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Swetha RG, Arakal BS, Rajendran S, Sekar K, Whitworth DE, Ramaiah S, James PE, Livingstone PG, Anbarasu A. MyxoPortal: a database of myxobacterial genomic features. Database (Oxford) 2024; 2024:baae056. [PMID: 38958433 PMCID: PMC11219305 DOI: 10.1093/database/baae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/02/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
Myxobacteria are predatory bacteria with antimicrobial activity, utilizing complex mechanisms to kill their prey and assimilate their macromolecules. Having large genomes encoding hundreds of secondary metabolites, hydrolytic enzymes and antimicrobial peptides, these organisms are widely studied for their antibiotic potential. MyxoPortal is a comprehensive genomic database hosting 262 genomes of myxobacterial strains. Datasets included provide genome annotations with gene locations, functions, amino acids and nucleotide sequences, allowing analysis of evolutionary and taxonomical relationships between strains and genes. Biosynthetic gene clusters are identified by AntiSMASH, and dbAMP-generated antimicrobial peptide sequences are included as a resource for novel antimicrobial discoveries, while curated datasets of CRISPR/Cas genes, regulatory protein sequences, and phage associated genes give useful insights into each strain's biological properties. MyxoPortal is an intuitive open-source database that brings together application-oriented genomic features that can be used in taxonomy, evolution, predation and antimicrobial research. MyxoPortal can be accessed at http://dicsoft1.physics.iisc.ac.in/MyxoPortal/. Database URL: http://dicsoft1.physics.iisc.ac.in/MyxoPortal/. Graphical Abstract.
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Affiliation(s)
- Rayapadi G Swetha
- School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore Campus, Tiruvalam Road, Katpadi, Vellore, Tamil Nadu 632 014, India
| | - Benita S Arakal
- School of Sports and Health Sciences, Cardiff Metropolitan University, Llandaff campus, Western Avenue, Cardiff CF5 2YB, UK
| | - Santhosh Rajendran
- Department of Computational and Data Sciences, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka 560 012, India
| | - K Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka 560 012, India
| | - David E Whitworth
- Department of Life Sciences, Aberystwyth University, Cledwyn Building, Penglais Campus, Aberystwyth, Ceredigion, Wales SY23 3FL, UK
| | - Sudha Ramaiah
- School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore Campus, Tiruvalam Road, Katpadi, Vellore, Tamil Nadu 632 014, India
| | - Philip E James
- School of Sports and Health Sciences, Cardiff Metropolitan University, Llandaff campus, Western Avenue, Cardiff CF5 2YB, UK
| | - Paul G Livingstone
- School of Sports and Health Sciences, Cardiff Metropolitan University, Llandaff campus, Western Avenue, Cardiff CF5 2YB, UK
| | - Anand Anbarasu
- School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore Campus, Tiruvalam Road, Katpadi, Vellore, Tamil Nadu 632 014, India
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Cook E, Olivares CI, Antell EH, Tsou K, Kim TK, Cuthbertson A, Higgins CP, Sedlak DL, Alvarez-Cohen L. Sulfonamide Per- and Polyfluoroalkyl Substances Can Impact Microorganisms Used in Aromatic Hydrocarbon and Trichloroethene Bioremediation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8792-8802. [PMID: 38719742 PMCID: PMC11112735 DOI: 10.1021/acs.est.3c09715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 05/22/2024]
Abstract
Per- and polyfluoroalkyl substances (PFASs) from aqueous film forming foams (AFFFs) can hinder bioremediation of co-contaminants such as trichloroethene (TCE) and benzene, toluene, ethylbenzene, and xylene (BTEX). Anaerobic dechlorination can require bioaugmentation of Dehalococcoides, and for BTEX, oxygen is often sparged to stimulate in situ aerobic biodegradation. We tested PFAS inhibition to TCE and BTEX bioremediation by exposing an anaerobic TCE-dechlorinating coculture, an aerobic BTEX-degrading enrichment culture, and an anaerobic toluene-degrading enrichment culture to n-dimethyl perfluorohexane sulfonamido amine (AmPr-FHxSA), perfluorohexane sulfonamide (FHxSA), perfluorohexanesulfonic acid (PFHxS), or nonfluorinated surfactant sodium dodecyl sulfate (SDS). The anaerobic TCE-dechlorinating coculture was resistant to individual PFAS exposures but was inhibited by >1000× diluted AFFF. FHxSA and AmPr-FHxSA inhibited the aerobic BTEX-degrading enrichment. The anaerobic toluene-degrading enrichment was not inhibited by AFFF or individual PFASs. Increases in amino acids in the anaerobic TCE-dechlorinating coculture compared to the control indicated stress response, whereas the BTEX culture exhibited lower concentrations of all amino acids upon exposure to most surfactants (both fluorinated and nonfluorinated) compared to the control. These data suggest the main mechanisms of microbial toxicity are related to interactions with cell membrane synthesis as well as protein stress signaling.
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Affiliation(s)
- Emily
K. Cook
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Christopher I. Olivares
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
- Department
of Civil and Environmental Engineering, University of California, Irvine, California 92697, United States
| | - Edmund H. Antell
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Katerina Tsou
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Tae-Kyoung Kim
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Amy Cuthbertson
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Christopher P. Higgins
- Department
of Civil & Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - David L. Sedlak
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Lisa Alvarez-Cohen
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
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Wang Y, Han Z, Liu J, Song C, Wei Z. The biotic effects of lignite on humic acid components conversion during chicken manure composting. BIORESOURCE TECHNOLOGY 2024; 398:130503. [PMID: 38442847 DOI: 10.1016/j.biortech.2024.130503] [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: 12/07/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/07/2024]
Abstract
Targeted regulation of composting to convert organic matter into humic acid (HA) holds significant importance in compost quality. Owing to its low carbon content, chicken manure compost often requires carbon supplements to promote the humification progress. The addition of lignite can increase HA content through biotic pathways, however, its structure was not explored. The Parallel factor analysis revealed that lignite can significantly increase the complexity of highly humified components. The lignite addition improved phenol oxidase activity, particularly laccase, during the thermophilic and cooling phases. The abundance and transformation functions of core bacteria also indicated that lignite addition can influence the activity of microbial transformation of HA components. The structural equation model further confirmed that lignite addition had a direct and indirect impact on enhancing the complexity of HA components through core bacteria and phenol oxidase. Therefore, lignite addition can improve HA structure complexity during composting through biotic pathways.
