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Freches A, Fradinho JC. The biotechnological potential of the Chloroflexota phylum. Appl Environ Microbiol 2024; 90:e0175623. [PMID: 38709098 PMCID: PMC11218635 DOI: 10.1128/aem.01756-23] [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] [Indexed: 05/07/2024] Open
Abstract
In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of Chloroflexota, spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled Chloroflexota to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the Chloroflexota phylum, specific members exemplify the diverse capabilities of these microorganisms: Chloroflexus aurantiacus showcases adaptability through its thermophilic and phototrophic growth, whereas members of the Anaerolineae class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of Chloroflexota must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of Chloroflexota in such environments with the potential application of their metabolisms in biotechnological approaches.
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Affiliation(s)
- André Freches
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, Portugal
- Department of Chemistry, UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Joana Costa Fradinho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, Portugal
- Department of Chemistry, UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
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2
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Doré H, Eisenberg AR, Junkins EN, Leventhal GE, Ganesh A, Cordero OX, Paul BG, Valentine DL, O’Malley MA, Wilbanks EG. Targeted hypermutation of putative antigen sensors in multicellular bacteria. Proc Natl Acad Sci U S A 2024; 121:e2316469121. [PMID: 38354254 PMCID: PMC10907252 DOI: 10.1073/pnas.2316469121] [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: 09/29/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Diversity-generating retroelements (DGRs) are used by bacteria, archaea, and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remain elusive. We find that 82% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 as an example, we characterized nine distinct DGR loci capable of generating 10282 different combinations of target proteins. With environmental metagenomes from individual Thiohalocapsa aggregates, we show that most of PB-PSB1's DGR target genes are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In Thiohalocapsa PB-PSB1 and other bacteria hosting this lineage of cellular DGRs, the diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified targets act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia, though this remains to be experimentally tested. These findings could have implications for understanding the evolution of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans.
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Affiliation(s)
- H. Doré
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
| | - A. R. Eisenberg
- Department of Chemical Engineering, University of California, Santa Barbara, CA93106
| | - E. N. Junkins
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
| | - G. E. Leventhal
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Anakha Ganesh
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA02543
| | - O. X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - B. G. Paul
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA02543
| | - D. L. Valentine
- Department of Earth Science, University of California, Santa Barbara, CA93106
- Marine Science Institute, University of California, Santa Barbara, CA93106
| | - M. A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA93106
- Department of Bioengineering, University of California, Santa Barbara, CA93106
| | - E. G. Wilbanks
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
- Department of Bioengineering, University of California, Santa Barbara, CA93106
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Carvalho VCF, Fradinho JC, Oehmen A, Reis MAM. Long term operation of a phototrophic biological nutrient removal system: Impact of CO 2 concentration and light exposure on process performance. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 334:117490. [PMID: 36801686 DOI: 10.1016/j.jenvman.2023.117490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
The utilization of non-aerated microalgae-bacterial consortia for phototrophic biological nutrient removal (photo-BNR) has emerged as an alternative to conventional wastewater treatment. Photo-BNR systems are operated under transient illumination, with alternating dark-anaerobic, light-aerobic and dark-anoxic conditions. A deep understanding of the impact of operational parameters on the microbial consortium and respective nutrient removal efficiency in photo-BNR systems is required. The present study evaluates, for the first time, the long-term operation (260 days) of a photo-BNR system, fed with a COD:N:P mass ratio of 7.5:1:1, to understand its operational limitations. In particular, different CO2 concentrations in the feed (between 22 and 60 mg C/L of Na2CO3) and variations of light exposure (from 2.75 h to 5.25 h per 8 h cycle) were studied to determine their impact on key parameters, like oxygen production and availability of polyhydroxyalkanoates (PHA), on the performance of anoxic denitrification by polyphosphate accumulating organisms. Results indicate that oxygen production was more dependent on the light availability than on the CO2 concentration. Also, under operational conditions with a COD:Na2CO3 ratio of 8.3 mg COD/mg C and an average light availability of 5.4 ± 1.3 W h/g TSS, no internal PHA limitation was observed, and 95 ± 7%, 92 ± 5% and 86 ± 5% of removal efficiency could be achieved for phosphorus, ammonia and total nitrogen, respectively. 81 ± 1.7% of the ammonia was assimilated into the microbial biomass and 19 ± 1.7% was nitrified, showing that biomass assimilation was the main N removal mechanism taking place in the bioreactor. Overall, the photo-BNR system presented a good settling capacity (SVI ∼60 mL/g TSS) and was able to remove 38 ± 3.3 mg P/L and 33 ± 1.7 mg N/L, highlighting its potential for achieving wastewater treatment without the need of aeration.
