremely acidic conditions, known as extreme acidophiles, are catalysts for rock weathering, metal cycling, and mineral formation in naturally acidic environments. They are also important drivers of large-scale industrial processes such as biomining and contaminant remediation. Understanding the factors that govern their ecology and distribution can help us better predict and utilize their activities in natural and engineered systems. However, extremely acidic habitats are unusual in that they are almost always isolated within circumneutral landscapes. So where did their acid-adapted inhabitants come from, and how do new colonists arrive and become established? In this study, we took advantage of a unique natural experiment in Earth's subsurface to show how isolation may have played a role in the colonization history, community assembly, and diversity of highly acidic microbial biofilms.
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12
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Konno N, Iwasaki W. Machine learning enables prediction of metabolic system evolution in bacteria. SCIENCE ADVANCES 2023; 9:eadc9130. [PMID: 36630500 PMCID: PMC9833677 DOI: 10.1126/sciadv.adc9130] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Evolution prediction is a long-standing goal in evolutionary biology, with potential impacts on strategic pathogen control, genome engineering, and synthetic biology. While laboratory evolution studies have shown the predictability of short-term and sequence-level evolution, that of long-term and system-level evolution has not been systematically examined. Here, we show that the gene content evolution of metabolic systems is generally predictable by applying ancestral gene content reconstruction and machine learning techniques to ~3000 bacterial genomes. Our framework, Evodictor, successfully predicted gene gain and loss evolution at the branches of the reference phylogenetic tree, suggesting that evolutionary pressures and constraints on metabolic systems are universally shared. Investigation of pathway architectures and meta-analysis of metagenomic datasets confirmed that these evolutionary patterns have physiological and ecological bases as functional dependencies among metabolic reactions and bacterial habitat changes. Last, pan-genomic analysis of intraspecies gene content variations proved that even "ongoing" evolution in extant bacterial species is predictable in our framework.
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Affiliation(s)
- Naoki Konno
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Corresponding author. (N.K.); (W.I.)
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Corresponding author. (N.K.); (W.I.)
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13
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Beltrán OG, Torres Higuera LD, Rodríguez Bautista JL, Patiño Burbano RE. Evaluation of the genetic stability of Leptospira reference strains maintained under two conservation methods. NOVA 2022. [DOI: 10.22490/24629448.6585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Objective. The genetic stability of Strains of Leptospira spp., maintained under two conservation systems, was evaluated. Methodology. The degree of conservation of the 16S rRNA and ompL1 genes of 10 reference serovars from the Leptospira spp. collection, belonging to the Sistema de Bancos de Germoplasma de la Nación para la Alimentación y la Agricultura (SBGNAA), was determined. Results. It was corroborated that the genes evaluated these have not undergone considerable changes, since similarities greater than 99.69 % were evidenced for 16S rRNA and 99.02% for ompL1, in the paired alignments. Conclusion. The genetic stability and purity of the reference strains of Leptospira spp. were verified. spp., kept in cryopreservation in liquid nitrogen at -196 °C and at room temperature for approximately eight years.
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14
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Manthey JD, Girón JC, Hruska JP. Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genus Camponotus) and their Blochmannia endosymbionts. Ecol Evol 2022; 12:e9026. [PMID: 35795355 PMCID: PMC9251289 DOI: 10.1002/ece3.9026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/28/2022] Open
Abstract
Obligate endosymbioses are tight associations between symbionts and the hosts they live inside. Hosts and their associated obligate endosymbionts generally exhibit codiversification, which has been documented in taxonomically diverse insect lineages. Host demography (e.g., effective population sizes) may impact the demography of endosymbionts, which may lead to an association between host demography and the patterns and processes of endosymbiont molecular evolution. Here, we used whole-genome sequencing data for carpenter ants (Genus Camponotus; subgenera Camponotus and Tanaemyrmex) and their Blochmannia endosymbionts as our study system to address whether Camponotus demography shapes Blochmannia molecular evolution. Using whole-genome phylogenomics, we confirmed previous work identifying codiversification between carpenter ants and their Blochmannia endosymbionts. We found that Blochmannia genes have evolved at a pace ~30× faster than that of their hosts' molecular evolution and that these rates are positively associated with host rates of molecular evolution. Using multiple tests for selection in Blochmannia genes, we found signatures of positive selection and shifts in selection strength across the phylogeny. Host demography was associated with Blochmannia shifts toward increased selection strengths, but not associated with Blochmannia selection relaxation, positive selection, genetic drift rates, or genome size evolution. Mixed support for relationships between host effective population sizes and Blochmannia molecular evolution suggests weak or uncoupled relationships between host demography and Blochmannia population genomic processes. Finally, we found that Blochmannia genome size evolution was associated with genome-wide estimates of genetic drift and number of genes with relaxed selection pressures.
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Affiliation(s)
- Joseph D. Manthey
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
| | - Jennifer C. Girón
- Department of EntomologyPurdue UniversityWest LafayetteIndianaUSA
- Natural Science Research LaboratoryMuseum of Texas Tech UniversityLubbockTexasUSA
| | - Jack P. Hruska
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
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15
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Bendová B, Mikula O, Bímová BV, Čížková D, Daniszová K, Ďureje Ľ, Hiadlovská Z, Macholán M, Martin JF, Piálek J, Schmiedová L, Kreisinger J. Divergent gut microbiota in two closely related house mouse subspecies under common garden conditions. FEMS Microbiol Ecol 2022; 98:6620832. [PMID: 35767862 DOI: 10.1093/femsec/fiac078] [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: 12/03/2021] [Revised: 06/02/2022] [Accepted: 06/27/2022] [Indexed: 11/14/2022] Open
Abstract
The gastrointestinal microbiota (GM) is considered an important component of the vertebrate holobiont. GM-host interactions influence the fitness of holobionts and are therefore an integral part of evolution. The house mouse is a prominent model for GM-host interactions, and evidence suggests a role for GM in mouse speciation. However, previous studies based on short 16S rRNA GM profiles of wild house mouse subspecies failed to detect GM divergence, which is a prerequisite for the inclusion of GM in Dobzhansky-Muller incompatibilities. Here, we used standard 16S rRNA GM profiling in two mouse subspecies, Mus musculus musculus and M. m. domesticus, including the intestinal mucosa and content of three gut sections (ileum, caecum, and colon). We reduced environmental variability by sampling GM in the offspring of wild mice bred under semi-natural conditions. Although the breeding conditions allowed a contact between the subspecies, we found a clear differentiation of GM between them, in all three gut sections. Differentiation was mainly driven by several Helicobacters and two H. ganmani variants showed a signal of co-divergence with their hosts. Helicobacters represent promising candidates for studying GM-host co-adaptations and the fitness effects of their interactions.
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Affiliation(s)
- Barbora Bendová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ondřej Mikula
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | | | - Dagmar Čížková
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Kristina Daniszová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Ľudovít Ďureje
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Zuzana Hiadlovská
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Miloš Macholán
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | | | - Jaroslav Piálek
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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16
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Buresova‐Faitova A, Kopecky J, Sagova‐Mareckova M, Alonso L, Vautrin F, Moënne‐Loccoz Y, Rodriguez‐Nava V. Comparison of
Actinobacteria
communities from human‐impacted and pristine karst caves. Microbiologyopen 2022; 11:e1276. [PMID: 35478281 PMCID: PMC8988830 DOI: 10.1002/mbo3.1276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 11/07/2022] Open
Abstract
Actinobacteria are important cave inhabitants, but knowledge of how anthropization and anthropization‐related visual marks affect this community on cave walls is lacking. We compared Actinobacteria communities among four French limestone caves (Mouflon, Reille, Rouffignac, and Lascaux) ranging from pristine to anthropized, and within Lascaux Cave between marked (wall visual marks) and unmarked areas in different rooms (Sas‐1, Passage, Apse, and Diaclase). In addition to the 16S rRNA gene marker, 441 bp fragments of the hsp65 gene were used and an hsp65‐related taxonomic database was constructed for the identification of Actinobacteria to the species level by Illumina‐MiSeq analysis. The hsp65 marker revealed higher resolution for species and higher richness (99% operational taxonomic units cutoff) versus the 16S rRNA gene; however, more taxa were identified at higher taxonomic ranks. Actinobacteria communities varied between Mouflon and Reille caves (both pristine), and Rouffignac and Lascaux (both anthropized). Rouffignac displayed high diversity of Nocardia, suggesting human inputs, and Lascaux exhibited high Mycobacterium relative abundance, whereas Gaiellales were typical in pristine caves and the Diaclase (least affected area of Lascaux Cave). Within Lascaux, Pseudonocardiaceae dominated on unmarked walls and Streptomycetaceae (especially Streptomyces mirabilis) on marked walls, indicating a possible role in mark formation. A new taxonomic database was developed. Although not all Actinobacteria species were represented, the use of the hsp65 marker enabled species‐level variations of the Actinobacteria community to be documented based on the extent of anthropogenic pressure. This approach proved effective when comparing different limestone caves or specific conditions within one cave.