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Affiliation(s)
- Yumeng Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Ziyi Han
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Junping Liu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Caihong Song
- College of Life Science, Liaocheng University, Liaocheng 252000, China
| | - Zimin Wei
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China.
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Saggu SK, Nath A, Kumar S. Myxobacteria: biology and bioactive secondary metabolites. Res Microbiol 2023; 174:104079. [PMID: 37169232 DOI: 10.1016/j.resmic.2023.104079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/22/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Myxobacteria are Gram-negative eubacteria and they thrive in a variety of habitats including soil rich in organic matter, rotting wood, animal dung and marine environment. Myxobacteria are a promising source of new compounds associated with diverse bioactive spectrum and unique mode of action. The genome information of myxobacteria has revealed many orphan biosynthetic pathways indicating that these bacteria can be the source of several novel natural products. In this review, we highlight the biology of myxobacteria with emphasis on their habitat, life cycle, isolation methods and enlist all the bioactive secondary metabolites purified till date and their mode of action.
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Affiliation(s)
- Sandeep Kaur Saggu
- Department of Biotechnology, Kanya Maha Vidyalaya, Jalandhar, Punjab, India - 144004.
| | - Amar Nath
- University Centre of Excellence in Research, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
| | - Shiv Kumar
- Guru Gobind Singh Medical College, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
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Riley R, Bowers RM, Camargo AP, Campbell A, Egan R, Eloe-Fadrosh EA, Foster B, Hofmeyr S, Huntemann M, Kellom M, Kimbrel JA, Oliker L, Yelick K, Pett-Ridge J, Salamov A, Varghese NJ, Clum A. Terabase-Scale Coassembly of a Tropical Soil Microbiome. Microbiol Spectr 2023; 11:e0020023. [PMID: 37310219 PMCID: PMC10434106 DOI: 10.1128/spectrum.00200-23] [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] [Received: 01/12/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023] Open
Abstract
Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes' sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 terabases (Tbp) of metagenome data from a tropical soil in the Luquillo Experimental Forest (LEF), Puerto Rico. The resulting coassembly yielded 39 high-quality (>90% complete, <5% contaminated, with predicted 23S, 16S, and 5S rRNA genes and ≥18 tRNAs) metagenome-assembled genomes (MAGs), including two from the candidate phylum Eremiobacterota. Another 268 medium-quality (≥50% complete, <10% contaminated) MAGs were extracted, including the candidate phyla Dependentiae, Dormibacterota, and Methylomirabilota. In total, 307 medium- or higher-quality MAGs were assigned to 23 phyla, compared to 294 MAGs assigned to nine phyla in the same samples individually assembled. The low-quality (<50% complete, <10% contaminated) MAGs from the coassembly revealed a 49% complete rare biosphere microbe from the candidate phylum FCPU426 among other low-abundance microbes, an 81% complete fungal genome from the phylum Ascomycota, and 30 partial eukaryotic MAGs with ≥10% completeness, possibly representing protist lineages. A total of 22,254 viruses, many of them low abundance, were identified. Estimation of metagenome coverage and diversity indicates that we may have characterized ≥87.5% of the sequence diversity in this humid tropical soil and indicates the value of future terabase-scale sequencing and coassembly of complex environments. IMPORTANCE Petabases of reads are being produced by environmental metagenome sequencing. An essential step in analyzing these data is metagenome assembly, the computational reconstruction of genome sequences from microbial communities. "Coassembly" of metagenomic sequence data, in which multiple samples are assembled together, enables more complete detection of microbial genomes in an environment than "multiassembly," in which samples are assembled individually. To demonstrate the potential for coassembling terabases of metagenome data to drive biological discovery, we applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 Tbp of reads from a humid tropical soil environment. The resulting coassembly, its functional annotation, and analysis are presented here. The coassembly yielded more, and phylogenetically more diverse, microbial, eukaryotic, and viral genomes than the multiassembly of the same data. Our resource may facilitate the discovery of novel microbial biology in tropical soils and demonstrates the value of terabase-scale metagenome sequencing.
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Affiliation(s)
- Robert Riley
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Robert M. Bowers
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Antonio Pedro Camargo
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Ashley Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Rob Egan
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | | | - Brian Foster
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Steven Hofmeyr
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marcel Huntemann
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Matthew Kellom
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Leonid Oliker
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Katherine Yelick
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, California, USA
| | - Asaf Salamov
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Neha J. Varghese
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Alicia Clum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
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6
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Ahearne A, Phillips KE, Knehans T, Hoing M, Dowd SE, Stevens DC. Chromosomal organization of biosynthetic gene clusters, including those of nine novel species, suggests plasticity of myxobacterial specialized metabolism. Front Microbiol 2023; 14:1227206. [PMID: 37601375 PMCID: PMC10435759 DOI: 10.3389/fmicb.2023.1227206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Natural products discovered from bacteria provide critically needed therapeutic leads for drug discovery, and myxobacteria are an established source for metabolites with unique chemical scaffolds and biological activities. Myxobacterial genomes accommodate an exceptional number and variety of biosynthetic gene clusters (BGCs) which encode for features involved in specialized metabolism. Methods In this study, we describe the collection, sequencing, and genome mining of 20 myxobacteria isolated from rhizospheric soil samples collected in North America. Results Nine isolates were determined to be novel species of myxobacteria including representatives from the genera Archangium, Myxococcus, Nannocystis, Polyangium, Pyxidicoccus, Sorangium, and Stigmatella. Growth profiles, biochemical assays, and descriptions were provided for all proposed novel species. We assess the BGC content of all isolates and observe differences between Myxococcia and Polyangiia clusters. Discussion Continued discovery and sequencing of novel myxobacteria from the environment provide BGCs for the genome mining pipeline. Utilizing complete or near-complete genome sequences, we compare the chromosomal organization of BGCs of related myxobacteria from various genera and suggest that the spatial proximity of hybrid, modular clusters contributes to the metabolic adaptability of myxobacteria.