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Affiliation(s)
- V C F Carvalho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal
| | - J C Fradinho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal.
| | - A Oehmen
- School of Chemical Engineering, University of Queensland, Brisbane, QLD, 4072, Australia
| | - M A M Reis
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516, Caparica, Portugal
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Bryantseva IA, Grouzdev DS, Krutkina MS, Ashikhmin AA, Kostrikina NA, Koziaeva VV, Gorlenko VM. 'Candidatus Chloroploca mongolica' sp. nov. a new mesophilic filamentous anoxygenic phototrophic bacterium. FEMS Microbiol Lett 2021; 368:6352337. [PMID: 34390245 DOI: 10.1093/femsle/fnab107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/12/2021] [Indexed: 12/25/2022] Open
Abstract
A mesophilic filamentous anoxygenic phototrophic bacterium, designated M50-1, was isolated from a microbial mat of the Chukhyn Nur soda lake (northeastern Mongolia) with salinity of 5-14 g/L and pH 8.0-9.3. The organism is a strictly anaerobic phototrophic bacterium, which required sulfide for phototrophic growth. The cells formed short undulate trichomes surrounded by a thin sheath and containing gas vesicles. Motility of the trichomes was not observed. The cells contained chlorosomes. The antenna pigments were bacteriochlorophyll d and β- and γ-carotenes. Analysis of the genome assembled from the metagenome of the enrichment culture revealed all the enzymes of the 3-hydroxypropionate bi-cycle for autotrophic CO2 assimilation. The genome also contained the genes encoding a type IV sulfide:quinone oxidoreductase (sqrX). The organism had no nifHDBK genes, encoding the proteins of the nitrogenase complex responsible for dinitrogen fixation. The DNA G + C content was 58.6%. The values for in silico DNA‒DNA hybridization and average nucleotide identity between M50-1 and a closely related bacterium 'Ca. Chloroploca asiatica' B7-9 containing bacteriochlorophyll c were 53.4% and 94.0%, respectively, which corresponds to interspecies differences. Classification of the filamentous anoxygenic phototrophic bacterium M50-1 as a new 'Ca. Chloroploca' species was proposed, with the species name 'Candidatus Chloroploca mongolica' sp. nov.
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Affiliation(s)
- Irina A Bryantseva
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Denis S Grouzdev
- SciBear LLC, Tartu mnt 67/1-13b, Kesklinna linnaosa, Tallin 10115, Estonia
| | - Maria S Krutkina
- SciBear LLC, Tartu mnt 67/1-13b, Kesklinna linnaosa, Tallin 10115, Estonia
| | - Aleksandr A Ashikhmin
- Institute of Basic Biological Problems of Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of Russian Academy of Sciences', Institutskaya ave. 2, Pushchino 142290, Russian Federation
| | - Nadezda A Kostrikina
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Veronika V Koziaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Vladimir M Gorlenko
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
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Gorlenko VM, Bryantseva IA, Samylina OS, Ashikhmin AA, Sinetova MA, Kostrikina NA, Kozyaeva VV. Filamentous Anoxygenic Phototrophic Bacteria in Microbial Communities of the Kulunda Steppe Soda Lakes (Altai Krai, Russia). Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720060053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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‘Candidatus Oscillochloris kuznetsovii’ a novel mesophilic filamentous anoxygenic phototrophic Chloroflexales bacterium from Arctic coastal environments. FEMS Microbiol Lett 2020; 367:5917981. [DOI: 10.1093/femsle/fnaa158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022] Open
Abstract
ABSTRACT
Chloroflexales bacteria are mostly known as filamentous anoxygenic phototrophs that thrive as members of the microbial communities of hot spring cyanobacterial mats. Recently, we described many new Chloroflexales species from non-thermal environments and showed that mesophilic Chloroflexales are more diverse than previously expected. Most of these species were isolated from aquatic environments of mid-latitudes. Here, we present the comprehensive characterization of a new filamentous multicellular anoxygenic phototrophic Chloroflexales bacterium from an Arctic coastal environment (Kandalaksha Gulf, the White Sea). Phylogenomic analysis and 16S rRNA phylogeny indicated that this bacterium belongs to the Oscillochloridaceae family as a new species. We propose that this species be named ‘Candidatus Oscillochloris kuznetsovii’. The genomes of this species possessed genes encoding sulfide:quinone reductase, the nitrogenase complex and the Calvin cycle, which indicate potential for photoautotrophic metabolism. We observed only mesophilic anaerobic anoxygenic phototrophic growth of this novel bacterium. Electron microphotography showed the presence of chlorosomes, polyhydroxyalkanoate-like granules and polyphosphate-like granules in the cells. High-performance liquid chromatography also revealed the presence of bacteriochlorophylls a, c and d as well as carotenoids. In addition, we found that this bacterium is present in benthic microbial communities of various coastal environments of the Kandalaksha Gulf.
