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Tomasch J, Kopejtka K, Bílý T, Gardiner AT, Gardian Z, Shivaramu S, Koblížek M, Kaftan D. A photoheterotrophic bacterium from Iceland has adapted its photosynthetic machinery to the long days of polar summer. mSystems 2024; 9:e0131123. [PMID: 38376261 PMCID: PMC10949492 DOI: 10.1128/msystems.01311-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
During their long evolution, anoxygenic phototrophic bacteria have inhabited a wide variety of natural habitats and developed specific strategies to cope with the challenges of any particular environment. Expression, assembly, and safe operation of the photosynthetic apparatus must be regulated to prevent reactive oxygen species generation under illumination in the presence of oxygen. Here, we report on the photoheterotrophic Sediminicoccus sp. strain KRV36, which was isolated from a cold stream in north-western Iceland, 30 km south of the Arctic Circle. In contrast to most aerobic anoxygenic phototrophs, which stop pigment synthesis when illuminated, strain KRV36 maintained its bacteriochlorophyll synthesis even under continuous light. Its cells also contained between 100 and 180 chromatophores, each accommodating photosynthetic complexes that exhibit an unusually large carotenoid absorption spectrum. The expression of photosynthesis genes in dark-adapted cells was transiently downregulated in the first 2 hours exposed to light but recovered to the initial level within 24 hours. An excess of membrane-bound carotenoids as well as high, constitutive expression of oxidative stress response genes provided the required potential for scavenging reactive oxygen species, safeguarding bacteriochlorophyll synthesis and photosystem assembly. The unique cellular architecture and an unusual gene expression pattern represent a specific adaptation that allows the maintenance of anoxygenic phototrophy under arctic conditions characterized by long summer days with relatively low irradiance.IMPORTANCEThe photoheterotrophic bacterium Sediminicoccus sp. KRV36 was isolated from a cold stream in Iceland. It expresses its photosynthesis genes, synthesizes bacteriochlorophyll, and assembles functional photosynthetic complexes under continuous light in the presence of oxygen. Unraveling the molecular basis of this ability, which is exceptional among aerobic anoxygenic phototrophic species, will help to understand the evolution of bacterial photosynthesis in response to changing environmental conditions. It might also open new possibilities for genetic engineering of biotechnologically relevant phototrophs, with the aim of increasing photosynthetic activity and their tolerance to reactive oxygen species.
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Affiliation(s)
- Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Tomáš Bílý
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Alastair T. Gardiner
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Zdenko Gardian
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Sahana Shivaramu
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - David Kaftan
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department Chemistry, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
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Muñoz-Gómez SA, Cadena LR, Gardiner AT, Leger MM, Sheikh S, Connell LB, Bilý T, Kopejtka K, Beatty JT, Koblížek M, Roger AJ, Slamovits CH, Lukeš J, Hashimi H. Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60. Curr Biol 2023; 33:1396. [PMID: 37040698 DOI: 10.1016/j.cub.2023.03.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
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Gardiner AT, Mujakić I, Bína D, Gardian Z, Kopejtka K, Nupur, Qian P, Koblížek M. Characterisation of the photosynthetic complexes from the marine gammaproteobacterium Congregibacter litoralis KT71. Biochim Biophys Acta Bioenerg 2023; 1864:148946. [PMID: 36455648 DOI: 10.1016/j.bbabio.2022.148946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/02/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
Possibly the most abundant group of anoxygenic phototrophs are marine photoheterotrophic Gammaproteobacteria belonging to the NOR5/OM60 clade. As little is known about their photosynthetic apparatus, the photosynthetic complexes from the marine phototrophic bacterium Congregibacter litoralis KT71 were purified and spectroscopically characterised. The intra-cytoplasmic membranes contain a smaller amount of photosynthetic complexes when compared with anaerobic purple bacteria. Moreover, the intra-cytoplasmic membranes contain only a minimum amount of peripheral LH2 complexes. The complexes are populated by bacteriochlorophyll a, spirilloxanthin and two novel ketocarotenoids, with biophysical and biochemical properties similar to previously characterised complexes from purple bacteria. The organization of the RC-LH1 complex has been further characterised using cryo-electron microscopy. The overall organisation is similar to the complex from the gammaproteobacterium Thermochromatium tepidum, with the type-II reaction centre surrounded by a slightly elliptical LH1 antenna ring composed of 16 αβ-subunits with no discernible gap or pore. The RC-LH1 and LH2 apoproteins are phylogenetically related to other halophilic species but LH2 also to some alphaproteobacterial species. It seems that the reduction of light-harvesting apparatus and acquisition of novel ketocarotenoids in Congregibacter litoralis KT71 represent specific adaptations for operating the anoxygenic photosynthesis under aerobic conditions at sea.