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Affiliation(s)
- Andrew Ahearne
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Kayleigh E. Phillips
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Thomas Knehans
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Miranda Hoing
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Scot E. Dowd
- Molecular Research LP (MR DNA), Shallowater, TX, United States
| | - David Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
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7
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Ahearne A, Phillips K, Knehans T, Hoing M, Dowd SE, Stevens DC. Chromosomal organization of biosynthetic gene clusters suggests plasticity of myxobacterial specialized metabolism including descriptions for nine novel species: Archangium lansinium sp. nov., Myxococcus landrumus sp. nov., Nannocystis bainbridgea sp. nov., Nannocystis poenicansa sp. nov., Nannocystis radixulma sp. nov., Polyangium mundeleinium sp. nov., Pyxidicoccus parkwaysis sp. nov., Sorangium aterium sp. nov., Stigmatella ashevillena sp. nov. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531766. [PMID: 36945379 PMCID: PMC10028903 DOI: 10.1101/2023.03.08.531766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Natural products discovered from bacteria provide critically needed therapeutic leads for drug discovery, and myxobacteria are an established source for metabolites with unique chemical scaffolds and biological activities. Myxobacterial genomes accommodate an exceptional number and variety of biosynthetic gene clusters (BGCs) which encode for features involved in specialized metabolism. Continued discovery and sequencing of novel myxobacteria from the environment provides BGCs for the genome mining pipeline. Herein, we describe the collection, sequencing, and genome mining of 20 myxobacteria isolated from rhizospheric soil samples collected in North America. Nine isolates where determined to be novel species of myxobacteria including representatives from the genera Archangium, Myxococcus, Nannocystis, Polyangium, Pyxidicoccus, Sorangium, and Stigmatella. Growth profiles, biochemical assays, and descriptions are provided for all proposed novel species. We assess the BGC content of all isolates and observe differences between Myxococcia and Polyangiia clusters. Utilizing complete or near complete genome sequences we compare the chromosomal organization of BGCs of related myxobacteria from various genera and suggest spatial proximity of hybrid, modular clusters contributes to the metabolic adaptability of myxobacteria.
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Affiliation(s)
- Andrew Ahearne
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Kayleigh Phillips
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Thomas Knehans
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Miranda Hoing
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Scot E. Dowd
- MR DNA, Molecular Research LP, Shallowater, TX 79363, USA
| | - D. Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
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Phillips KE, Akbar S, Stevens DC. Concepts and conjectures concerning predatory performance of myxobacteria. Front Microbiol 2022; 13:1031346. [PMID: 36246230 PMCID: PMC9556981 DOI: 10.3389/fmicb.2022.1031346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/14/2022] [Indexed: 01/28/2023] Open
Abstract
Myxobacteria are excellent model organisms for investigation of predator-prey interactions and predatory shaping of microbial communities. This review covers interdisciplinary topics related to myxobacterial predation and provides current concepts and challenges for determining predatory performance. Discussed topics include the role of specialized metabolites during predation, genetic determinants for predatory performance, challenges associated with methodological differences, discrepancies between sequenced and environmental myxobacteria, and factors that influence predation.
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Affiliation(s)
- Kayleigh E. Phillips
- Department of BioMolecular Sciences, The University of Mississippi, Oxford, MS, United States
| | - Shukria Akbar
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - D. Cole Stevens
- Department of BioMolecular Sciences, The University of Mississippi, Oxford, MS, United States,*Correspondence: D. Cole Stevens,
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Pérez-Castaño R, Bastida-Martínez E, Fernández Zapata J, Polanco MDC, Galbis-Martínez ML, Iniesta AA, Fontes M, Padmanabhan S, Elías-Arnanz M. Coenzyme B 12 -dependent and independent photoregulation of carotenogenesis across Myxococcales. Environ Microbiol 2022; 24:1865-1886. [PMID: 35005822 PMCID: PMC9304148 DOI: 10.1111/1462-2920.15895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/27/2021] [Accepted: 01/01/2022] [Indexed: 11/28/2022]
Abstract
Light-induced carotenogenesis in Myxococcus xanthus is controlled by the B12 -based CarH repressor and photoreceptor, and by a separate intricate pathway involving singlet oxygen, the B12 -independent CarH paralog CarA and various other proteins, some eukaryotic-like. Whether other myxobacteria conserve these pathways and undergo photoregulated carotenogenesis is unknown. Here, comparative analyses across 27 Myxococcales genomes identified carotenogenic genes, albeit arranged differently, with carH often in their genomic vicinity, in all three Myxococcales suborders. However, CarA and its associated factors were found exclusively in suborder Cystobacterineae, with carA-carH invariably in tandem in a syntenic carotenogenic operon, except for Cystobacter/Melittangium, which lack CarA but retain all other factors. We experimentally show B12 -mediated photoregulated carotenogenesis in representative myxobacteria, and a remarkably plastic CarH operator design and DNA binding across Myxococcales. Unlike the two characterized CarH from other phyla, which are tetrameric, Cystobacter CarH (the first myxobacterial homolog amenable to analysis in vitro) is a dimer that combines direct CarH-like B12 -based photoregulation with CarA-like DNA-binding and inhibition by an antirepressor. This study provides new molecular insights into B12 -dependent photoreceptors. It further establishes the B12 -dependent pathway for photoregulated carotenogenesis as broadly prevalent across myxobacteria and its evolution, exclusively in one suborder, into a parallel complex B12 -independent circuit. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Eva Bastida-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Jesús Fernández Zapata
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - María Del Carmen Polanco
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - María Luisa Galbis-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Antonio A Iniesta
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Marta Fontes
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
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Li J, Chen X, Yang Z, Liu Z, Chen Y, Wang YE, Xie H. Denitrification performance and mechanism of sequencing batch reactor with a novel iron-polyurethane foam composite carrier. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Wang J, Ran Q, Du X, Wu S, Wang J, Sheng D, Chen Q, Du Z, Li YZ. Two new Polyangium species, P. aurulentum sp. nov. and P. jinanense sp. nov., isolated from a soil sample. Syst Appl Microbiol 2021; 44:126274. [PMID: 34763291 DOI: 10.1016/j.syapm.2021.126274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022]
Abstract
Polyangium belongs to Polyangiaceae family of Myxococcales, a taxonomic group well-known for their extraordinary social lifestyle and diverse novel gene clusters of secondary metabolites. A yellow-golden strain, designated SDU3-1T, and two rose pink strains, designated SDU13 and SDU14T, were isolated from a soil sample. These three strains were aerobic, mesophilic, not salt-tolerant and were able to prey on living microorganisms. SDU13 and SDU14T formed solitary sporangioles under starvation conditions, while SDU3-1T had no fruiting body structures. They showed 95.9-97.0% (SDU3-1T) or 98.7-98.9% (SDU13 and SDU14T) 16S rRNA gene similarity with the type strains of Polyangium, but were phylogenetically separate from them based on the 16S rRNA gene and genome sequences. Their genomes were 12.3 Mbp (SDU3-1T), 13.9 Mbp (SDU13) and 13.8 Mbp (SDU14T) with the G + C content range of 68.3-69.4 mol%. The average nucleotide identity and DNA-DNA hybridization analyses of genomes further indicated that these three strains belonged to two new species in Polyangium. Their major fatty acids were C18:1ω9c, C16:0 and C18:0. The polyphasic taxonomic characterization suggest that the three strains represent two novel species in the genus Polyangium, for which the names Polyangium aurulentum sp. nov. and Polyangium jinanense sp. nov. are proposed, and the type strains are SDU3-1T (=CGMCC 1.16875T = KCTC 72136T) and SDU14T (=CCTCC AB 2021123T = KCTC 82625T), respectively.