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Affiliation(s)
- Andrea Buresova‐Faitova
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
- Department of Ecology, Faculty of ScienceCharles University in PraguePrague 2PragueCzech Republic
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Jan Kopecky
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Marketa Sagova‐Mareckova
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Lise Alonso
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Florian Vautrin
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Yvan Moënne‐Loccoz
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Veronica Rodriguez‐Nava
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
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17
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Hugoson E, Guliaev A, Ammunét T, Guy L. Host-adaptation in Legionellales is 1.9 Ga, coincident with eukaryogenesis. Mol Biol Evol 2022; 39:6527638. [PMID: 35167692 PMCID: PMC8896642 DOI: 10.1093/molbev/msac037] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacteria adapting to living in a host cell caused the most salient events in the evolution of eukaryotes, namely the seminal fusion with an archaeon, and the emergence of both mitochondrion and chloroplast. A bacterial clade that may hold the key to understanding these events is the deep-branching gammaproteobacterial order Legionellales-containing among others Coxiella and Legionella-of which all known members grow inside eukaryotic cells. Here, by analyzing 35 novel Legionellales genomes mainly acquired through metagenomics, we show that this group is much more diverse than previously thought, and that key host-adaptation events took place very early in its evolution. Crucial virulence factors like the Type IVB secretion (Dot/Icm) system and two shared effector proteins were gained in the last Legionellales common ancestor (LLCA). Many metabolic gene families were lost in LLCA and its immediate descendants, including functions directly and indirectly related to molybdenum metabolism. On the other hand, genome sizes increased in the ancestors of the Legionella genus. We estimate that LLCA lived circa 1.89 Ga ago, probably predating the last eukaryotic common ancestor (LECA) by circa 0.4-1.0 Ga. These elements strongly indicate that host-adaptation arose only once in Legionellales, and that these bacteria were using advanced molecular machinery to exploit and manipulate host cells early in eukaryogenesis.
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Affiliation(s)
- Eric Hugoson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratories, Uppsala University, Box 582, 75123, Uppsala, Sweden.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, D-24306, Germany
| | - Andrei Guliaev
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratories, Uppsala University, Box 582, 75123, Uppsala, Sweden
| | - Tea Ammunét
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratories, Uppsala University, Box 582, 75123, Uppsala, Sweden
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratories, Uppsala University, Box 582, 75123, Uppsala, Sweden
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18
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Chou L, Lin YC, Haryono M, Santos MNM, Cho ST, Weisberg AJ, Wu CF, Chang JH, Lai EM, Kuo CH. Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biol 2022; 20:16. [PMID: 35022048 PMCID: PMC8756689 DOI: 10.1186/s12915-021-01221-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Many named species as defined in current bacterial taxonomy correspond to species complexes. Uncertainties regarding the organization of their genetic diversity challenge research efforts. We utilized the Agrobacterium tumefaciens species complex (a.k.a. Agrobacterium biovar 1), a taxon known for its phytopathogenicity and applications in transformation, as a study system and devised strategies for investigating genome diversity and evolution of species complexes. RESULTS We utilized 35 genome assemblies, including 14 newly generated ones, to achieve a phylogenetically balanced sampling of A. tumefaciens. Our genomic analysis suggested that the 10 genomospecies described previously are distinct biological species and supported a quantitative guideline for species delineation. Furthermore, our inference of gene content and core-genome phylogeny allowed for investigations of genes critical in fitness and ecology. For the type VI secretion system (T6SS) involved in interbacterial competition and thought to be conserved, we detected multiple losses and one horizontal gene transfer. For the tumor-inducing plasmids (pTi) and pTi-encoded type IV secretion system (T4SS) that are essential for agrobacterial phytopathogenicity, we uncovered novel diversity and hypothesized their involvement in shaping this species complex. Intriguingly, for both T6SS and T4SS, genes encoding structural components are highly conserved, whereas extensive diversity exists for genes encoding effectors and other proteins. CONCLUSIONS We demonstrate that the combination of a phylogeny-guided sampling scheme and an emphasis on high-quality assemblies provides a cost-effective approach for robust analysis in evolutionary genomics. We show that the T6SS VgrG proteins involved in specific effector binding and delivery can be classified into distinct types based on domain organization. The co-occurrence patterns of VgrG-associated domains and the neighboring genes that encode different chaperones/effectors can be used to infer possible interacting partners. Similarly, the associations between plant host preference and the pTi type among these strains can be used to infer phenotype-genotype correspondence. Our strategies for multi-level investigations at scales that range from whole genomes to intragenic domains and phylogenetic depths from between- to within-species are applicable to other bacteria. Furthermore, modularity observed in the molecular evolution of genes and domains is useful for inferring functional constraints and informing experimental works.
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Affiliation(s)
- Lin Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chen Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mindia Haryono
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mary Nia M Santos
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Chih-Feng Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.,Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan. .,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan. .,Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
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19
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Louca S. The rates of global bacterial and archaeal dispersal. THE ISME JOURNAL 2022; 16:159-167. [PMID: 34282284 PMCID: PMC8692594 DOI: 10.1038/s41396-021-01069-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/28/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
The phylogenetic resolution at which microorganisms display geographic endemism, the rates at which they disperse at global scales, and the role of humans on global microbial dispersal are largely unknown. Answering these questions is necessary for interpreting microbial biogeography, ecology, and macroevolution and for predicting the spread of emerging pathogenic strains. To resolve these questions, I analyzed the geographic and evolutionary relationships between 36,795 bacterial and archaeal ("prokaryotic") genomes from ∼7000 locations around the world. I find clear signs of continental-scale endemism, including strong correlations between phylogenetic divergence and geographic distance. However, the phylogenetic scale at which endemism generally occurs is extremely small, and most "species" (defined by an average nucleotide identity ≥ 95%) and even closely related strains (average nucleotide identity ≥ 99.9%) are globally distributed. Human-associated lineages display faster dispersal rates than other terrestrial lineages; the average net distance between any two human-associated cell lineages diverging 50 years ago is roughly 580 km. These results suggest that many previously reported global-scale microbial biogeographical patterns are likely the result of recent or current environmental filtering rather than geographic endemism. For human-associated lineages, estimated transition rates between Europe and North America are particularly high, and much higher than for non-human associated terrestrial lineages, highlighting the role that human movement plays in global microbial dispersal. Dispersal was slowest for hot spring- and terrestrial subsurface-associated lineages, indicating that these environments may act as "isolated islands" of microbial evolution.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, OR, USA.
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA.
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20
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Weinstein SB, Martínez-Mota R, Stapleton TE, Klure DM, Greenhalgh R, Orr TJ, Dale C, Kohl KD, Dearing MD. Microbiome stability and structure is governed by host phylogeny over diet and geography in woodrats ( Neotoma spp.). Proc Natl Acad Sci U S A 2021; 118:e2108787118. [PMID: 34799446 PMCID: PMC8617456 DOI: 10.1073/pnas.2108787118] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2021] [Indexed: 01/17/2023] Open
Abstract
The microbiome is critical for host survival and fitness, but gaps remain in our understanding of how this symbiotic community is structured. Despite evidence that related hosts often harbor similar bacterial communities, it is unclear whether this pattern is due to genetic similarities between hosts or to common ecological selection pressures. Here, using herbivorous rodents in the genus Neotoma, we quantify how geography, diet, and host genetics, alongside neutral processes, influence microbiome structure and stability under natural and captive conditions. Using bacterial and plant metabarcoding, we first characterized dietary and microbiome compositions for animals from 25 populations, representing seven species from 19 sites across the southwestern United States. We then brought wild animals into captivity, reducing the influence of environmental variation. In nature, geography, diet, and phylogeny collectively explained ∼50% of observed microbiome variation. Diet and microbiome diversity were correlated, with different toxin-enriched diets selecting for distinct microbial symbionts. Although diet and geography influenced natural microbiome structure, the effects of host phylogeny were stronger for both wild and captive animals. In captivity, gut microbiomes were altered; however, responses were species specific, indicating again that host genetic background is the most significant predictor of microbiome composition and stability. In captivity, diet effects declined and the effects of host genetic similarity increased. By bridging a critical divide between studies in wild and captive animals, this work underscores the extent to which genetics shape microbiome structure and stability in closely related hosts.