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Affiliation(s)
- Alastair T Gardiner
- Institute of Microbiology of the Czech Academy of Sciences, 379 81 Třeboň, Czech Republic
| | - Izabela Mujakić
- Institute of Microbiology of the Czech Academy of Sciences, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - David Bína
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Zdenko Gardian
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Karel Kopejtka
- Institute of Microbiology of the Czech Academy of Sciences, 379 81 Třeboň, Czech Republic
| | - Nupur
- Institute of Microbiology of the Czech Academy of Sciences, 379 81 Třeboň, Czech Republic
| | - Pu Qian
- Materials and Structure Analysis, Thermofisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - Michal Koblížek
- Institute of Microbiology of the Czech Academy of Sciences, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic.
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Muñoz-Gómez SA, Cadena LR, Gardiner AT, Leger MM, Sheikh S, Connell LB, Bilý T, Kopejtka K, Beatty JT, Koblížek M, Roger AJ, Slamovits CH, Lukeš J, Hashimi H. Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60. Curr Biol 2023; 33:1099-1111.e6. [PMID: 36921606 DOI: 10.1016/j.cub.2023.02.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/06/2023] [Accepted: 02/16/2023] [Indexed: 03/16/2023]
Abstract
Mitochondrial cristae expand the surface area of respiratory membranes and ultimately allow for the evolutionary scaling of respiration with cell volume across eukaryotes. The discovery of Mic60 homologs among alphaproteobacteria, the closest extant relatives of mitochondria, suggested that cristae might have evolved from bacterial intracytoplasmic membranes (ICMs). Here, we investigated the predicted structure and function of alphaproteobacterial Mic60, and a protein encoded by an adjacent gene Orf52, in two distantly related purple alphaproteobacteria, Rhodobacter sphaeroides and Rhodopseudomonas palustris. In addition, we assessed the potential physical interactors of Mic60 and Orf52 in R. sphaeroides. We show that the three α helices of mitochondrial Mic60's mitofilin domain, as well as its adjacent membrane-binding amphipathic helix, are present in alphaproteobacterial Mic60. The disruption of Mic60 and Orf52 caused photoheterotrophic growth defects, which are most severe under low light conditions, and both their disruption and overexpression led to enlarged ICMs in both studied alphaproteobacteria. We also found that alphaproteobacterial Mic60 physically interacts with BamA, the homolog of Sam50, one of the main physical interactors of eukaryotic Mic60. This interaction, responsible for making contact sites at mitochondrial envelopes, has been conserved in modern alphaproteobacteria despite more than a billion years of evolutionary divergence. Our results suggest a role for Mic60 in photosynthetic ICM development and contact site formation at alphaproteobacterial envelopes. Overall, we provide support for the hypothesis that mitochondrial cristae evolved from alphaproteobacterial ICMs and have therefore improved our understanding of the nature of the mitochondrial ancestor.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
| | - Lawrence Rudy Cadena
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Alastair T Gardiner
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Michelle M Leger
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, 08003 Catalonia, Spain
| | - Shaghayegh Sheikh
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Louise B Connell
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Tomáš Bilý
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Karel Kopejtka
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Claudio H Slamovits
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Hassan Hashimi
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic.