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Affiliation(s)
- Jingjing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Qi Ran
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Xinran Du
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Shuge Wu
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Duohong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Qi Chen
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Zongjun Du
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China; College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China.
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12
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Genomes of Novel Myxococcota Reveal Severely Curtailed Machineries for Predation and Cellular Differentiation. Appl Environ Microbiol 2021; 87:e0170621. [PMID: 34524899 DOI: 10.1128/aem.01706-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, nonsoil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring (Zodletone Spring) in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of 13 distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g., FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine learning approaches based on a set of 634 genes informative of social lifestyle predicted a nonsocial behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities but carried genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 million years ago (Mya) in response to the rise of soil as a distinct habitat on Earth. IMPORTANCE The phylum Myxococcota is a phylogenetically coherent bacterial lineage that exhibits unique social traits. Cultured Myxococcota are predominantly aerobic soil-dwelling microorganisms that are capable of predation and fruiting body formation. However, multiple yet-uncultured lineages within the Myxococcota have been encountered in a wide range of nonsoil, predominantly anaerobic habitats, and the metabolic capabilities, physiological preferences, and capacity of social behavior of such lineages remain unclear. Here, we analyzed genomes recovered from a metagenomic analysis of an anoxic freshwater spring in Oklahoma, USA, that represent novel, yet-uncultured, orders and families in the Myxococcota. The genomes appear to lack the characteristic hallmarks for social behavior encountered in Myxococcota genomes and displayed a significantly smaller genome size and a smaller number of genes encoding biosynthetic gene clusters, peptidases, signal transduction systems, and transcriptional regulators. Such perceived lack of social capacity was confirmed through detailed comparative genomic analysis of 13 pathways associated with Myxococcota social behavior, as well as the implementation of machine learning approaches to predict social behavior based on genome composition. Metabolically, these novel Myxococcota are predicted to be strict anaerobes, utilizing fermentation, nitrate reduction, and dissimilarity sulfate reduction for energy acquisition. Our results highlight the broad patterns of metabolic diversity within the yet-uncultured Myxococcota and suggest that the evolution of predation and fruiting body formation in the Myxococcota has occurred in response to soil formation as a distinct habitat on Earth.
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13
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Loakasikarn T, Kubota Y, Koyama M, Nakasaki K. Effect of seeding materials on organic matter degradation and microbial community succession during model organic waste composting. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Ahearne A, Albataineh H, Dowd SE, Stevens DC. Assessment of Evolutionary Relationships for Prioritization of Myxobacteria for Natural Product Discovery. Microorganisms 2021; 9:microorganisms9071376. [PMID: 34202719 PMCID: PMC8307915 DOI: 10.3390/microorganisms9071376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/03/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
Discoveries of novel myxobacteria have started to unveil the potentially vast phylogenetic diversity within the family Myxococcaceae and have brought about an updated approach to myxobacterial classification. While traditional approaches focused on morphology, 16S gene sequences, and biochemistry, modern methods including comparative genomics have provided a more thorough assessment of myxobacterial taxonomy. Herein, we utilize long-read genome sequencing for two myxobacteria previously classified as Archangium primigenium and Chondrococcus macrosporus, as well as four environmental myxobacteria newly isolated for this study. Average nucleotide identity and digital DNA-DNA hybridization scores from comparative genomics suggest previously classified as A. primigenium to instead be a novel member of the genus Melittangium, C. macrosporus to be a potentially novel member of the genus Corallococcus with high similarity to Corallococcus exercitus, and the four isolated myxobacteria to include another novel Corallococcus species, a novel Pyxidicoccus species, a strain of Corallococcus exiguus, and a potentially novel Myxococcus species with high similarity to Myxococcus stipitatus. We assess the biosynthetic potential of each sequenced myxobacterium and suggest that genus-level conservation of biosynthetic pathways support our preliminary taxonomic assignment. Altogether, we suggest that long-read genome sequencing benefits the classification of myxobacteria and improves determination of biosynthetic potential for prioritization of natural product discovery.
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Affiliation(s)
- Andrew Ahearne
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (A.A.); (H.A.)
| | - Hanan Albataineh
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (A.A.); (H.A.)
| | - Scot E. Dowd
- MR DNA, Molecular Research LP, Shallowater, TX 79363, USA;
| | - D. Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (A.A.); (H.A.)
- Correspondence: ; Tel.: +1-662-915-5730
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15
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Shrivastava A, Sharma RK. Myxobacteria and their products: current trends and future perspectives in industrial applications. Folia Microbiol (Praha) 2021; 66:483-507. [PMID: 34060028 DOI: 10.1007/s12223-021-00875-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 05/13/2021] [Indexed: 12/12/2022]
Abstract
Myxobacteria belong to a group of bacteria that are known for their well-developed communication system and synchronized or coordinated movement. This typical behavior of myxobacteria is mediated through secondary metabolites. They are capable of producing secondary metabolites belonging to several chemical classes with unique and wide spectrum of bioactivities. It is predominantly significant that myxobacteria specialize in mechanisms of action that are very rare with other producers. Most of the metabolites have been explored for their medical and pharmaceutical values while a lot of them are still unexplored. This review is an attempt to understand the role of potential metabolites produced by myxobacteria in different applications. Different myxobacterial metabolites have demonstrated antibacterial, antifungal, and antiviral properties along with cytotoxic activity against various cell lines. Beside their metabolites, these myxobacteria have also been discussed for better exploitation and implementation in different industrial sectors.
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Affiliation(s)
- Akansha Shrivastava
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, Jaipur, India
| | - Rakesh Kumar Sharma
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, Jaipur, India.
