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Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota. Nat Microbiol 2023; 8:727-744. [PMID: 36928026 PMCID: PMC10066038 DOI: 10.1038/s41564-022-01319-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 12/30/2022] [Indexed: 03/18/2023]
Abstract
Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites.
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Kolinko S, Richter M, Glöckner FO, Brachmann A, Schüler D. Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes. Environ Microbiol 2015; 18:21-37. [PMID: 26060021 DOI: 10.1111/1462-2920.12907] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/10/2015] [Accepted: 05/14/2015] [Indexed: 11/26/2022]
Abstract
While magnetosome biosynthesis within the magnetotactic Proteobacteria is increasingly well understood, much less is known about the genetic control within deep-branching phyla, which have a unique ultrastructure and biosynthesize up to several hundreds of bullet-shaped magnetite magnetosomes arranged in multiple bundles of chains, but have no cultured representatives. Recent metagenomic analysis identified magnetosome genes in the genus 'Candidatus Magnetobacterium' homologous to those in Proteobacteria. However, metagenomic analysis has been limited to highly abundant members of the community, and therefore only little is known about the magnetosome biosynthesis, ecophysiology and metabolic capacity in deep-branching MTB. Here we report the analysis of single-cell derived draft genomes of three deep-branching uncultivated MTB. Single-cell sorting followed by whole genome amplification generated draft genomes of Candidatus Magnetobacterium bavaricum and Candidatus Magnetoovum chiemensis CS-04 of the Nitrospirae phylum. Furthermore, we present the first, nearly complete draft genome of a magnetotactic representative from the candidate phylum Omnitrophica, tentatively named Candidatus Omnitrophus magneticus SKK-01. Besides key metabolic features consistent with a common chemolithoautotrophic lifestyle, we identified numerous, partly novel genes most likely involved in magnetosome biosynthesis of bullet-shaped magnetosomes and their arrangement in multiple bundles of chains.
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Affiliation(s)
- Sebastian Kolinko
- Department of Biology I, LMU Biozentrum, Ludwig-Maximilians University Munich, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Michael Richter
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | - Frank-Oliver Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany.,Department of Life Sciences & Chemistry, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany
| | - Andreas Brachmann
- Department of Biology I, LMU Biozentrum, Ludwig-Maximilians University Munich, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany
| | - Dirk Schüler
- Department of Biology I, LMU Biozentrum, Ludwig-Maximilians University Munich, Großhaderner Str. 2-4, Planegg-Martinsried, 82152, Germany.,Department of Microbiology, University Bayreuth, Bayreuth, Germany
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Fernández ML, Granados-Chinchilla F, Rodríguez C. A single exposure of sediment sulphate-reducing bacteria to oxytetracycline concentrations relevant to aquaculture enduringly disturbed their activity, abundance and community structure. J Appl Microbiol 2015; 119:354-64. [PMID: 25973855 DOI: 10.1111/jam.12846] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/23/2015] [Accepted: 05/08/2015] [Indexed: 11/28/2022]
Abstract
AIM Although feed medicated with antibiotics is widely used in animal production to prevent and treat bacterial infections, the effect of these drugs on nontarget anaerobic bacteria is unknown. We aimed to clarify whether a single exposure of sulphate-reducing bacteria (SRB) from a tilapia pond to oxytetracycline (OTC) concentrations relevant to aquaculture impacts their function, abundance and community structure. METHODS AND RESULTS To demonstrate changes in SO4(2-) content, SRB abundance, dsrB copy number and SRB diversity, sediment mesocosms were spiked with 5, 25, 50 and 75 mg OTC kg(-1) and examined for 30 days by means of ion chromatography, qPCR, cultivation and fluorescent in situ hybridization (FISH). On day 3, we measured higher SO4(2-) concentrations (ca. two-fold) and a reduction in dsrB copy numbers of approximately 50% in the treatments compared to the controls. After 30 days, a subtle yet measurable enrichment of bacteria from the order Desulfovibrionales occurred in mesocosms receiving ≥ 50 mg OTC kg(-1), notwithstanding that SRB counts decreased two orders of magnitude. OTC was dynamically and reversibly converted into 4-epioxytetracycline and other related compounds in a dose-dependent manner during the experiment. CONCLUSIONS A single exposure to rather high OTC concentrations triggered functional and structural changes in a SRB community that manifested quickly and persisted for a month. SIGNIFICANCE AND IMPACT OF THE STUDY This study improves our limited knowledge on the ecotoxicology of antibiotics in anaerobic environments.