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Koblížek M, Hávová D, Kopejtka K, Tomasch J, Bišová K. Distribution of cycle threshold values in RT-qPCR tests during the autumn 2020 peak of the COVID-19 pandemic in the Czech Republic. Access Microbiol 2021; 3:000263. [PMID: 34712908 PMCID: PMC8549392 DOI: 10.1099/acmi.0.000263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/01/2021] [Indexed: 11/18/2022] Open
Abstract
Reverse-transcription quantitative PCR (RT-qPCR) is currently the most sensitive method to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19). We analysed 1927 samples collected in a local public hospital during the autumn 2020 peak of the pandemic in the Czech Republic. The tests were performed using the Seegene Allplex 2019-nCov assay, which simultaneously detects three SARS-CoV-2 genes. In all samples analysed, 44.5 % were negative for all three genes, and 37.6 % were undoubtedly positive, with all three viral genes being amplified. A high degree of correlation between Ct values among the genes confirmed the internal consistency of testing. Most of the positive samples were detected between the 15th and 35th cycles. We also registered a small number of samples with only one (13.2 %) or two (4.7 %) amplified genes, which may have originated from either freshly infected or already recovering patients. In addition, we did not detect any potentially false-positive samples from low-prevalence settings. Our results document that PCR testing represents a reliable and robust method for routine diagnostic detection of SARS-CoV-2.
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Affiliation(s)
- Michal Koblížek
- Institute of Microbiology of the Czech Acad. Sci., Centre Algatech, 37981 Třeboň, Czechia
| | - Daniela Hávová
- Institute of Microbiology of the Czech Acad. Sci., Centre Algatech, 37981 Třeboň, Czechia
| | - Karel Kopejtka
- Institute of Microbiology of the Czech Acad. Sci., Centre Algatech, 37981 Třeboň, Czechia
| | - Jürgen Tomasch
- Institute of Microbiology of the Czech Acad. Sci., Centre Algatech, 37981 Třeboň, Czechia
| | - Kateřina Bišová
- Institute of Microbiology of the Czech Acad. Sci., Centre Algatech, 37981 Třeboň, Czechia
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6
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Kopejtka K, Tomasch J, Zeng Y, Selyanin V, Dachev M, Piwosz K, Tichý M, Bína D, Gardian Z, Bunk B, Brinkmann H, Geffers R, Sommaruga R, Koblížek M. Simultaneous Presence of Bacteriochlorophyll and Xanthorhodopsin Genes in a Freshwater Bacterium. mSystems 2020; 5:e01044-20. [PMID: 33361324 PMCID: PMC7762795 DOI: 10.1128/msystems.01044-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023] Open
Abstract
Photoheterotrophic bacteria represent an important part of aquatic microbial communities. There exist two fundamentally different light-harvesting systems: bacteriochlorophyll-containing reaction centers or rhodopsins. Here, we report a photoheterotrophic Sphingomonas strain isolated from an oligotrophic lake, which contains complete sets of genes for both rhodopsin-based and bacteriochlorophyll-based phototrophy. Interestingly, the identified genes were not expressed when cultured in liquid organic media. Using reverse transcription quantitative PCR (RT-qPCR), RNA sequencing, and bacteriochlorophyll a quantification, we document that bacteriochlorophyll synthesis was repressed by high concentrations of glucose or galactose in the medium. Coactivation of photosynthesis genes together with genes for TonB-dependent transporters suggests the utilization of light energy for nutrient import. The photosynthetic units were formed by ring-shaped light-harvesting complex 1 and reaction centers with bacteriochlorophyll a and spirilloxanthin as the main light-harvesting pigments. The identified rhodopsin gene belonged to the xanthorhodopsin family, but it lacks salinixanthin antenna. In contrast to bacteriochlorophyll, the expression of xanthorhodopsin remained minimal under all experimental conditions tested. Since the gene was found in the same operon as a histidine kinase, we propose that it might serve as a light sensor. Our results document that photoheterotrophic Sphingomonas bacteria use the energy of light under carbon-limited conditions, while under carbon-replete conditions, they cover all their metabolic needs through oxidative phosphorylation.IMPORTANCE Phototrophic organisms are key components of many natural environments. There exist two main phototrophic groups: species that collect light energy using various kinds of (bacterio)chlorophylls and species that utilize rhodopsins. Here, we present a freshwater bacterium Sphingomonas sp. strain AAP5 which contains genes for both light-harvesting systems. We show that bacteriochlorophyll-based reaction centers are repressed by light and/or glucose. On the other hand, the rhodopsin gene was not expressed significantly under any of the experimental conditions. This may indicate that rhodopsin in Sphingomonas may have other functions not linked to bioenergetics.