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16
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Cervantes-Avilés P, Caretta CA, Brito EMS, Bertin P, Cuevas-Rodríguez G, Duran R. Changes in bacterial diversity of activated sludge exposed to titanium dioxide nanoparticles. Biodegradation 2021; 32:313-326. [PMID: 33811584 DOI: 10.1007/s10532-021-09939-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/24/2021] [Indexed: 11/29/2022]
Abstract
The rapid growth of the use of nanomaterials in different modern industrial branches makes the study of the impact of nanoparticles on the human health and environment an urgent matter. For instance, it has been reported that titanium dioxide nanoparticles (TiO2 NPs) can be found in wastewater treatment plants. Previous studies have found contrasting effects of these nanoparticles over the activated sludge process, including negative effects on the oxygen uptake. The non-utilization of oxygen reflects that aerobic bacteria were inhibited or decayed. The aim of this work was to study how TiO2 NPs affect the bacterial diversity and metabolic processes on an activated sludge. First, respirometry assays of 8 h were carried out at different concentrations of TiO2 NPs (0.5-2.0 mg/mL) to measure the oxygen uptake by the activated sludge. The bacterial diversity of these assays was determined by sequencing the amplified V3-V4 region of the 16S rRNA gene using Illumina MiSeq. According to the respirometry assays, the aerobic processes were inhibited in a range from 18.5 ± 4.8% to 37.5 ± 2.0% for concentrations of 0.5-2.0 mg/mL TiO2 NPs. The oxygen uptake rate was affected mainly after 4.5 h for concentrations higher than 1.0 mg/mL of these nanoparticles. Results indicated that, in the presence of TiO2 NPs, the bacterial community of activated sludge was altered mainly in the genera related to nitrogen removal (nitrogen assimilation, nitrification and denitrification). The metabolic pathways prediction suggested that genes related to biofilm formation were more sensitive than genes directly related to nitrification-denitrification and N-assimilation processes. These results indicated that TiO2 NPs might modify the bacteria diversity in the activated sludge according to their concentration and time of exposition, which in turn impact in the performance of the wastewater treatment processes.
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Affiliation(s)
- Pabel Cervantes-Avilés
- Departamento de Ingeniería Civil and Ambiental, DI-CGT, Universidad de Guanajuato, Av. Juárez 77, Col. Centro, 36000, Guanajuato, Gto, Mexico.,Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Reserva Territorial Atlixcayotl, vía Atlixcayotl 5718, 72453, Puebla, Pue, Mexico
| | - César Augusto Caretta
- Departamento de Astronomía, DCNE-CGT, Universidad de Guanajuato, Callejón de Jalisco S/N, Col. Valenciana, 36023, Guanajuato, Gto, Mexico
| | - Elcia Margareth Souza Brito
- Departamento de Ingeniería Civil and Ambiental, DI-CGT, Universidad de Guanajuato, Av. Juárez 77, Col. Centro, 36000, Guanajuato, Gto, Mexico.
| | - Pierre Bertin
- Institut de Biologie Intégrative de la Cellule, Université Paris Sud, Batiment 400, 91400, Orsay, France
| | - Germán Cuevas-Rodríguez
- Departamento de Ingeniería Civil and Ambiental, DI-CGT, Universidad de Guanajuato, Av. Juárez 77, Col. Centro, 36000, Guanajuato, Gto, Mexico
| | - Robert Duran
- Equipe Environment et Microbiologie, MELODY Group, IPREM UMR CNRS 5254, Université de pau et des pays de l'Adour, BP 1155, 64013, Pau Cedex, France
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17
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Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol 2020; 70:5972-6016. [DOI: 10.1099/ijsem.0.004213] [Citation(s) in RCA: 696] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class
Deltaproteobacteria
comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum
Proteobacteria
, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class
Deltaproteobacteria
encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the
Oligoflexia
. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes
Deltaproteobacteria
and
Oligoflexia
in the phylum
Proteobacteria
. Instead, the great majority of currently recognized members of the class
Deltaproteobacteria
are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class
Oligoflexia
represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum
Thermodesulfobacteria
, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the
Thermodesulfobacteria
rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.
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Affiliation(s)
- David W Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Maria Chuvochina
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Claus Pelikan
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | | | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Alexander Loy
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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18
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Pérez-Burgos M, García-Romero I, Valvano MA, Søgaard Andersen L. Identification of the Wzx flippase, Wzy polymerase and sugar-modifying enzymes for spore coat polysaccharide biosynthesis in Myxococcus xanthus. Mol Microbiol 2020; 113:1189-1208. [PMID: 32064693 DOI: 10.1111/mmi.14486] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/11/2020] [Indexed: 12/28/2022]
Abstract
The rod-shaped cells of Myxococcus xanthus, a Gram-negative deltaproteobacterium, differentiate to environmentally resistant spores upon starvation or chemical stress. The environmental resistance depends on a spore coat polysaccharide that is synthesised by the ExoA-I proteins, some of which are part of a Wzx/Wzy-dependent pathway for polysaccharide synthesis and export; however, key components of this pathway have remained unidentified. Here, we identify and characterise two additional loci encoding proteins with homology to enzymes involved in polysaccharide synthesis and export, as well as sugar modification and show that six of the proteins encoded by these loci are essential for the formation of environmentally resistant spores. Our data support that MXAN_3260, renamed ExoM and MXAN_3026, renamed ExoJ, are the Wzx flippase and Wzy polymerase, respectively, responsible for translocation and polymerisation of the repeat unit of the spore coat polysaccharide. Moreover, we provide evidence that three glycosyltransferases (MXAN_3027/ExoK, MXAN_3262/ExoO and MXAN_3263/ExoP) and a polysaccharide deacetylase (MXAN_3259/ExoL) are important for formation of the intact spore coat, while ExoE is the polyisoprenyl-phosphate hexose-1-phosphate transferase responsible for initiating repeat unit synthesis, likely by transferring N-acetylgalactosamine-1-P to undecaprenyl-phosphate. Together, our data generate a more complete model of the Exo pathway for spore coat polysaccharide biosynthesis and export.