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Affiliation(s)
- Sara B Weinstein
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112;
| | - Rodolfo Martínez-Mota
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
- Centro de Investigaciones Tropicales, Universidad Veracruzana, Veracruz, 91000, Mexico
| | - Tess E Stapleton
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Dylan M Klure
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Robert Greenhalgh
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Teri J Orr
- Department of Biology, New Mexico State University, Las Cruces, NM 88003
| | - Colin Dale
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15217
| | - M Denise Dearing
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
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21
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Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa. Microorganisms 2021; 9:microorganisms9091928. [PMID: 34576823 PMCID: PMC8466087 DOI: 10.3390/microorganisms9091928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/04/2021] [Accepted: 09/05/2021] [Indexed: 11/17/2022] Open
Abstract
Comparative genomics, in particular, pan-genome analysis, provides an in-depth understanding of the genetic variability and dynamics of a bacterial species. Coupled with whole-genome-based taxonomic analysis, these approaches can help to provide comprehensive, detailed insights into a bacterial species. Here, we report whole-genome-based taxonomic classification and comparative genomic analysis of potential human pathogenic Enterobacter hormaechei subsp. hoffmannii isolated from chlorinated wastewater. Genome Blast Distance Phylogeny (GBDP), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) confirmed the identity of the isolates. The algorithm PathogenFinder predicted the isolates to be human pathogens with a probability of greater than 0.78. The potential pathogenic nature of the isolates was supported by the presence of biosynthetic gene clusters (BGCs), aerobactin, and aryl polyenes (APEs), which are known to be associated with pathogenic/virulent strains. Moreover, analysis of the genome sequences of the isolates reflected the presence of an arsenal of virulence factors and antibiotic resistance genes that augment the predictions of the algorithm PathogenFinder. The study comprehensively elucidated the genomic features of pathogenic Enterobacter isolates from wastewaters, highlighting the role of wastewaters in the dissemination of pathogenic microbes, and the need for monitoring the effectiveness of the wastewater treatment process.
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Calland JK, Pascoe B, Bayliss SC, Mourkas E, Berthenet E, Thorpe HA, Hitchings MD, Feil EJ, Corander J, Blaser MJ, Falush D, Sheppard SK. Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages. PLoS Genet 2021; 17:e1009829. [PMID: 34582435 PMCID: PMC8500405 DOI: 10.1371/journal.pgen.1009829] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/08/2021] [Accepted: 09/20/2021] [Indexed: 11/20/2022] Open
Abstract
Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the 'birthday problem'. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter coli (2.4 x 10-6 s/s/y) and Campylobacter jejuni (3.4 x 10-6 s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame-analogous to a shared birthday-and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.
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Affiliation(s)
- Jessica K. Calland
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Ben Pascoe
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Sion C. Bayliss
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Evangelos Mourkas
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Elvire Berthenet
- French National Reference Center for Campylobacters and Helicobacters, University of Bordeaux, Bordeaux, France
- Institute of Life Sciences, Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Harry A. Thorpe
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Matthew D. Hitchings
- Institute of Life Sciences, Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Edward J. Feil
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Martin J. Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Daniel Falush
- Centre for Microbes, Development and Health, Institute Pasteur of Shanghai, Shanghai, China
- * E-mail: (DF); (SKS)
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (DF); (SKS)
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McKee CD, Bai Y, Webb CT, Kosoy MY. Bats are key hosts in the radiation of mammal-associated Bartonella bacteria. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 89:104719. [PMID: 33444855 PMCID: PMC10915969 DOI: 10.1016/j.meegid.2021.104719] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/25/2022]
Abstract
Bats are notorious reservoirs of several zoonotic diseases and may be uniquely tolerant of infection among mammals. Broad sampling has revealed the importance of bats in the diversification and spread of viruses and eukaryotes to other animal hosts. Vector-borne bacteria of the genus Bartonella are prevalent and diverse in mammals globally and recent surveys have revealed numerous Bartonella lineages in bats. We assembled a sequence database of Bartonella strains, consisting of nine genetic loci from 209 previously characterized Bartonella lineages and 121 new cultured isolates from bats, and used these data to perform a comprehensive phylogenetic analysis of the Bartonella genus. This analysis included estimation of divergence dates using a molecular clock and ancestral reconstruction of host associations and geography. We estimate that Bartonella began infecting mammals 62 million years ago near the Cretaceous-Paleogene boundary. Additionally, the radiation of particular Bartonella clades correlate strongly to the timing of diversification and biogeography of mammalian hosts. Bats were inferred to be the ancestral hosts of all mammal-associated Bartonella and appear to be responsible for the early geographic expansion of the genus. We conclude that bats have had a deep influence on the evolutionary radiation of Bartonella bacteria and their spread to other mammalian orders. These results support a 'bat seeding' hypothesis that could explain similar evolutionary patterns in other mammalian parasite taxa. Application of such phylogenetic tools as we have used to other taxa may reveal the general importance of bats in the ancient diversification of mammalian parasites.
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Affiliation(s)
- Clifton D McKee
- Graduate Degree Program in Ecology, Colorado State University, 1021 Campus Delivery, Fort Collins, CO 80523, USA; Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA.
| | - Ying Bai
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, USA
| | - Colleen T Webb
- Graduate Degree Program in Ecology, Colorado State University, 1021 Campus Delivery, Fort Collins, CO 80523, USA; Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA
| | - Michael Y Kosoy
- KB One Health, LLC, 3244 Reedgrass Court, Fort Collins, CO 80521, USA
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Ward LM, Johnston DT, Shih PM. Phanerozoic radiation of ammonia oxidizing bacteria. Sci Rep 2021; 11:2070. [PMID: 33483596 PMCID: PMC7822890 DOI: 10.1038/s41598-021-81718-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
The modern nitrogen cycle consists of a web of microbially mediated redox transformations. Among the most crucial reactions in this cycle is the oxidation of ammonia to nitrite, an obligately aerobic process performed by a limited number of lineages of bacteria (AOB) and archaea (AOA). As this process has an absolute requirement for O2, the timing of its evolution-especially as it relates to the Great Oxygenation Event ~ 2.3 billion years ago-remains contested and is pivotal to our understanding of nutrient cycles. To estimate the antiquity of bacterial ammonia oxidation, we performed phylogenetic and molecular clock analyses of AOB. Surprisingly, bacterial ammonia oxidation appears quite young, with crown group clades having originated during Neoproterozoic time (or later) with major radiations occurring during Paleozoic time. These results place the evolution of AOB broadly coincident with the pervasive oxygenation of the deep ocean. The late evolution AOB challenges earlier interpretations of the ancient nitrogen isotope record, predicts a more substantial role for AOA during Precambrian time, and may have implications for understanding of the size and structure of the biogeochemical nitrogen cycle through geologic time.
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Affiliation(s)
- L M Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA.
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.
| | - D T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
| | - P M Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Department of Energy, Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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25
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Harris HMB, Hill C. A Place for Viruses on the Tree of Life. Front Microbiol 2021; 11:604048. [PMID: 33519747 PMCID: PMC7840587 DOI: 10.3389/fmicb.2020.604048] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022] Open
Abstract
Viruses are ubiquitous. They infect almost every species and are probably the most abundant biological entities on the planet, yet they are excluded from the Tree of Life (ToL). However, there can be no doubt that viruses play a significant role in evolution, the force that facilitates all life on Earth. Conceptually, viruses are regarded by many as non-living entities that hijack living cells in order to propagate. A strict separation between living and non-living entities places viruses far from the ToL, but this may be theoretically unsound. Advances in sequencing technology and comparative genomics have expanded our understanding of the evolutionary relationships between viruses and cellular organisms. Genomic and metagenomic data have revealed that co-evolution between viral and cellular genomes involves frequent horizontal gene transfer and the occasional co-option of novel functions over evolutionary time. From the giant, ameba-infecting marine viruses to the tiny Porcine circovirus harboring only two genes, viruses and their cellular hosts are ecologically and evolutionarily intertwined. When deciding how, if, and where viruses should be placed on the ToL, we should remember that the Tree functions best as a model of biological evolution on Earth, and it is important that models themselves evolve with our increasing understanding of biological systems.
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Affiliation(s)
- Hugh M B Harris
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
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26
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Madi N, Vos M, Murall CL, Legendre P, Shapiro BJ. Does diversity beget diversity in microbiomes? eLife 2020; 9:e58999. [PMID: 33215610 PMCID: PMC7755399 DOI: 10.7554/elife.58999] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/19/2020] [Indexed: 11/29/2022] Open
Abstract
Microbes are embedded in complex communities where they engage in a wide array of intra- and inter-specific interactions. The extent to which these interactions drive or impede microbiome diversity is not well understood. Historically, two contrasting hypotheses have been suggested to explain how species interactions could influence diversity. 'Ecological Controls' (EC) predicts a negative relationship, where the evolution or migration of novel types is constrained as niches become filled. In contrast, 'Diversity Begets Diversity' (DBD) predicts a positive relationship, with existing diversity promoting the accumulation of further diversity via niche construction and other interactions. Using high-throughput amplicon sequencing data from the Earth Microbiome Project, we provide evidence that DBD is strongest in low-diversity biomes, but weaker in more diverse biomes, consistent with biotic interactions initially favouring the accumulation of diversity (as predicted by DBD). However, as niches become increasingly filled, diversity hits a plateau (as predicted by EC).