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Affiliation(s)
- Karel Kopejtka
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - Jürgen Tomasch
- Research Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany
| | - Yonghui Zeng
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
- Department of Environmental Science, Aarhus University, Aarhus, Denmark
| | - Vadim Selyanin
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - Marko Dachev
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - Kasia Piwosz
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - Martin Tichý
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - David Bína
- Institute of Plant Molecular Biology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czechia
- Institute of Parasitology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Zdenko Gardian
- Institute of Plant Molecular Biology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czechia
- Institute of Parasitology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Henner Brinkmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Robert Geffers
- Research Group Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ruben Sommaruga
- Laboratory of Aquatic Photobiology and Plankton Ecology, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
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Kopejtka K, Lin Y, Jakubovičová M, Koblížek M, Tomasch J. Clustered Core- and Pan-Genome Content on Rhodobacteraceae Chromosomes. Genome Biol Evol 2020; 11:2208-2217. [PMID: 31273387 PMCID: PMC6699656 DOI: 10.1093/gbe/evz138] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2019] [Indexed: 12/18/2022] Open
Abstract
In Bacteria, chromosome replication starts at a single origin of replication and proceeds on both replichores. Due to its asymmetric nature, replication influences chromosome structure and gene organization, mutation rate, and expression. To date, little is known about the distribution of highly conserved genes over the bacterial chromosome. Here, we used a set of 101 fully sequenced Rhodobacteraceae representatives to analyze the relationship between conservation of genes within this family and their distance from the origin of replication. Twenty-two of the analyzed species had core genes clustered significantly closer to the origin of replication with representatives of the genus Celeribacter being the most apparent example. Interestingly, there were also eight species with the opposite organization. In particular, Rhodobaca barguzinensis and Loktanella vestfoldensis showed a significant increase of core genes with distance from the origin of replication. The uneven distribution of low-conserved regions is in particular pronounced for genomes in which the halves of one replichore differ in their conserved gene content. Phage integration and horizontal gene transfer partially explain the scattered nature of Rhodobacteraceae genomes. Our findings lay the foundation for a better understanding of bacterial genome evolution and the role of replication therein.
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Affiliation(s)
- Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Center Algatech, Institute of Microbiology CAS, Třeboň, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Yan Lin
- Department of Physics, School of Science, Tianjin University, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Markéta Jakubovičová
- Faculty of Information Technology, Czech Technical University in Prague, Czech Republic
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Center Algatech, Institute of Microbiology CAS, Třeboň, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Piwosz K, Shabarova T, Tomasch J, Šimek K, Kopejtka K, Kahl S, Pieper DH, Koblížek M. Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS). ISME J 2018; 12:2640-2654. [PMID: 29980795 PMCID: PMC6194029 DOI: 10.1038/s41396-018-0213-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 06/01/2018] [Accepted: 06/09/2018] [Indexed: 01/07/2023]
Abstract
The growth rate is a fundamental characteristic of bacterial species, determining its contributions to the microbial community and carbon flow. High-throughput sequencing can reveal bacterial diversity, but its quantitative inaccuracy precludes estimation of abundances and growth rates from the read numbers. Here, we overcame this limitation by normalizing Illumina-derived amplicon reads using an internal standard: a constant amount of Escherichia coli cells added to samples just before biomass collection. This approach made it possible to reconstruct growth curves for 319 individual OTUs during the grazer-removal experiment conducted in a freshwater reservoir Římov. The high resolution data signalize significant functional heterogeneity inside the commonly investigated bacterial groups. For instance, many Actinobacterial phylotypes, a group considered to harbor slow-growing defense specialists, grew rapidly upon grazers' removal, demonstrating their considerable importance in carbon flow through food webs, while most Verrucomicrobial phylotypes were particle associated. Such differences indicate distinct life strategies and roles in food webs of specific bacterial phylotypes and groups. The impact of grazers on the specific growth rate distributions supports the hypothesis that bacterivory reduces competition and allows existence of diverse bacterial communities. It suggests that the community changes were driven mainly by abundant, fast, or moderately growing, and not by rare fast growing, phylotypes. We believe amplicon read normalization using internal standard (ARNIS) can shed new light on in situ growth dynamics of both abundant and rare bacteria.