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Affiliation(s)
- María Pérez-Burgos
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Lotte Søgaard Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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19
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Vermassen A, Leroy S, Talon R, Provot C, Popowska M, Desvaux M. Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan. Front Microbiol 2019; 10:331. [PMID: 30873139 PMCID: PMC6403190 DOI: 10.3389/fmicb.2019.00331] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/08/2019] [Indexed: 11/13/2022] Open
Abstract
The cell wall (CW) of bacteria is an intricate arrangement of macromolecules, at least constituted of peptidoglycan (PG) but also of (lipo)teichoic acids, various polysaccharides, polyglutamate and/or proteins. During bacterial growth and division, there is a constant balance between CW degradation and biosynthesis. The CW is remodeled by bacterial hydrolases, whose activities are carefully regulated to maintain cell integrity or lead to bacterial death. Each cell wall hydrolase (CWH) has a specific role regarding the PG: (i) cell wall amidase (CWA) cleaves the amide bond between N-acetylmuramic acid and L-alanine residue at the N-terminal of the stem peptide, (ii) cell wall glycosidase (CWG) catalyses the hydrolysis of the glycosidic linkages, whereas (iii) cell wall peptidase (CWP) cleaves amide bonds between amino acids within the PG chain. After an exhaustive overview of all known conserved catalytic domains responsible for CWA, CWG, and CWP activities, this review stresses that the CWHs frequently display a modular architecture combining multiple and/or different catalytic domains, including some lytic transglycosylases as well as CW binding domains. From there, direct physiological and collateral roles of CWHs in bacterial cells are further discussed.
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Affiliation(s)
- Aurore Vermassen
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | - Régine Talon
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | | | - Magdalena Popowska
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
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20
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A Highly Polymorphic Receptor Governs Many Distinct Self-Recognition Types within the Myxococcales Order. mBio 2019; 10:mBio.02751-18. [PMID: 30755513 PMCID: PMC6372800 DOI: 10.1128/mbio.02751-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Many biological species distinguish self from nonself by using different mechanisms. Higher animals recognize close kin via complex processes that often involve the five senses, cognition, and learning, whereas some microbes achieve self-recognition simply through the activity of a single genetic locus. Here we describe a single locus, traA, in myxobacteria that governs cell-cell recognition within natural populations. We found that traA is widespread across the order Myxococcales. TraA is highly polymorphic among diverse myxobacterial isolates, and such polymorphisms determine selectivity in self-recognition. Through bioinformatic and experimental analyses, we showed that traA governs many distinct recognition groups within Myxococcales. This report provides an example in which a single locus influences social recognition across a wide phylogenetic range of natural populations. Self-recognition underlies sociality in many group-living organisms. In bacteria, cells use various strategies to recognize kin to form social groups and, in some cases, to transition into multicellular life. One strategy relies on a single genetic locus that encodes a variable phenotypic tag (“greenbeard”) for recognizing other tag bearers. Previously, we discovered a polymorphic cell surface receptor called TraA that directs self-identification through homotypic interactions in the social bacterium Myxococcus xanthus. Recognition by TraA leads to cellular resource sharing in a process called outer membrane exchange (OME). A second gene in the traA operon, traB, is also required for OME but is not involved in recognition. Our prior studies of TraA identified only six recognition groups among closely related M. xanthus isolates. Here we hypothesize that the number of traA polymorphisms and, consequently, the diversity of recognition in wild isolates are much greater. To test this hypothesis, we expand the scope of TraA characterization to the order Myxococcales. From genomic sequences within the three suborders of Myxococcales, we identified 90 traA orthologs. Sequence analyses and functional characterization of traAB loci suggest that OME is well maintained among diverse myxobacterial taxonomic groups. Importantly, TraA orthologs are highly polymorphic within their variable domain, the region that confers selectivity in self-recognition. We experimentally defined 10 distinct recognition groups and, based on phylogenetic and experimental analyses, predicted >60 recognition groups among the 90 traA alleles. Taken together, our findings revealed a widespread greenbeard locus that mediates the diversity of self-recognition across the order Myxococcales.
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21
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In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides. BMC Genomics 2018; 19:757. [PMID: 30340510 PMCID: PMC6194562 DOI: 10.1186/s12864-018-5151-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/08/2018] [Indexed: 11/23/2022] Open
Abstract
Background An efficient signal transduction system allows a bacterium to sense environmental cues and then to respond positively or negatively to those signals; this process is referred to as taxis. In addition to external cues, the internal metabolic state of any bacterium plays a major role in determining its ability to reside and thrive in its current environment. Similar to external signaling molecules, cytoplasmic signals are also sensed by methyl-accepting chemotaxis proteins (MCPs) via diverse ligand binding domains. Myxobacteria are complex soil-dwelling social microbes that can perform a variety of physiologic and metabolic activities ranging from gliding motility, sporulation, biofilm formation, carotenoid and secondary metabolite biosynthesis, predation, and slime secretion. To live such complex lifestyles, they have evolved efficient signal transduction systems with numerous one- and two-component regulatory system along with a large array of chemosensory systems to perceive and integrate both external and internal cues. Results Here we report the in silico characterization of a putative energy taxis cluster, Cc-5, which is present in only one amongst 34 known and sequenced myxobacterial genomes, Corallococcus coralloides. In addition, we propose that this energy taxis cluster is involved in oxygen sensing, suggesting that C. coralloides can sense (either directly or indirectly) and then respond to changing concentrations of molecular oxygen. Conclusions This hypothesis is based on the presence of a unique MCP encoded in this gene cluster that contains two different oxygen-binding sensor domains, PAS and globin. In addition, the two monooxygenases encoded in this cluster may contribute to aerobic respiration via ubiquinone biosynthesis, which is part of the cytochrome bc1 complex. Finally, we suggest that this cluster was acquired from Actinobacteria, Gammaproteobacteria or Cyanobacteria. Overall, this in silico study has identified a potentially innovative and evolved mechanism of energy taxis in only one of the myxobacteria, C. coralloides. Electronic supplementary material The online version of this article (10.1186/s12864-018-5151-6) contains supplementary material, which is available to authorized users.
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22
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Garcia R, Müller R. Simulacricoccus ruber gen. nov., sp. nov., a microaerotolerant, non-fruiting, myxospore-forming soil myxobacterium and emended description of the family Myxococcaceae. Int J Syst Evol Microbiol 2018; 68:3101-3110. [PMID: 30113300 DOI: 10.1099/ijsem.0.002936] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
A non-fruiting group of myxobacteria was previously speculated to exist in nature based on metagenomics data containing uncultured members of the order Myxococcales. Here, we describe a myxobacterial strain, designated MCy10636T, which was isolated from a German soil sample collected in 2013. It exhibits swarming characteristics but atypically produces myxospores in the absence of fruiting bodies. The novel strain stains Gram-negative and Congo-red-negative and is characterized mesophilic, neutrophilic, chemoheterotrophic and microaerotolerant. Branched-chain fatty acids are the predominant cellular fatty acids over the straight-chain type, and contain the major fatty acids iso-C17 : 0 2-OH, C16 : 1, iso-C17 : 0 and iso-C15 : 0. Based on blastn results, the 16S rRNA gene sequence reveals similarity (97 %) to Aggregicoccus edonensis MCy1366T, (97 %) Myxococcus macrosporus DSM 14697T, (96 %) Corallococcus coralloides DSM2259T and Corallococcus exiguus Cc e167T. Phylogenetic analysis showed a novel lineage of MCy10636T in the family Myxococcaceae, suborder Cystobacterineae. Based on polyphasic taxonomic characterization, we propose that this unusual, non-fruiting, myxospore-forming and microaerotolerant myxobacterial strain, MCy10636T, represents a novel genus and species, Simulacricoccus ruber gen. nov., sp. nov. (DSM 106554T=NCCB 100651T).