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Affiliation(s)
- M L Fernández
- Instituto Clodomiro Picado, Universidad de Costa Rica, Coronado, San José, Costa Rica
| | - F Granados-Chinchilla
- Centro de Investigación en Nutrición Animal (CINA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, Costa Rica
| | - C Rodríguez
- Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, Costa Rica.,Facultad de Microbiología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, Costa Rica
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Abstract
Despite its reactivity and hence toxicity to living cells, sulfite is readily converted by various microorganisms using distinct assimilatory and dissimilatory metabolic routes. In respiratory pathways, sulfite either serves as a primary electron donor or terminal electron acceptor (yielding sulfate or sulfide, respectively), and its conversion drives electron transport chains that are coupled to chemiosmotic ATP synthesis. Notably, such processes are also seen to play a general role in sulfite detoxification, which is assumed to have an evolutionary ancient origin. The diversity of sulfite conversion is reflected by the fact that the range of microbial sulfite-converting enzymes displays different cofactors such as siroheme, heme c, or molybdopterin. This chapter aims to summarize the current knowledge of microbial sulfite metabolism and focuses on sulfite catabolism. The structure and function of sulfite-converting enzymes and the emerging picture of the modular architecture of the corresponding respiratory/detoxifying electron transport chains is emphasized.
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Affiliation(s)
- Jörg Simon
- Department of Biology, Microbial Energy Conversion and Biotechnology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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Parey K, Fritz G, Ermler U, Kroneck PMH. Conserving energy with sulfate around 100 °C – structure and mechanism of key metal enzymes in hyperthermophilic Archaeoglobus fulgidus. Metallomics 2013; 5:302-17. [DOI: 10.1039/c2mt20225e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Dissimilatory sulfate and sulfur reduction evolved billions of years ago and while the bacteria and archaea that use this unique metabolism employ a variety of electron donors, H(2) is most commonly used as the energy source. These prokaryotes use multiheme c-type proteins to shuttle electrons from electron donors, and electron transport complexes presumed to contain b-type hemoproteins contribute to proton charging of the membrane. Numerous sulfate and sulfur reducers use an alternate pathway for heme synthesis and, frequently, uniquely specific axial ligands are used to secure c-type heme to the protein. This review presents some of the types and functional activities of hemoproteins involved in these two dissimilatory reduction pathways.
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Structure of the Dissimilatory Sulfite Reductase from the Hyperthermophilic Archaeon Archaeoglobus fulgidus. J Mol Biol 2008; 379:1063-74. [DOI: 10.1016/j.jmb.2008.04.027] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 04/03/2008] [Accepted: 04/10/2008] [Indexed: 11/21/2022]
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Qin S, Ke Y, Lu S, Li J, Pei H, Wu X, Du W. Synthesis and structure characterization of three-coordinate silver (I) and seven-coordinate cobalt (II) coordination polymers with 4-pyridylthioacetate. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2003.10.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Grabielle-Madelmont C, Lesieur S, Ollivon M. Characterization of loaded liposomes by size exclusion chromatography. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 2003; 56:189-217. [PMID: 12834977 DOI: 10.1016/s0165-022x(03)00059-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This review focuses on the use of conventional (SEC) and high performance (HPSEC) size exclusion chromatography for the analysis of liposomes. The suitability of both techniques is examined regarding the field of liposome applications. The potentiality of conventional SEC is strongly improved by using a HPLC system associated to gel columns with a size selectivity range allowing liposome characterization in addition to particle fractionation. Practical aspects of size exclusion chromatography are described and a methodology based on HPSEC coupled to multidetection modes for on-line analysis of liposomes via label or substance encapsulation is presented. Examples of conventional SEC and HPSEC applications are described which concern polydispersity, size and encapsulation stability, bilayer permeabilization, liposome formation and reconstitution, incorporation of amphiphilic molecules. Size exclusion chromatography is a simple and powerful technique for investigation of encapsulation, insertion/interaction of substances from small solutes (ions, surfactants, drugs, etc.) up to large molecules (proteins, peptides and nucleic acids) in liposomes.