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Affiliation(s)
- Naïma Madi
- Département de sciences biologiques, Université de MontréalMontrealCanada
| | - Michiel Vos
- European Centre for Environment and Human Health, University of ExeterPenrynUnited Kingdom
| | - Carmen Lia Murall
- Département de sciences biologiques, Université de MontréalMontrealCanada
| | - Pierre Legendre
- Département de sciences biologiques, Université de MontréalMontrealCanada
| | - B Jesse Shapiro
- Département de sciences biologiques, Université de MontréalMontrealCanada
- Department of Microbiology and Immunology, McGill UniversityMontrealCanada
- McGill Genome Centre, McGill UniversityMontrealCanada
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27
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A Persisting Nontropical Focus of Burkholderia pseudomallei with Limited Genome Evolution over Five Decades. mSystems 2020; 5:5/6/e00726-20. [PMID: 33172968 PMCID: PMC7657595 DOI: 10.1128/msystems.00726-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Burkholderia pseudomallei is predominantly a tropical pathogen uncommonly found in the environment of temperate climatic regions. It is unclear if introduction into temperate regions is sporadic and temporary or if B. pseudomallei can persist in such environments. B. pseudomallei was identified in the environment of southwest Western Australia with melioidosis cases between 1966 and 1991. We report a new cluster with 23 animal fatalities in the same region from 2017, with B. pseudomallei again being recovered from the environment. Comparison of the isolates from the first and second clusters using genomics revealed a single sequence type, high clonality, and limited recombination, even though the time of recovery of the isolates spanned 51 years. This is a major contrast to the extensive genomic diversity seen in the tropics. Our data support the suggestion that B. pseudomallei has the ability to persist in nontropical environments, potentially in a latent state, and has the ability to activate following favorable conditions (rainfall) and then infect animals and humans. Burkholderia pseudomallei is the causative agent of the high-mortality disease melioidosis. Although melioidosis is classified as a tropical disease, rare autochthonous cases have been reported from temperate climatic regions, with uncertainty as to whether B. pseudomallei is persistent in the local environment and whether specific genetic mechanisms facilitate the survival of B. pseudomallei outside the tropics. Sporadic cases of melioidosis occurred in a valley region (latitude 31.6°S) in southwest Western Australia, Australia, between 1966 and 1992. We report a new melioidosis cluster in the same region following high rainfall in January 2017. More than 20 animals died, and B. pseudomallei was isolated from four alpacas, a parrot, and three environmental samples taken from the farm where the alpacas resided. Epidemiological data and genomics revealed that two locations on the farm were the probable sources of the alpaca infections. We determined that B. pseudomallei isolates from the 2017 cluster belonged to sequence type 284 (ST-284), as did all isolates recovered from 1966 to 1992. Genomic analysis confirmed that the ST-284 isolates were clonal and contained conserved genomic islands and limited evidence of recombination. We identified protein-coding regions unique to these isolates that might influence the persistence of B. pseudomallei in this temperate region. We demonstrate the environmental persistence of B. pseudomallei in a temperate region for over 50 years, with limited genetic changes suggesting a latent state and with activation, potential aerosolization, and local dispersal following unusually high rainfall. IMPORTANCEBurkholderia pseudomallei is predominantly a tropical pathogen uncommonly found in the environment of temperate climatic regions. It is unclear if introduction into temperate regions is sporadic and temporary or if B. pseudomallei can persist in such environments. B. pseudomallei was identified in the environment of southwest Western Australia with melioidosis cases between 1966 and 1991. We report a new cluster with 23 animal fatalities in the same region from 2017, with B. pseudomallei again being recovered from the environment. Comparison of the isolates from the first and second clusters using genomics revealed a single sequence type, high clonality, and limited recombination, even though the time of recovery of the isolates spanned 51 years. This is a major contrast to the extensive genomic diversity seen in the tropics. Our data support the suggestion that B. pseudomallei has the ability to persist in nontropical environments, potentially in a latent state, and has the ability to activate following favorable conditions (rainfall) and then infect animals and humans.
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28
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Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts. ISME JOURNAL 2020; 15:503-519. [PMID: 33011742 DOI: 10.1038/s41396-020-00791-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 01/17/2023]
Abstract
The symbiosis between bacteria and sponges has arguably the longest evolutionary history for any extant metazoan lineage, yet little is known about bacterial evolution or adaptation in this process. An example of often dominant and widespread bacterial symbionts of sponges is a clade of uncultured and uncharacterised Proteobacteria. Here we set out to characterise this group using metagenomics, in-depth phylogenetic analyses, metatranscriptomics, and fluorescence in situ hybridisation microscopy. We obtained five metagenome-assembled-genomes (MAGs) from different sponge species that, together with a previously published MAG (AqS2), comprise two families within a new gammaproteobacterial order that we named UTethybacterales. Members of this order share a heterotrophic lifestyle but vary in their predicted ability to use various carbon, nitrogen and sulfur sources, including taurine, spermidine and dimethylsulfoniopropionate. The deep branching of the UTethybacterales within the Gammaproteobacteria and their almost exclusive presence in sponges suggests they have entered a symbiosis with their host relatively early in evolutionary time and have subsequently functionally radiated. This is reflected in quite distinct lifestyles of various species of UTethybacterales, most notably their diverse morphologies, predicted substrate preferences, and localisation within the sponge tissue. This study provides new insight into the evolution of metazoan-bacteria symbiosis.
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29
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Cho ST, Kung HJ, Huang W, Hogenhout SA, Kuo CH. Species Boundaries and Molecular Markers for the Classification of 16SrI Phytoplasmas Inferred by Genome Analysis. Front Microbiol 2020; 11:1531. [PMID: 32754131 PMCID: PMC7366425 DOI: 10.3389/fmicb.2020.01531] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/12/2020] [Indexed: 11/29/2022] Open
Abstract
Phytoplasmas are plant-pathogenic bacteria that impact agriculture worldwide. The commonly adopted classification system for phytoplasmas is based on the restriction fragment length polymorphism (RFLP) analysis of their 16S rRNA genes. With the increased availability of phytoplasma genome sequences, the classification system can now be refined. This work examined 11 strains in the 16SrI group within the genus ‘Candidatus Phytoplasma’ and investigated the possible species boundaries. We confirmed that the RFLP classification method is problematic due to intragenomic variation of the 16S rRNA genes and uneven weighing of different nucleotide positions. Importantly, our results based on the molecular phylogeny, differentiations in chromosomal segments and gene content, and divergence in homologous sequences, all supported that these strains may be classified into multiple operational taxonomic units (OTUs) equivalent to species. Strains assigned to the same OTU share >97% genome-wide average nucleotide identity (ANI) and >78% of their protein-coding genes. In comparison, strains assigned to different OTUs share < 94% ANI and < 75% of their genes. Reduction in homologous recombination between OTUs is one possible explanation for the discontinuity in genome similarities, and these findings supported the proposal that 95% ANI could serve as a cutoff for distinguishing species in bacteria. Additionally, critical examination of these results and the raw sequencing reads led to the identification of one genome that was presumably mis-assembled by combining two sequencing libraries built from phytoplasmas belonging to different OTUs. This finding provided a cautionary tale for working on uncultivated bacteria. Based on the new understanding of phytoplasma divergence and the current genome availability, we developed five molecular markers that could be used for multilocus sequence analysis (MLSA). By selecting markers that are short yet highly informative, and are distributed evenly across the chromosome, these markers provided a cost-effective system that is robust against recombination. Finally, examination of the effector gene distribution further confirmed the rapid gains and losses of these genes, as well as the involvement of potential mobile units (PMUs) in their molecular evolution. Future improvements on the taxon sampling of phytoplasma genomes will allow further expansions of similar analysis, and thus contribute to phytoplasma taxonomy and diagnostics.
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Affiliation(s)
- Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hung-Jui Kung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Weijie Huang
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | | | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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30
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Afouda P, Dubourg G, Raoult D. Archeomicrobiology applied to environmental samples. Microb Pathog 2020; 143:104140. [DOI: 10.1016/j.micpath.2020.104140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
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31
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Xue CX, Zhang H, Lin HY, Sun Y, Luo D, Huang Y, Zhang XH, Luo H. Ancestral niche separation and evolutionary rate differentiation between sister marine flavobacteria lineages. Environ Microbiol 2020; 22:3234-3247. [PMID: 32390223 DOI: 10.1111/1462-2920.15065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/30/2022]
Abstract
Marine flavobacteria are specialists for polysaccharide degradation. They dominate in habitats enriched with polysaccharides, but are also prevalent in pelagic environments where polysaccharides are less available. These niches are likely occupied by distinct lineages, but evolutionary processes underlying their niche differentiation remain elusive. Here, genomic analyses and physiological assays indicate that the sister flavobacteria lineages Leeuwenhoekiella and Nonlabens likely explore polysaccharide-rich macroalgae and polysaccharide-poor pelagic niches respectively. Phylogenomic analyses inferred that the niche separation likely occurred anciently and coincided with increased sequence evolutionary rate in Nonlabens compared with Leeuwenhoekiella. Further analyses ruled out the known mechanisms likely driving evolutionary rate acceleration, including reduced selection efficiency, decreased generation time and increased mutation rate. In particular, the mutation rates were determined using an unbiased experimental method, which measures the present-day populations and may not reflect ancestral populations. These data collectively lead to a new hypothesis that an ancestral and transient mutation rate increase resulted in evolutionary rate increase in Nonlabens. This hypothesis was supported by inferring that gains and losses of genes involved in SOS response, a mechanism known to drive transiently increased mutation rate, coincided with evolutionary rate acceleration. Our analyses highlight the evolutionary mechanisms underlying niche differentiation of flavobacteria lineages.