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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8
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Gaisin VA, Kooger R, Grouzdev DS, Gorlenko VM, Pilhofer M. Cryo-Electron Tomography Reveals the Complex Ultrastructural Organization of Multicellular Filamentous Chloroflexota ( Chloroflexi) Bacteria. Front Microbiol 2020; 11:1373. [PMID: 32670237 PMCID: PMC7332563 DOI: 10.3389/fmicb.2020.01373] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/27/2020] [Indexed: 11/13/2022] Open
Abstract
The cell biology of Chloroflexota is poorly studied. We applied cryo-focused ion beam milling and cryo-electron tomography to study the ultrastructural organization of thermophilic Roseiflexus castenholzii and Chloroflexus aggregans, and mesophilic “Ca. Viridilinea mediisalina.” These species represent the three main lineages within a group of multicellular filamentous anoxygenic phototrophic Chloroflexota bacteria belonging to the Chloroflexales order. We found surprising structural complexity in the Chloroflexales. As with filamentous cyanobacteria, cells of C. aggregans and “Ca. Viridilinea mediisalina” share the outer membrane-like layers of their intricate multilayer cell envelope. Additionally, cells of R. castenholzii and “Ca. Viridilinea mediisalina” are connected by septal channels that resemble cyanobacterial septal junctions. All three strains possess long pili anchored close to cell-to-cell junctions, a morphological feature comparable to that observed in cyanobacteria. The cytoplasm of the Chloroflexales bacteria is crowded with intracellular organelles such as different types of storage granules, membrane vesicles, chlorosomes, gas vesicles, chemoreceptor-like arrays, and cytoplasmic filaments. We observed a higher level of complexity in the mesophilic strain compared to the thermophilic strains with regards to the composition of intracellular bodies and the organization of the cell envelope. The ultrastructural details that we describe in these Chloroflexales bacteria will motivate further cell biological studies, given that the function and evolution of the many discovered morphological traits remain enigmatic in this diverse and widespread bacterial group.
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Affiliation(s)
- Vasil A Gaisin
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.,Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Romain Kooger
- Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Denis S Grouzdev
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Vladimir M Gorlenko
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Martin Pilhofer
- Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
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Gaisin VA, Burganskaya EI, Grouzdev DS, Osipova NS, Ashikhmin AA, Sinetova MA, Krutkina MS, Bryantseva IA, Sukhacheva MV, Kochetkova TV, Koziaeva VV, Kalashnikov AM, Gorlenko VM. ‘Candidatus Oscillochloris fontis’: a novel mesophilic phototrophic Chloroflexota bacterium belonging to the ubiquitous Oscillochloris genus. FEMS Microbiol Lett 2019; 366:5485639. [DOI: 10.1093/femsle/fnz097] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 05/02/2019] [Indexed: 01/02/2023] Open
Affiliation(s)
- Vasil A Gaisin
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Ekaterina I Burganskaya
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Denis S Grouzdev
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Natalya S Osipova
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Aleksandr A Ashikhmin
- Institute of Basic Biological Problems of Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences”, Institutskaya ave. 2, Pushchino, 142290, Russian Federation
| | - Maria A Sinetova
- К.А. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Botanicheskaya St. 35, Moscow, 127276, Russian Federation
| | - Maria S Krutkina
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Irina A Bryantseva
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Marina V Sukhacheva
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Tatiana V Kochetkova
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Veronika V Koziaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Aleksandr M Kalashnikov
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Vladimir M Gorlenko
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow, 119071, Russian Federation
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Gaisin VA, Burganskaya EI, Grouzdev DS, Ashikhmin AA, Kostrikina NA, Bryantseva IA, Koziaeva VV, Gorlenko VM. ‘Candidatus Viridilinea mediisalina’, a novel phototrophic Chloroflexi bacterium from a Siberian soda lake. FEMS Microbiol Lett 2019; 366:5364544. [DOI: 10.1093/femsle/fnz043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 02/22/2019] [Indexed: 12/23/2022] Open
Affiliation(s)
- Vasil A Gaisin
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Ekaterina I Burganskaya
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Denis S Grouzdev