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Affiliation(s)
- Kasia Piwosz
- Center Algatech, Institute of Microbiology CAS, Novohradská 237, 37981, Třeboň, Czech Republic
| | - Tanja Shabarova
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, 37005, Česke Budějovice, Czech Republic
| | - Jürgen Tomasch
- Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Karel Šimek
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, 37005, Česke Budějovice, Czech Republic
| | - Karel Kopejtka
- Center Algatech, Institute of Microbiology CAS, Novohradská 237, 37981, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, CZ-37005, České Budějovice, Czech Republic
| | - Silke Kahl
- Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Dietmar H Pieper
- Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology CAS, Novohradská 237, 37981, Třeboň, Czech Republic.
- Faculty of Science, University of South Bohemia in České Budějovice, CZ-37005, České Budějovice, Czech Republic.
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Strunecký O, Kopejtka K, Goecke F, Tomasch J, Lukavský J, Neori A, Kahl S, Pieper DH, Pilarski P, Kaftan D, Koblížek M. High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy, cultivation, single-cell PCR and amplicon sequencing. Extremophiles 2018; 23:35-48. [PMID: 30284641 DOI: 10.1007/s00792-018-1058-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022]
Abstract
Genotypic and morphological diversity of cyanobacteria in the Rupite hot spring (Bulgaria) was investigated by means of optical microscopy, cultivation, single-cell PCR, and 16S rRNA gene amplicon sequencing. Altogether, 34 sites were investigated along the 71-39 °C temperature gradient. Analysis of samples from eight representative sites shown that Illumina, optical microscopy, and Roche 454 identified 72, 45 and 19% respective occurrences of all cumulatively present taxa. Optical microscopy failed to detect species of minor occurrence; whereas, amplicon sequencing technologies suffered from failed primer annealing and the presence of species with extensive extracellular polysaccharides production. Amplicon sequencing of the 16S rRNA gene V5-V6 region performed by Illumina identified the cyanobacteria most reliably to the generic level. Nevertheless, only the combined use of optical microscopy, cultivation and sequencing methods allowed for reliable estimate of the cyanobacterial diversity. Here, we show that Rupite hot-spring system hosts one of the richest cyanobacterial flora reported from a single site above 50 °C. Chlorogloeopsis sp. was the most abundant at the highest temperature (68 °C), followed by Leptolyngbya boryana, Thermoleptolyngbya albertanoae, Synechococcus bigranulatus, Oculatella sp., and Desertifilum sp. thriving above 60 °C, while Leptolyngbya geysericola, Geitlerinema splendidum, and Cyanobacterium aponinum were found above 50 °C.
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Affiliation(s)
- Otakar Strunecký
- Institute of Aquaculture, CENAKVA, Faculty of Fisheries and Protection of Waters, University of South Bohemia, 37005, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia, 37005, České Budějovice, Czech Republic.