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Affiliation(s)
- Chun-Xu Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.,Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - He-Yu Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Ying Sun
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Danli Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Yongjie Huang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000, China
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32
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Cao Y, Trivellone V, Dietrich CH. A timetree for phytoplasmas (Mollicutes) with new insights on patterns of evolution and diversification. Mol Phylogenet Evol 2020; 149:106826. [PMID: 32283136 DOI: 10.1016/j.ympev.2020.106826] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/12/2020] [Accepted: 04/07/2020] [Indexed: 11/16/2022]
Abstract
The first comprehensive timetree is presented for phytoplasmas, a diverse group of obligate intracellular bacteria restricted to phloem sieve elements of vascular plants and tissues of their hemipteran insect vectors. Maximum likelihood-based phylogenetic analysis of DNA sequence data from the 16S rRNA and methionine aminopeptidase (map) genes yielded well resolved estimates of phylogenetic relationships among major phytoplasma lineages, 16Sr groups and known strains of phytoplasmas. Age estimates for divergences among two major lineages of Mollicutes based on a previous comprehensive bacterial timetree were used to calibrate an initial 16S timetree. A separate timetree was estimated based on the more rapidly-evolving map gene, with an internal calibration based on a recent divergence within two related 16Sr phytoplasma subgroups in group 16SrV thought to have been driven by the introduction of the North American leafhopper vector Scaphoideus titanus Ball into Europe during the early part of the 20th century. Combining the resulting divergence time estimates into a final 16S timetree suggests that evolutionary rates have remained relatively constant overall through the evolution of phytoplasmas and that the origin of this lineage, at ~641 million years ago (Ma), preceded the origin of land plants and hemipteran insects. Nevertheless, the crown group of phytoplasmas is estimated to have begun diversifying ~316 Ma, roughly coinciding with the origin of seed plants and Hemiptera. Some phytoplasma groups apparently associated with particular plant families or insect vector lineages generally arose more recently than their respective hosts and vectors, suggesting that vector-mediated host shifts have been an important mechanism in the evolutionary diversification of phytoplasmas. Further progress in understanding macroevolutionary patterns in phytoplasmas is hindered by large gaps in knowledge of the identity of competent vectors and lack of data on phytoplasma associations with non-economically important plants.
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Affiliation(s)
- Yanghui Cao
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
| | - Valeria Trivellone
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA.
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
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33
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Sapriel G, Brosch R. Shared Pathogenomic Patterns Characterize a New Phylotype, Revealing Transition toward Host-Adaptation Long before Speciation of Mycobacterium tuberculosis. Genome Biol Evol 2020; 11:2420-2438. [PMID: 31368488 PMCID: PMC6736058 DOI: 10.1093/gbe/evz162] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis remains one of the deadliest infectious diseases of humanity. To better understand the evolutionary history of host-adaptation of tubercle bacilli (MTB), we sought for mycobacterial species that were more closely related to MTB than the previously used comparator species Mycobacterium marinum and Mycobacterium kansasii. Our phylogenomic approach revealed some recently sequenced opportunistic mycobacterial pathogens, Mycobacterium decipiens, Mycobacterium lacus, Mycobacterium riyadhense, and Mycobacterium shinjukuense, to constitute a common clade with MTB, hereafter called MTB-associated phylotype (MTBAP), from which MTB have emerged. Multivariate and clustering analyses of genomic functional content revealed that the MTBAP lineage forms a clearly distinct cluster of species that share common genomic characteristics, such as loss of core genes, shift in dN/dS ratios, and massive expansion of toxin–antitoxin systems. Consistently, analysis of predicted horizontal gene transfer regions suggests that putative functions acquired by MTBAP members were markedly associated with changes in microbial ecology, for example adaption to intracellular stress resistance. Our study thus considerably deepens our view on MTB evolutionary history, unveiling a decisive shift that promoted conversion to host-adaptation among ancestral founders of the MTBAP lineage long before Mycobacterium tuberculosis has adapted to the human host.
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Affiliation(s)
- Guillaume Sapriel
- UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France.,Atelier de Bioinformatique, ISYEB, UMR 7205, Paris, France
| | - Roland Brosch
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
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Nuy JK, Hoetzinger M, Hahn MW, Beisser D, Boenigk J. Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients. Front Microbiol 2020; 11:154. [PMID: 32117171 PMCID: PMC7031163 DOI: 10.3389/fmicb.2020.00154] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/22/2020] [Indexed: 12/05/2022] Open
Abstract
Polynucleobacter (Burkholderiaceae, Betaproteobacteria) and Limnohabitans (Comamonadaceae, Betaproteobacteria) are abundant freshwater bacteria comprising large genetic and taxonomic diversities, with species adapted to physico-chemically distinct types of freshwater systems. The relative importance of environmental drivers, i.e., physico-chemistry, presence of microeukaryotes and geographic position for the diversity and prevalence has not been investigated for both taxa before. Here, we present the first pan-European study on this topic, comprising 255 freshwater lakes. We investigated Limnohabitans and Polynucleobacter using an amplicon sequencing approach of partial 16S rRNA genes along environmental gradients. We show that physico-chemical factors had the greatest impact on both genera. Analyses on environmental gradients revealed an exceptionally broad ecological spectrum of operational taxonomic units (OTUs). Despite the coarse resolution of the genetic marker, we found OTUs with contrasting environmental preferences within Polynucleobacter and Limnohabitans subclusters. Such an ecological differentiation has been characterized for PnecC and LimC before but was so far unknown for less well studied subclusters such as PnecA and PnecB. Richness and abundance of OTUs are geographically clustered, suggesting that geographic diversity patterns are attributable to region-specific physico-chemical characteristics (e.g., pH and temperature) rather than latitudinal gradients or lake sizes.
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Affiliation(s)
- Julia K Nuy
- Department of Biodiversity, University of Duisburg Essen, Essen, Germany
| | - Matthias Hoetzinger
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg Essen, Essen, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg Essen, Essen, Germany
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Cohen ML, Mashanova EV, Jagannathan SV, Soto W. Adaptation to pH stress by Vibrio fischeri can affect its symbiosis with the Hawaiian bobtail squid ( Euprymna scolopes). MICROBIOLOGY-SGM 2020; 166:262-277. [PMID: 31967537 PMCID: PMC7376262 DOI: 10.1099/mic.0.000884] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many microorganisms engaged in host-microbe interactions pendulate between a free-living phase and a host-affiliated stage. How adaptation to stress during the free-living phase affects host-microbe associations is unclear and understudied. To explore this topic, the symbiosis between Hawaiian bobtail squid (Euprymna scolopes) and the luminous bacterium Vibrio fischeri was leveraged for a microbial experimental evolution study. V. fischeri experienced adaptation to extreme pH while apart from the squid host. V. fischeri was serially passaged for 2000 generations to the lower and upper pH growth limits for this microorganism, which were pH 6.0 and 10.0, respectively. V. fischeri was also serially passaged for 2000 generations to vacillating pH 6.0 and 10.0. Evolution to pH stress both facilitated and impaired symbiosis. Microbial evolution to acid stress promoted squid colonization and increased bioluminescence for V. fischeri, while symbiont adaptation to alkaline stress diminished these two traits. Oscillatory selection to acid and alkaline stress also improved symbiosis for V. fischeri, but the facilitating effects were less than that provided by microbial adaptation to acid stress. In summary, microbial adaptation to harsh environments amid the free-living phase may impact the evolution of host-microbe interactions in ways that were not formerly considered.