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Aleksandr A Ashikhmin
- Institute of Basic Biological Problems of Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences”, Institutskaya ave. 2, Pushchino 142290, Russian Federation
| | - Nadezda A Kostrikina
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Irina A Bryantseva
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Veronika V Koziaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
| | - Vladimir M Gorlenko
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky ave. 33, bld. 2, Moscow 119071, Russian Federation
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11
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Genome Sequence of " Candidatus Viridilinea halotolerans" Chok-6, Isolated from a Saline Sulfide-Rich Spring. Microbiol Resour Announc 2019; 8:MRA01614-18. [PMID: 30701256 PMCID: PMC6346205 DOI: 10.1128/mra.01614-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 12/17/2018] [Indexed: 12/25/2022] Open
Abstract
The draft genome sequence of the green filamentous anoxygenic phototrophic (FAP) bacterium “Candidatus Viridilinea halotolerans” strain Chok-6, isolated from a cold saline sulfide-rich spring near Lake Chokrak, is presented. The genome sequence is annotated for elucidation of the taxonomic position of Chok-6 and to extend the public genome database. The draft genome sequence of the green filamentous anoxygenic phototrophic (FAP) bacterium “Candidatus Viridilinea halotolerans” strain Chok-6, isolated from a cold saline sulfide-rich spring near Lake Chokrak, is presented. The genome sequence is annotated for elucidation of the taxonomic position of Chok-6 and to extend the public genome database.
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12
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Grouzdev DS, Rysina MS, Bryantseva IA, Gorlenko VM, Gaisin VA. Draft genome sequences of ' Candidatus Chloroploca asiatica' and ' Candidatus Viridilinea mediisalina', candidate representatives of the Chloroflexales order: phylogenetic and taxonomic implications. Stand Genomic Sci 2018; 13:24. [PMID: 30338027 PMCID: PMC6180586 DOI: 10.1186/s40793-018-0329-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 09/28/2018] [Indexed: 11/10/2022] Open
Abstract
'Candidatus Chloroploca asiatica' B7-9 and 'Candidatus Viridilinea mediisalina' Kir15-3F are mesophilic filamentous anoxygenic phototrophic bacteria from alkaline aquatic environments. Both bacteria became available in the last few years and only in stable enrichment culture. In this study, we report the draft genomic sequences of 'Ca. Chloroploca asiatica' B7-9 and 'Ca. Viridilinea mediisalina' Kir15-3F, which were assembled from metagenomes of their cultures with a fold coverage 86.3× and 163.8×, respectively. The B7-9 (5.8 Mb) and the Kir15-3F (5.6 Mb) draft genome harbors 4818 and 4595 predicted protein-coding genes, respectively. In this article, we analyzed the phylogeny of representatives of the Chloroflexineae suborder in view of the appearance of new genomic data. These data were used for the revision of earlier published group-specific conserved signature indels and for searching for novel signatures for taxons in the Chloroflexineae suborder.
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Affiliation(s)
- Denis S. Grouzdev
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria S. Rysina
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
| | - Irina A. Bryantseva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir M. Gorlenko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vasil A. Gaisin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
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Thiel V, Tank M, Bryant DA. Diversity of Chlorophototrophic Bacteria Revealed in the Omics Era. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:21-49. [PMID: 29505738 DOI: 10.1146/annurev-arplant-042817-040500] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Because of recent advances in omics methodologies, knowledge of chlorophototrophy (i.e., chlorophyll-based phototrophy) in bacteria has rapidly increased. Chlorophototrophs currently are known to occur in seven bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Other organisms that can produce chlorophylls and photochemical reaction centers may still be undiscovered. Here we summarize the current status of the taxonomy and phylogeny of chlorophototrophic bacteria as revealed by genomic methods. In specific cases, we briefly describe important ecophysiological and metabolic insights that have been gained from the application of genomic methods to these bacteria. In the 20 years since the completion of the Synechocystis sp. PCC 6803 genome in 1996, approximately 1,100 genomes have been sequenced, which represents nearly the complete diversity of known chlorophototrophic bacteria. These data are leading to new insights into many important processes, including photosynthesis, nitrogen and carbon fixation, cellular differentiation and development, symbiosis, and ecosystem functionality.