| | - Karel Kopejtka
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic
| | - Franz Goecke
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic.,Department of Plant and Environmental Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Jürgen Tomasch
- Group Microbial Communication, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Jaromír Lukavský
- Department of Plant Ecology, Institute of Botany CAS, 37901, Třeboň, Czech Republic
| | - Amir Neori
- Israel Oceanographic and Limnological Research Ltd., National Center for Mariculture, 88112, Eilat, Israel
| | - Silke Kahl
- Group Microbial Interactions and Processes, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Dietmar H Pieper
- Group Microbial Interactions and Processes, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Plamen Pilarski
- Institute of Plant Physiology and Genetics BAS, 1113, Sofia, Bulgaria
| | - David Kaftan
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic.,Faculty of Science, University of South Bohemia, 37005, České Budějovice, Czech Republic
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic
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10
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Kopejtka K, Tomasch J, Bunk B, Spröer C, Wagner-Döbler I, Koblížek M. The complete genome sequence of Rhodobaca barguzinensis alga05 (DSM 19920) documents its adaptation for life in soda lakes. Extremophiles 2018; 22:839-849. [PMID: 30022245 DOI: 10.1007/s00792-018-1041-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/09/2018] [Indexed: 12/19/2022]
Abstract
Soda lakes, with their high salinity and high pH, pose a very challenging environment for life. Microorganisms living in these harsh conditions have had to adapt their physiology and gene inventory. Therefore, we analyzed the complete genome of the haloalkaliphilic photoheterotrophic bacterium Rhodobaca barguzinensis strain alga05. It consists of a 3,899,419 bp circular chromosome with 3624 predicted coding sequences. In contrast to most of Rhodobacterales, this strain lacks any extrachromosomal elements. To identify the genes responsible for adaptation to high pH, we compared the gene inventory in the alga05 genome with genomes of 17 reference strains belonging to order Rhodobacterales. We found that all haloalkaliphilic strains contain the mrpB gene coding for the B subunit of the MRP Na+/H+ antiporter, while this gene is absent in all non-alkaliphilic strains, which indicates its importance for adaptation to high pH. Further analysis showed that alga05 requires organic carbon sources for growth, but it also contains genes encoding the ethylmalonyl-CoA pathway for CO2 fixation. Remarkable is the genetic potential to utilize organophosphorus compounds as a source of phosphorus. In summary, its genetic inventory indicates a large flexibility of the alga05 metabolism, which is advantageous in rapidly changing environmental conditions in soda lakes.
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Affiliation(s)
- Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Center Algatech, Institute of Microbiology CAS, Třeboň, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Boyke Bunk
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Irene Wagner-Döbler
- Institute of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Center Algatech, Institute of Microbiology CAS, Třeboň, Czech Republic. .,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
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11
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Kopejtka K, Tomasch J, Zeng Y, Tichý M, Sorokin DY, Koblížek M. Genomic Analysis of the Evolution of Phototrophy among Haloalkaliphilic Rhodobacterales. Genome Biol Evol 2017; 9:1950-1962. [PMID: 28810712 PMCID: PMC5553392 DOI: 10.1093/gbe/evx141] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2017] [Indexed: 11/12/2022] Open
Abstract
A characteristic feature of the order Rhodobacterales is the presence of a large number of photoautotrophic and photoheterotrophic species containing bacteriochlorophyll. Interestingly, these phototrophic species are phylogenetically mixed with chemotrophs. To better understand the origin of such variability, we sequenced the genomes of three closely related haloalkaliphilic species, differing in their phototrophic capacity and oxygen preference: the photoheterotrophic and facultatively anaerobic bacterium Rhodobaca barguzinensis, aerobic photoheterotroph Roseinatronobacter thiooxidans, and aerobic heterotrophic bacterium Natronohydrobacter thiooxidans. These three haloalcaliphilic species are phylogenetically related and share many common characteristics with the Rhodobacter species, forming together the Rhodobacter-Rhodobaca (RR) group. A comparative genomic analysis showed close homology of photosynthetic proteins and similarity in photosynthesis gene organization among the investigated phototrophic RR species. On the other hand, Rhodobaca barguzinensis and Roseinatronobacter thiooxidans lack an inorganic carbon fixation pathway and outer light-harvesting genes. This documents the reduction of their photosynthetic machinery towards a mostly photoheterotrophic lifestyle. Moreover, both phototrophic species contain 5-aminolevulinate synthase (encoded by the hemA gene) incorporated into their photosynthesis gene clusters, which seems to be a common feature of all aerobic anoxygenic phototrophic Alphaproteobacteria. Interestingly, the chrR-rpoE (sigma24) operon, which is part of singlet oxygen defense in phototrophic species, was found in the heterotrophic strain Natronohydrobacter thiooxidans. This suggests that this organism evolved from a photoheterotrophic ancestor through the loss of its photosynthesis genes. The overall evolution of phototrophy among the haloalkaliphilic members of the RR group is discussed.
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Affiliation(s)
- Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, CAS, Center Algatech, Třeboň, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jürgen Tomasch
- Research Group Microbial Communication, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yonghui Zeng
- Aarhus Institute of Advanced Studies, Aarhus, Denmark
| | - Martin Tichý
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, CAS, Center Algatech, Trebon, Czech Republic
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, The Netherlands
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, CAS, Center Algatech, Třeboň, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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