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Affiliation(s)
- Meagan Leah Cohen
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Ekaterina Vadimovna Mashanova
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Sveta Vivian Jagannathan
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - William Soto
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
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36
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Hossain S, De Silva BCJ, Dahanayake PS, Heo GJ. Phylogenetic relationships, virulence and antimicrobial resistance properties of Klebsiella sp. isolated from pet turtles in Korea. Lett Appl Microbiol 2019; 70:71-78. [PMID: 31671218 DOI: 10.1111/lam.13245] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 10/05/2019] [Accepted: 10/29/2019] [Indexed: 12/17/2022]
Abstract
Klebsiella sp. are responsible for a multitude of infectious diseases in both humans and animals. In this study, phylogenetic relationships, virulence and antimicrobial resistance gene properties of 16 Klebsiella sp. isolated from 49 pet turtles were investigated. The isolates including Klebsiella oxytoca (n = 13) and Klebsiella pneumoniae (n = 3) were identified using 16S rRNA gene sequencing and each species formed distinct clusters in the neighbour-joining phylogenetic tree. The prevalence of virulence genes including ureC (100%) and kfu (68·75%) was observed among the isolates using Polymerase chain reaction (PCR) assay. The fimH, mrkD and rmpA genes were detected in all K. pneumoniae while these were absent in every K. oxytoca isolate. In antimicrobial susceptibility testing, high resistance rates were observed against ampicillin (100%) and cephalothin (62·50%). The resistance rates against imipenem, tetracycline, trimethoprim/sulfamethoxazole, nalidixic acid and ciprofloxacin were 12·50, 12·50, 12·50, 6·25 and 6·25% respectively. The presence of antimicrobial resistance genes such as plasmid-mediated quinolone resistance (PMQR) [qnrB (37·50%), qnrA (31·25%), qnrS (12·50%) and aac(6')-Ib-cr (12·50%)], extended-spectrum β-lactamase (ESBL) [blaCTX-M (18·75%)], β-lactamase [blaSHV-1 (18·75%)] and tetracycline resistance [tetE (12·50%)] was observed. The results revealed that pet turtle-borne Klebsiella sp. may carry different types of virulence and antimicrobial resistance genes which represents a potential threat to public health. SIGNIFICANCE AND IMPACT OF THE STUDY: Klebsiella sp. are nonmotile Gram-negative bacteria that are found in different environments. The virulence and antimicrobial resistance properties of pet turtle-borne Klebsiella sp. have not been studied before. Phylogenetic relationships, virulence traits and antimicrobial resistance profiles of pet turtle-borne Klebsiella sp. were characterized for the first time in Korea. Multiple virulence and antimicrobial resistance genes were observed among the isolates. The occurrence of virulence and antimicrobial resistance determinants in Klebsiella sp. may represent a potential threat to public health.
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Affiliation(s)
- S Hossain
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
| | - B C J De Silva
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
| | - P S Dahanayake
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
| | - G-J Heo
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
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37
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de Oliveira Martins L, Page AJ, Mather AE, Charles IG. Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing. NAR Genom Bioinform 2019; 2:lqz016. [PMID: 33575567 PMCID: PMC7671355 DOI: 10.1093/nargab/lqz016] [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: 06/12/2019] [Revised: 10/03/2019] [Accepted: 10/24/2019] [Indexed: 01/02/2023] Open
Abstract
DNA barcoding through the use of amplified regions of the ribosomal operon, such as the 16S gene, is a routine method to gain an overview of the microbial taxonomic diversity within a sample without the need to isolate and culture the microbes present. However, bacterial cells usually have multiple copies of this ribosomal operon, and choosing the 'wrong' copy could provide a misleading species classification. While this presents less of a problem for well-characterized organisms with large sequence databases to interrogate, it is a significant challenge for lesser known organisms with unknown copy number and diversity. Using the entire length of the ribosomal operon, which encompasses the 16S, 23S, 5S and internal transcribed spacer regions, should provide greater taxonomic resolution but has not been well explored. Here, we use publicly available reference genomes and explore the theoretical boundaries when using concatenated genes and the full-length ribosomal operons, which has been made possible by the development and uptake of long-read sequencing technologies. We quantify the issues of both copy choice and operon length in a phylogenetic context to demonstrate that longer regions improve the phylogenetic signal while maintaining taxonomic accuracy.
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Affiliation(s)
| | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.,Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Ian G Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.,Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Salmaso N. Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes. Front Microbiol 2019; 10:2257. [PMID: 31636614 PMCID: PMC6788347 DOI: 10.3389/fmicb.2019.02257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/17/2019] [Indexed: 12/04/2022] Open
Abstract
In deep lakes, many investigations highlighted the existence of exclusive groups of bacteria adapted to deep oxygenated and hypoxic and anoxic hypolimnia. Nevertheless, the extent of bacterial strain diversity has been much less scrutinized. This aspect is essential for an unbiased estimation of genetic variation, biodiversity, and population structure, which are essential for studying important research questions such as biogeographical patterns, temporal and spatial variability and the environmental factors affecting this variability. This study investigated the bacterioplankton community in the epilimnetic layers and in the oxygenated and hypoxic/anoxic hypolimnia of five large and deep lakes located at the southern border of the Alps using high throughput sequencing (HTS) analyses (16S rDNA) and identification of amplicon sequence variants (ASVs) resolving reads differing by as little as one nucleotide. The study sites, which included two oligomictic (Garda and Como) and three meromictic lakes (Iseo, Lugano, and Idro) with maximum depths spanning from 124 to 410 m, were chosen among large lakes to represent an oxic-hypoxic gradient. The analyses showed the existence of several unique ASVs in the three layers of the five lakes. In the case of cyanobacteria, this confirmed previous analyses made at the level of strains or based on oligotyping methods. As expected, the communities in the hypoxic/anoxic monimolimnia showed a strong differentiation from the oxygenated layer, with the exclusive presence in single lakes of several unique ASVs. In the meromictic lakes, results supported the hypothesis that the formation of isolated monimolimnia sustained the development of highly diversified bacterial communities through ecological selection, leading to the establishment of distinctive biodiversity zones. The genera identified in these layers are well-known to activate a wide range of redox reactions at low O2 conditions. As inferred from 16S rDNA data, the highly diversified and coupled processes sustained by the monimolimnetic microbiota are essential ecosystem services that enhance mineralization of organic matter and formation of reduced compounds, and also abatement of undesirable greenhouse gasses.
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Affiliation(s)
- Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
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39
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Rausch P, Rühlemann M, Hermes BM, Doms S, Dagan T, Dierking K, Domin H, Fraune S, von Frieling J, Hentschel U, Heinsen FA, Höppner M, Jahn MT, Jaspers C, Kissoyan KAB, Langfeldt D, Rehman A, Reusch TBH, Roeder T, Schmitz RA, Schulenburg H, Soluch R, Sommer F, Stukenbrock E, Weiland-Bräuer N, Rosenstiel P, Franke A, Bosch T, Baines JF. Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms. MICROBIOME 2019; 7:133. [PMID: 31521200 PMCID: PMC6744666 DOI: 10.1186/s40168-019-0743-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 08/23/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as "metaorganisms." The goal of the Collaborative Research Center "Origin and Function of Metaorganisms" is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants. METHODS In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample. CONCLUSION While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3 V4 over the V1 V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.
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Affiliation(s)
- Philipp Rausch
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen Ø, Denmark
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Britt M. Hermes
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Shauni Doms
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Katja Dierking
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Hanna Domin
- Zoological Institute, Kiel University, Kiel, Germany
| | | | - Jakob von Frieling
- Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany
| | - Ute Hentschel
- Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Kiel University, Kiel, Germany
| | | | - Marc Höppner
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Martin T. Jahn
- Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Cornelia Jaspers
- Kiel University, Kiel, Germany
- Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Kohar Annie B. Kissoyan
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | | | - Ateequr Rehman
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Thorsten B. H. Reusch
- Kiel University, Kiel, Germany
- Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Thomas Roeder
- Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany
| | - Ruth A. Schmitz
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Ryszard Soluch
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Felix Sommer
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Eva Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Botanical Institute, Kiel University, Kiel, Germany
| | | | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Thomas Bosch
- Zoological Institute, Kiel University, Kiel, Germany
| | - John F. Baines
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
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Patané JSL, Martins J, Rangel LT, Belasque J, Digiampietri LA, Facincani AP, Ferreira RM, Jaciani FJ, Zhang Y, Varani AM, Almeida NF, Wang N, Ferro JA, Moreira LM, Setubal JC. Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses. BMC Genomics 2019; 20:700. [PMID: 31500575 PMCID: PMC6734499 DOI: 10.1186/s12864-019-6007-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A* and Aw are more restricted both in hosts and in geography. Two previous phylogenomic studies led to contrasting well-supported clades for sequenced genomes of these pathotypes. No extensive biogeographical or divergence dating analytic approaches have been so far applied to available genomes. RESULTS Based on a larger sampling of genomes than in previous studies (including six new genomes sequenced by our group, adding to a total of 95 genomes), phylogenomic analyses resulted in different resolutions, though overall indicating that A + AW is the most likely true clade. Our results suggest the high degree of recombination at some branches and the fast diversification of lineages are probable causes for this phylogenetic blurring effect. One of the genomes analyzed, X. campestris pv. durantae, was shown to be an A* strain; this strain has been reported to infect a plant of the family Verbenaceae, though there are no reports of any X. citri subsp. citri pathotypes infecting any plant outside the Citrus genus. Host reconstruction indicated the pathotype ancestor likely had plant hosts in the family Fabaceae, implying an ancient jump to the current Rutaceae hosts. Extensive dating analyses indicated that the origin of X. citri subsp. citri occurred more recently than the main phylogenetic splits of Citrus plants, suggesting dispersion rather than host-directed vicariance as the main driver of geographic expansion. An analysis of 120 pathogenic-related genes revealed pathotype-associated patterns of presence/absence. CONCLUSIONS Our results provide novel insights into the evolutionary history of X. citri subsp. citri as well as a sound phylogenetic foundation for future evolutionary and genomic studies of its pathotypes.