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Affiliation(s)
- Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; ,
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; ,
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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Benthic phototrophic community from Kiran soda lake, south-eastern Siberia. Extremophiles 2017; 22:211-220. [PMID: 29270850 DOI: 10.1007/s00792-017-0989-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
Abstract
Phototrophic bacterial mats from Kiran soda lake (south-eastern Siberia) were studied using integrated approach including analysis of the ion composition of water, pigments composition, bacterial diversity and the vertical distribution of phototrophic microorganisms in the mats. Bacterial diversity was investigated using microscopic examination, 16S rRNA gene Illumina sequencing and culturing methods. The mats were formed as a result of decomposition of sedimented planktonic microorganisms, among which cyanobacteria of the genus Arthrospira predominated. Cyanobacteria were the largest part of phototrophs in the mats, but anoxygenic phototrophs were significant fraction. The prevailing species of the anoxygenic phototrophic bacteria are typical for soda lakes. The mats harbored aerobic anoxygenic phototrophic bacteria, purple sulfur and non-sulfur bacteria, as well as new filamentous phototrophic Chloroflexi. New strains of Thiocapsa sp. Kir-1, Ectothiorhodospira sp. Kir-2 and Kir-4, Thiorhodospira sp. Kir-3 and novel phototrophic Chloroflexi bacterium Kir15-3F were isolated and identified.
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15
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Gaisin VA, Kalashnikov AM, Sukhacheva MV, Namsaraev ZB, Barhutova DD, Gorlenko VM, Kuznetsov BB. Filamentous anoxygenic phototrophic bacteria from cyanobacterial mats of Alla hot springs (Barguzin Valley, Russia). Extremophiles 2015; 19:1067-76. [PMID: 26290358 DOI: 10.1007/s00792-015-0777-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 07/23/2015] [Indexed: 11/25/2022]
Abstract
Alkaline hydrotherms of the Baikal rift zone are unique systems to study the diversity of thermophilic bacteria. In this study, we present data on the phototrophic bacterial community of cyanobacterial mats from the alkaline Alla hot spring. Using a clonal analysis approach, this study evaluated the species diversity, the proportion of oxygenic and anoxygenic phototrophs and their distribution between various areas of the spring. Novel group-specific PCR primers were designed and applied to detect representatives of the Chloroflexus and Roseiflexus genera in mat samples. For the first time, the presence of Roseiflexus-like bacteria was detected in the Baikal rift zone.
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Affiliation(s)
- Vasil A Gaisin
- Centre Bioengineering RAS, Prospekt 60-Letiya Oktyabrya, 7/1, 117312, Moscow, Russia.
| | - Alexander M Kalashnikov
- Winogradsky Institute of Microbiology RAS, Prospekt 60-Letiya Oktyabrya, 7/2, 117312, Moscow, Russia
| | - Marina V Sukhacheva
- Centre Bioengineering RAS, Prospekt 60-Letiya Oktyabrya, 7/1, 117312, Moscow, Russia
| | - Zorigto B Namsaraev
- Winogradsky Institute of Microbiology RAS, Prospekt 60-Letiya Oktyabrya, 7/2, 117312, Moscow, Russia
- National Research Centre "Kurchatov Institute", Akademika Kurchatova pl., 1, 123182, Moscow, Russia
| | - Darima D Barhutova
- Institute of General and Experimental Biology RAS, Sakhyanovoy st., 6, 670047, Ulan-Ude, Russia
| | - Vladimir M Gorlenko
- Winogradsky Institute of Microbiology RAS, Prospekt 60-Letiya Oktyabrya, 7/2, 117312, Moscow, Russia
| | - Boris B Kuznetsov
- Centre Bioengineering RAS, Prospekt 60-Letiya Oktyabrya, 7/1, 117312, Moscow, Russia.
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