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Affiliation(s)
- Cécile Grabielle-Madelmont
- Equipe Physico-chimie des Systèmes Polyphasés, UMR CNRS 8612, Université Paris-Sud, Châtenay-Malabry Cedex 92296, France.
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Einsle O, Foerster S, Mann K, Fritz G, Messerschmidt A, Kroneck PM. Spectroscopic investigation and determination of reactivity and structure of the tetraheme cytochromec3fromDesulfovibrio desulfuricansEssex 6. ACTA ACUST UNITED AC 2001; 268:3028-35. [PMID: 11358521 DOI: 10.1046/j.1432-1327.2001.02195.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cytochrome c3, a small (14-kDa) soluble tetraheme protein was isolated from the periplasmic fraction of Desulfovibrio desulfuricans strain Essex 6. Its major physiological function appears to be that of an electron carrier for the periplasmic hydrogenase. It has been also shown to interact with the high-molecular-mass cytochrome complex in the cytoplasmic membrane, which eventually feeds electrons into the membraneous quinone pool, as well as with the membrane-associated dissimilatory sulfite reductase. The EPR spectra show features of four different low-spin Fe(III) hemes. Orthorhombic crystals of cytochrome c3 were obtained and X-ray diffraction data were collected to below 2 A resolution. The structure was solved by molecular replacement using cytochrome c3 from D. desulfuricans ATCC 27774 as a search model.
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Affiliation(s)
- O Einsle
- Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, Martinsried, Germany
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Cort JR, Mariappan SV, Kim CY, Park MS, Peat TS, Waldo GS, Terwilliger TC, Kennedy MA. Solution structure of Pyrobaculum aerophilum DsrC, an archaeal homologue of the gamma subunit of dissimilatory sulfite reductase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:5842-50. [PMID: 11722571 DOI: 10.1046/j.0014-2956.2001.02529.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The solution structure of DsrC, an archaeal homologue of the gamma subunit of dissimilatory sulfite reductase, has been determined by NMR spectroscopy. This 12.7-kDa protein from the hyperthermophilic archaeon Pyrobaculum aerophilum adopts a novel fold consisting of an orthogonal helical bundle with a beta hairpin along one side. A portion of the structure resembles the helix-turn-helix DNA-binding motif common in transcriptional regulator proteins. The protein contains two disulfide bonds but remains folded following reduction of the disulfides. DsrC proteins from organisms other than Pyrobaculum species do not contain these disulfide bonds. A conserved cysteine next to the C-terminus, which is not involved in the disulfide bonds, is located on a seven-residue C-terminal arm that is not part of the globular protein and is likely to dynamically sample more than one conformation.
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Affiliation(s)
- J R Cort
- Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Richland, Washington, USA
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Morse R, Gibson GR, Collins MD. Secondary structure analysis of the dissimilatory sulphite reductase in Desulfovibrio desulfuricans. Lett Appl Microbiol 2000; 30:375-8. [PMID: 10792666 DOI: 10.1046/j.1472-765x.2000.00659.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete sequences of the dsrA and dsrB genes coding for the alpha- and beta-subunits, respectively, of the sulphite reductase enzyme in Desulfovibrio desulfuricans were determined. Analyses of the amino acid sequences indicated a number of serohaem/Fe4S4 binding consensus sequences whilst predictive secondary structure analysis revealed a similar pattern of alpha-helix and beta-strand structures between the two subunits which was indicative of gene duplication.
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Affiliation(s)
- R Morse
- Department of Food Science and Technology, The University of Reading, Reading, UK.
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