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Affiliation(s)
- Ronald Garcia
- 1Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarland University Campus Building E8 1, 66123 Saarbrücken, Germany.,2German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- 1Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarland University Campus Building E8 1, 66123 Saarbrücken, Germany.,2German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, 38124 Braunschweig, Germany.,3Department of Pharmacy, Saarland University, Building E8 1, 66123 Saarbrücken, Germany
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23
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Six Heterocyclic Metabolites from the Myxobacterium Labilithrix luteola. Molecules 2018; 23:molecules23030542. [PMID: 29495640 PMCID: PMC6017429 DOI: 10.3390/molecules23030542] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 11/17/2022] Open
Abstract
Two new secondary metabolites, labindole A [2-methyl-3-(2-nitroethyl)-3H-indole] (1) and labindole B [2-methyl-3-(2-nitrovinyl)-3H-indole] (2), were isolated from the myxobacterium Labilithrixluteola (DSM 27648T). Additionally, four metabolites 3, 4, 5 and 6 already known from other sources were obtained. Their structures were elucidated from high resolution electrospray ionisation mass spectrometry (HRESIMS) and 1D and 2D nuclear magnetic resonance (NMR) spectroscopy data and their relative configuration was assigned based on nuclear Overhauser effect (NOE) and vicinal ¹H-NMR coupling data. The compounds where tested for biological activities; labindoles A (1) and B (2) exhibited significant activity against Hepatitis C Virus, 9H-carbazole (3), 3-chloro-9H-carbazole (4) and 4-hydroxymethyl-quinoline (5) showed antifungal activities. Moreover, compound 3 had weak to moderate antibacterial activities, while labindoles A (1) and B (2) were devoid of significant antifungal and antibacterial effects.
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Complete Genome Sequence of the Fruiting Myxobacterium Melittangium boletus DSM 14713. GENOME ANNOUNCEMENTS 2017; 5:5/45/e01262-17. [PMID: 29122879 PMCID: PMC5679812 DOI: 10.1128/genomea.01262-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The formation of spore-filled fruiting bodies in response to starvation represents a hallmark of many members of the order Myxococcales. Here, we present the complete 9.9-Mb genome of the fruiting type strain Melittangium boletus DSM 14713, the first member of this genus to have its genome sequenced.
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Draft Genome Sequence of the Fruiting Myxobacterium Nannocystis exedens DSM 71. GENOME ANNOUNCEMENTS 2017; 5:5/43/e01227-17. [PMID: 29074673 PMCID: PMC5658511 DOI: 10.1128/genomea.01227-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In response to starvation, members of the order Myxococcales form morphologically very different fruiting bodies. To determine whether fruiting myxobacteria share a common genetic program that leads to fruiting body formation, we sequenced and assembled the genome of Nannocystis exedens DSM 71 as two contigs with a total GC content of 72%.
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Whole-Genome Sequence of the Fruiting Myxobacterium Cystobacter fuscus DSM 52655. GENOME ANNOUNCEMENTS 2017; 5:5/43/e01196-17. [PMID: 29074667 PMCID: PMC5658505 DOI: 10.1128/genomea.01196-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Among myxobacteria, the genus Cystobacter is known not only for fruiting body formation but also for formation of secondary metabolites, such as cystobactamids and cystothiazols. Here, we present the complete genome sequence of the Cystobacter fuscus strain DSM 52655, which comprises 12,349,744 bp and 9,836 putative protein-coding sequences.
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Arias Del Angel JA, Escalante AE, Martínez-Castilla LP, Benítez M. An Evo-Devo Perspective on Multicellular Development of Myxobacteria. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:165-178. [PMID: 28217903 DOI: 10.1002/jez.b.22727] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 12/12/2016] [Accepted: 12/25/2016] [Indexed: 11/07/2022]
Abstract
The transition to multicellularity, recognized as one the major transitions in evolution, has occurred independently several times. While multicellular development has been extensively studied in zygotic organisms including plant and animal groups, just a few aggregative multicellular organisms have been employed as model organisms for the study of multicellularity. Studying different evolutionary origins and modes of multicellularity enables comparative analyses that can help identifying lineage-specific aspects of multicellular evolution and generic factors and mechanisms involved in the transition to multicellularity. Among aggregative multicellular organisms, myxobacteria are a valuable system to explore the particularities that aggregation confers to the evolution of multicellularity and mechanisms shared with clonal organisms. Moreover, myxobacteria species develop fruiting bodies displaying a range of morphological diversity. In this review, we aim to synthesize diverse lines of evidence regarding myxobacteria development and discuss them in the context of Evo-Devo concepts and approaches. First, we briefly describe the developmental processes in myxobacteria, present an updated comparative analysis of the genes involved in their developmental processes and discuss these and other lines of evidence in terms of co-option and developmental system drift, two concepts key to Evo-Devo studies. Next, as has been suggested from Evo-Devo approaches, we discuss how broad comparative studies and integration of diverse genetic, physicochemical, and environmental factors into experimental and theoretical models can further our understanding of myxobacterial development, phenotypic variation, and evolution.
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Affiliation(s)
- Juan A Arias Del Angel
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecologiía, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana E Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecologiía, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - León Patricio Martínez-Castilla
- Departamento de Bioquímica, Facultad de Quiímica, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecologiía, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Complete Genome Sequence of the Fruiting Myxobacterium Myxococcus macrosporus Strain DSM 14697, Generated by PacBio Sequencing. GENOME ANNOUNCEMENTS 2017; 5:5/40/e01127-17. [PMID: 28983009 PMCID: PMC5629066 DOI: 10.1128/genomea.01127-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Members of the Myxococcales order initiate a developmental program in response to starvation that culminates in formation of spore-filled fruiting bodies. To investigate the genetic basis for fruiting body formation, we present the complete 8.9-Mb genome sequence of Myxococcus macrosporus strain DSM 14697, generated using the PacBio sequencing platform.