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Affiliation(s)
- José S L Patané
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - Joaquim Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luiz Thiberio Rangel
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - José Belasque
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Luciano A Digiampietri
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Agda Paula Facincani
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Rafael Marini Ferreira
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Fabrício José Jaciani
- Departamento de Pesquisa e Desenvolvimento, Fundo de Defesa da Citricultura (Fundecitrus), Araraquara, SP, Brazil
| | - Yunzeng Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA
| | - Alessandro M Varani
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Nalvo F Almeida
- Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA
| | - Jesus A Ferro
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Leandro M Moreira
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
- Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA.
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Moran NA, Ochman H, Hammer TJ. Evolutionary and ecological consequences of gut microbial communities. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019; 50:451-475. [PMID: 32733173 DOI: 10.1146/annurev-ecolsys-110617-062453] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Animals are distinguished by having guts: organs that must extract nutrients from food while barring invasion by pathogens. Most guts are colonized by non-pathogenic microorganisms, but the functions of these microbes, or even the reasons why they occur in the gut, vary widely among animals. Sometimes these microorganisms have co-diversified with hosts; sometimes they live mostly elsewhere in the environment. Either way, gut microorganisms often benefit hosts. Benefits may reflect evolutionary "addiction" whereby hosts incorporate gut microorganisms into normal developmental processes. But benefits often include novel ecological capabilities; for example, many metazoan clades exist by virtue of gut communities enabling new dietary niches. Animals vary immensely in their dependence on gut microorganisms, from lacking them entirely, to using them as food, to obligate dependence for development, nutrition, or protection. Many consequences of gut microorganisms for hosts can be ascribed to microbial community processes and the host's ability to shape these processes.
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Affiliation(s)
- Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78703 USA
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78703 USA
| | - Tobin J Hammer
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78703 USA
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Stimson J, Gardy J, Mathema B, Crudu V, Cohen T, Colijn C. Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions. Mol Biol Evol 2019; 36:587-603. [PMID: 30690464 DOI: 10.1093/molbev/msy242] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Whole-genome sequencing (WGS) is increasingly used to aid the understanding of pathogen transmission. A first step in analyzing WGS data is usually to define "transmission clusters," sets of cases that are potentially linked by direct transmission. This is often done by including two cases in the same cluster if they are separated by fewer single-nucleotide polymorphisms (SNPs) than a specified threshold. However, there is little agreement as to what an appropriate threshold should be. We propose a probabilistic alternative, suggesting that the key inferential target for transmission clusters is the number of transmissions separating cases. We characterize this by combining the number of SNP differences and the length of time over which those differences have accumulated, using information about case timing, molecular clock, and transmission processes. Our framework has the advantage of allowing for variable mutation rates across the genome and can incorporate other epidemiological data. We use two tuberculosis studies to illustrate the impact of our approach: with British Columbia data by using spatial divisions; with Republic of Moldova data by incorporating antibiotic resistance. Simulation results indicate that our transmission-based method is better in identifying direct transmissions than a SNP threshold, with dissimilarity between clusterings of on average 0.27 bits compared with 0.37 bits for the SNP-threshold method and 0.84 bits for randomly permuted data. These results show that it is likely to outperform the SNP-threshold method where clock rates are variable and sample collection times are spread out. We implement the method in the R package transcluster.
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Affiliation(s)
- James Stimson
- Department of Mathematics, Imperial College London, London, UK
| | - Jennifer Gardy
- British Columbia Centre for Disease Control, Communicable Disease Prevention and Control Services, Vancouver, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Ted Cohen
- Yale University School of Public Health, New Haven
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, London, UK.,Department of Mathematics, Simon Fraser University, Vancouver, Canada
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Louca S, Mazel F, Doebeli M, Parfrey LW. A census-based estimate of Earth's bacterial and archaeal diversity. PLoS Biol 2019; 17:e3000106. [PMID: 30716065 PMCID: PMC6361415 DOI: 10.1371/journal.pbio.3000106] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/21/2018] [Indexed: 12/17/2022] Open
Abstract
The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8–1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%–96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%–93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2–4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs. A massive survey of Earth's Bacteria and Archaea reveals that their diversity is orders of magnitude lower than previously thought. The study also indicates that extinctions played an important role in prokaryotic evolution. The global diversity of Bacteria and Archaea ("prokaryotes"), the most ancient and most widespread forms of life on Earth, is subject to high uncertainty. Here, to estimate the global diversity of prokaryotes, we analyzed a large number of 16S ribosomal RNA gene sequences, found in all prokaryotes and commonly used to catalogue prokaryotic diversity. Sequences were obtained from a multitude of environments across thousands of geographic locations worldwide. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs), i.e., 16S gene clusters sharing 97% similarity, roughly corresponding to prokaryotic species. Using several statistical approaches and through comparison with existing databases and previous independent surveys, we estimate that there exist globally between 0.8 and 1.6 million prokaryotic OTUs. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar estimates as for the global data set, suggesting that most OTUs are not restricted to a single continent but are instead globally distributed. Our estimates constrain the extent of a commonly hypothesized but poorly quantified rare prokaryotic biosphere and refute recent predictions that there exists trillions of prokaryotic OTUs. Our findings also indicate that, contrary to common speculation, extinctions may strongly influence global prokaryotic diversity.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- * E-mail:
| | - Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
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Music MS, Samarzija I, Hogenhout SA, Haryono M, Cho ST, Kuo CH. The genome of 'Candidatus Phytoplasma solani' strain SA-1 is highly dynamic and prone to adopting foreign sequences. Syst Appl Microbiol 2018; 42:117-127. [PMID: 30455068 DOI: 10.1016/j.syapm.2018.10.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 10/15/2018] [Accepted: 10/25/2018] [Indexed: 11/15/2022]
Abstract
Bacteria of the genus 'Candidatus Phytoplasma' are uncultivated intracellular plant pathogens transmitted by phloem-feeding insects. They have small genomes lacking genes for essential metabolites, which they acquire from either plant or insect hosts. Nonetheless, some phytoplasmas, such as 'Ca. P. solani', have broad plant host range and are transmitted by several polyphagous insect species. To understand better how these obligate symbionts can colonize such a wide range of hosts, the genome of 'Ca. P. solani' strain SA-1 was sequenced from infected periwinkle via a metagenomics approach. The de novo assembly generated a draft genome with 19 contigs totalling 821,322bp, which corresponded to more than 80% of the estimated genome size. Further completion of the genome was challenging due to the high occurrence of repetitive sequences. The majority of repeats consisted of gene arrangements characteristic of phytoplasma potential mobile units (PMUs). These regions showed variation in gene orders intermixed with genes of unknown functions and lack of similarity to other phytoplasma genes, suggesting that they were prone to rearrangements and acquisition of new sequences via recombination. The availability of this high-quality draft genome also provided a foundation for genome-scale genotypic analysis (e.g., average nucleotide identity and average amino acid identity) and molecular phylogenetic analysis. Phylogenetic analyses provided evidence of horizontal transfer for PMU-like elements from various phytoplasmas, including distantly related ones. The 'Ca. P. solani' SA-1 genome also contained putative secreted protein/effector genes, including a homologue of SAP11, found in many other phytoplasma species.
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Affiliation(s)
- Martina Seruga Music
- Department of Biology, Faculty of Science, University of Zagreb, Marulicev trg 9A, HR-10000 Zagreb, Croatia.
| | - Ivana Samarzija
- Department of Biology, Faculty of Science, University of Zagreb, Marulicev trg 9A, HR-10000 Zagreb, Croatia.
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Ln, Norwich NR4 7UH, UK.
| | - Mindia Haryono
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd., Taipei 11529, Taiwan.
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd., Taipei 11529, Taiwan.
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd., Taipei 11529, Taiwan.
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Novel Cardinium strains in non-marine ostracod (Crustacea) hosts from natural populations. Mol Phylogenet Evol 2018; 130:406-415. [PMID: 30244151 DOI: 10.1016/j.ympev.2018.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
Endosymbiotic bacteria are known from many metazoan taxa, where they manipulate host biology and reproduction. Here, we used classic PCR amplification and direct DNA sequencing with universal primers for four different endosymbionts to test for their presence in more than 300 specimens of three recent non-marine ostracod superfamilies from different geographic areas and aquatic habitats. We verified these results with "high throughput" amplicon sequencing of 16S of nine selected specimens and evolutionary placement algorithms. The phylogenetic position of endosymbionts detected in ostracod hosts was compared to known endosymbionts from other metazoans. While Wolbachia, Spiroplasma and Rickettsia are absent, we find evidence for the general presence of Cardinium bacteria in natural populations of various non-marine ostracod species. Phylogenetic reconstructions based on Cardinium 16S data and estimates of genetic distances both indicate that Cardinium from ostracods are distantly related to Cardinium from Diptera and Nematoda but represent novel strains with a monophyletic origin. Cardinium bacteria from different ostracod hosts have genetic distances of up to 3.8%, providing evidence against recent and frequent horizontal transmissions amongst the three ostracod superfamilies. High throughput sequencing reveals more than 400 different 16S amplicon sequence variants in the investigated ostracods as well as the presence of different Cardinium strains within individual Eucypris virens and Heterocypris hosts. These results call for future, more in-depth investigations. Mapping Cardinium infections on COI trees of non-marine ostracod hosts shows that the occurrence of these endosymbionts is not linked to genetic species identity or phylogenetic host groups and, except for one ostracod morphospecies, prevalence never reaches 100%.
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Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota. mBio 2018; 9:mBio.01348-18. [PMID: 30206171 PMCID: PMC6134092 DOI: 10.1128/mbio.01348-18] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Our understanding of mammalian evolution has become microbiome-aware. While emerging research links mammalian biodiversity and the gut microbiome, we lack insight into which microbes potentially impact mammalian evolution. Microbes common to diverse mammalian species may be strong candidates, as their absence in the gut may affect how the microbiome functionally contributes to mammalian physiology to adversely affect fitness. Identifying such conserved gut microbes is thus important to ultimately assessing the microbiome’s potential role in mammalian evolution. To advance their discovery, we developed an approach that identifies ancestrally related groups of microbes that distribute across mammals in a way that indicates their collective conservation. These conserved clades are presumed to have evolved a trait in their ancestor that matters to their distribution across mammals and which has been retained among clade members. We found not only that such clades do exist among mammals but also that they appear to be subject to natural selection and characterize human evolution. Our knowledge of how the gut microbiome relates to mammalian evolution benefits from the identification of gut microbial taxa that are unexpectedly prevalent or unexpectedly conserved across mammals. Such taxa enable experimental determination of the traits needed for such microbes to succeed as gut generalists, as well as those traits that impact mammalian fitness. However, the punctuated resolution of microbial taxonomy may limit our ability to detect conserved gut microbes, especially in cases in which broadly related microbial lineages possess shared traits that drive their apparent ubiquity across mammals. To advance the discovery of conserved mammalian gut microbes, we developed a novel ecophylogenetic approach to taxonomy that groups microbes into taxonomic units based on their shared ancestry and their common distribution across mammals. Applying this approach to previously generated gut microbiome data uncovered monophyletic clades of gut bacteria that are conserved across mammals. It also resolved microbial clades exclusive to and conserved among particular mammalian lineages. Conserved clades often manifest phylogenetic patterns, such as cophylogeny with their host, that indicate that they are subject to selective processes, such as host filtering. Moreover, this analysis identified variation in the rate at which mammals acquire or lose conserved microbial clades and resolved a human-accelerated loss of conserved clades. Collectively, the data from this study reveal mammalian gut microbiota that possess traits linked to mammalian phylogeny, point to the existence of a core set of microbes that comprise the mammalian gut microbiome, and clarify potential evolutionary or ecologic mechanisms driving the gut microbiome’s diversification throughout mammalian evolution.
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Chen NWG, Serres-Giardi L, Ruh M, Briand M, Bonneau S, Darrasse A, Barbe V, Gagnevin L, Koebnik R, Jacques MA. Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean. BMC Genomics 2018; 19:606. [PMID: 30103675 PMCID: PMC6090828 DOI: 10.1186/s12864-018-4975-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 07/31/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Host specialization is a hallmark of numerous plant pathogens including bacteria, fungi, oomycetes and viruses. Yet, the molecular and evolutionary bases of host specificity are poorly understood. In some cases, pathological convergence is observed for individuals belonging to distant phylogenetic clades. This is the case for Xanthomonas strains responsible for common bacterial blight of bean, spread across four genetic lineages. All the strains from these four lineages converged for pathogenicity on common bean, implying possible gene convergences and/or sharing of a common arsenal of genes conferring the ability to infect common bean. RESULTS To search for genes involved in common bean specificity, we used a combination of whole-genome analyses without a priori, including a genome scan based on k-mer search. Analysis of 72 genomes from a collection of Xanthomonas pathovars unveiled 115 genes bearing DNA sequences specific to strains responsible for common bacterial blight, including 20 genes located on a plasmid. Of these 115 genes, 88 were involved in successive events of horizontal gene transfers among the four genetic lineages, and 44 contained nonsynonymous polymorphisms unique to the causal agents of common bacterial blight. CONCLUSIONS Our study revealed that host specificity of common bacterial blight agents is associated with a combination of horizontal transfers of genes, and highlights the role of plasmids in these horizontal transfers.
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Affiliation(s)
- Nicolas W. G. Chen
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Laurana Serres-Giardi
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Martial Briand
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Sophie Bonneau
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Armelle Darrasse
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Valérie Barbe
- CEA/DSV/IG/Genoscope, 2 rue Gaston Crémieux, BP5706, 91057 Evry, France
| | - Lionel Gagnevin
- CIRAD, UMR PVBMT, F-97410 Saint-Pierre, La Réunion France
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
| | - Ralf Koebnik
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
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Louca S, Shih PM, Pennell MW, Fischer WW, Parfrey LW, Doebeli M. Bacterial diversification through geological time. Nat Ecol Evol 2018; 2:1458-1467. [DOI: 10.1038/s41559-018-0625-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/28/2018] [Indexed: 11/09/2022]
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Espejo RT, Plaza N. Multiple Ribosomal RNA Operons in Bacteria; Their Concerted Evolution and Potential Consequences on the Rate of Evolution of Their 16S rRNA. Front Microbiol 2018; 9:1232. [PMID: 29937760 PMCID: PMC6002687 DOI: 10.3389/fmicb.2018.01232] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/22/2018] [Indexed: 12/12/2022] Open
Abstract
Bacterial species differ greatly in the number and location of the rRNA operons which may be present in the bacterial chromosomes and plasmids. Most bacterial species contain more than one ribosomal RNA operon copy in their genomes, with some species containing up to 15 such copies. We review the number and location of the rRNA operons and discuss evolution of 16S rRNA (rrs) genes -which are considered as ultimate chronometers for phylogenetic classification- in bacteria with multiple copies of these genes. In these bacterial species, the rrs genes must evolve in concert and sequence changes generated by mutation or horizontal gene transfer must be either erased or spread to every gene copy to avoid divergence, as it occurs when they are present in different species. Analysis of polymorphic sites in intra-genomic rrs copies identifies putative conversion events and demonstrates that sequence conversion is patchy and occurs in small conversion tracts. Sequence conversion probably arises by a non-reciprocal transfer between two or more copies where one copy contributes only a small contiguous segment of DNA, whereas the other copy contributes the rest of the genome in a fairly well understood molecular process. Because concerted evolution implies that a mutation in any of the rrs copies is either eliminated or transferred to every rrs gene in the genome, this process should slow their evolution rate relative to that of single copy genes. However, available data on the rrs genes in bacterial genomes do not show a clear relationship between their evolution rates and the number of their copies in the genome.
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Affiliation(s)
- Romilio T Espejo
- Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Nicolás Plaza
- Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile.,Centro de Investigación Biomédica, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
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Martínez-Cano DJ, Bor G, Moya A, Delaye L. Testing the Domino Theory of Gene Loss in Buchnera aphidicola: The Relevance of Epistatic Interactions. Life (Basel) 2018; 8:life8020017. [PMID: 29843462 PMCID: PMC6027505 DOI: 10.3390/life8020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 02/07/2023] Open
Abstract
The domino theory of gene loss states that when some particular gene loses its function and cripples a cellular function, selection will relax in all functionally related genes, which may allow for the non-functionalization and loss of these genes. Here we study the role of epistasis in determining the pattern of gene losses in a set of genes participating in cell envelope biogenesis in the endosymbiotic bacteria Buchnera aphidicola. We provide statistical evidence indicating pairs of genes in B. aphidicola showing correlated gene loss tend to have orthologs in Escherichia coli known to have alleviating epistasis. In contrast, pairs of genes in B. aphidicola not showing correlated gene loss tend to have orthologs in E. coli known to have aggravating epistasis. These results suggest that during the process of genome reduction in B. aphidicola by gene loss, positive or alleviating epistasis facilitates correlated gene losses while negative or aggravating epistasis impairs correlated gene losses. We interpret this as evidence that the reduced proteome of B. aphidicola contains less pathway redundancy and more compensatory interactions, mimicking the situation of E. coli when grown under environmental constrains.
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Affiliation(s)
- David J Martínez-Cano
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico.
| | - Gil Bor
- CIMAT, A.P. 402, Guanajuato 36000, Gto., Mexico.
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, Avenida de Catalunya 21, 46020 València, Spain.
- Institute for Integrative Systems Biology, Universitat de València, Calle Catedrático José Beltrán 2, 46980 Paterna, València, Spain.
| | - Luis Delaye
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico.
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