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Affiliation(s)
- Silke C. Wenzel
- Saarland University; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology; Saarland University Campus, Building E8.1 66123 Saarbrücken Germany
| | - Rolf Müller
- Saarland University; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology; Saarland University Campus, Building E8.1 66123 Saarbrücken Germany
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Wei JH, Yin X, Welander PV. Sterol Synthesis in Diverse Bacteria. Front Microbiol 2016; 7:990. [PMID: 27446030 PMCID: PMC4919349 DOI: 10.3389/fmicb.2016.00990] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/09/2016] [Indexed: 11/13/2022] Open
Abstract
Sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. Sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. However, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. Phylogenomic studies have identified genes encoding homologs of sterol biosynthesis proteins in the genomes of several additional species, indicating that sterol production may be more widespread in the bacterial domain than previously thought. Although the occurrence of sterol synthesis genes in a genome indicates the potential for sterol production, it provides neither conclusive evidence of sterol synthesis nor information about the composition and abundance of basic and modified sterols that are actually being produced. Here, we coupled bioinformatics with lipid analyses to investigate the scope of bacterial sterol production. We identified oxidosqualene cyclase (Osc), which catalyzes the initial cyclization of oxidosqualene to the basic sterol structure, in 34 bacterial genomes from five phyla (Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia) and in 176 metagenomes. Our data indicate that bacterial sterol synthesis likely occurs in diverse organisms and environments and also provides evidence that there are as yet uncultured groups of bacterial sterol producers. Phylogenetic analysis of bacterial and eukaryotic Osc sequences confirmed a complex evolutionary history of sterol synthesis in this domain. Finally, we characterized the lipids produced by Osc-containing bacteria and found that we could generally predict the ability to synthesize sterols. However, predicting the final modified sterol based on our current knowledge of sterol synthesis was difficult. Some bacteria produced demethylated and saturated sterol products even though they lacked homologs of the eukaryotic proteins required for these modifications emphasizing that several aspects of bacterial sterol synthesis are still completely unknown.
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Affiliation(s)
| | | | - Paula V. Welander
- Department of Earth System Science, Stanford UniversityStanford, CA, USA
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Craig JM, Logan AC, Prescott SL. Natural environments, nature relatedness and the ecological theater: connecting satellites and sequencing to shinrin-yoku. J Physiol Anthropol 2016; 35:1. [PMID: 26763049 PMCID: PMC4712592 DOI: 10.1186/s40101-016-0083-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/07/2016] [Indexed: 02/08/2023] Open
Abstract
Recent advances in research concerning the public health value of natural environments have been remarkable. The growing interest in this topic (often housed under terms such as green and/or blue space) has been occurring in parallel with the microbiome revolution and an increased use of remote sensing technology in public health. In the context of biodiversity loss, rapid urbanization, and alarming rates of global non-communicable diseases (many associated with chronic, low-grade inflammation), discussions of natural vis-a-vis built environments are not merely fodder for intellectual curiosity. Here, we argue for increased interdisciplinary collaboration with the aim of better understanding the mechanisms—including aerobiological and epigenetic—that might help explain some of the noted positive health outcomes. It is our contention that some of these mechanisms are related to ecodiversity (i.e., the sum of biodiversity and geodiversity, including biotic and abiotic constituents). We also encourage researchers to more closely examine individual nature relatedness and how it might influence many outcomes that are at the interface of lifestyle habits and contact with ecodiversity.
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Affiliation(s)
- Jeffrey M Craig
- Murdoch Childrens Research Institute; Department of Paediatrics, University of Melbourne, The Royal Children's Hospital, Flemington Road, Parkville, Victoria, 3052, Australia. .,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN), Perth, Australia.
| | - Alan C Logan
- CAMNR, 23679 Calabassas Road, Suite 542, Calabassas, CA, 91302, USA. .,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN), Perth, Australia.
| | - Susan L Prescott
- School of Paediatrics and Child Health, Princess Margaret Hospital for Children, University of Western Australia, GPO Box D 184, Perth, WA, 6840, Australia. .,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN), Perth, Australia.
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Mohr KI, Stechling M, Wink J, Wilharm E, Stadler M. Comparison of myxobacterial diversity and evaluation of isolation success in two niches: Kiritimati Island and German compost. Microbiologyopen 2015; 5:268-78. [PMID: 26669488 PMCID: PMC4831471 DOI: 10.1002/mbo3.325] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/08/2015] [Accepted: 11/09/2015] [Indexed: 02/05/2023] Open
Abstract
Myxobacteria harbor an enormous potential for new bioactive secondary metabolites and therefore the isolation of in particular new groups is of great interest. The diversity of myxobacteria present in two ecological habitats, namely sand from Kiritimati Island and German compost, was evaluated by both cultivation‐based and cultivation‐independent methods. Phylogenetic analyses of the strains in comparison with 16S rRNA gene sequences from cultured and uncultured material in GenBank revealed a great potential of undescribed myxobacteria in both sampling sites. Several OTUs (operational taxonomic units) represent unknown taxa and were detected by clone bank analyses, but not by cultivation. Clone bank analyses indicated that the myxobacterial community is predominantly indigenous. The 16S rDNA libraries from the two samples were generated from total community DNA with myxobacterial specific forward and universal reverse primer sets. The clones were partially sequenced. Cultivation was successful for exclusively bacteriolytic, but not for cellulolytic myxobacteria and revealed 42 strains from the genera Corallococcus, Myxococcus, and Polyangium. The genera of Myxococcaceae family were represented by both approaches. But, even in this well studied family, as well as in the suborders Sorangiineae and Nannocystineae, a considerable number of clones were assigned to, if any, uncultivated organisms. Our study shows an overrepresentation of the genera Myxococcus spp. and Corallococcus spp. with standard cultivation methods. However, high deficits are demonstrated in the cultivation success of the myxobacterial diversity detected by exclusively cultivation‐independent approaches. Especially, clades which are exclusively represented by clones are of high interest with regard to the cultivation of new bioactive secondary metabolite producers.
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Affiliation(s)
- Kathrin I Mohr
- Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, D-38124, Germany
| | - Marc Stechling
- Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, D-38124, Germany.,Department of Supply Engineering, Ostfalia, Salzdahlumer Straße 46/48, Wolfenbüttel, D-38302, Germany
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, D-38124, Germany
| | - Elke Wilharm
- Department of Supply Engineering, Ostfalia, Salzdahlumer Straße 46/48, Wolfenbüttel, D-38302, Germany
| | - Marc Stadler
- Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, D-38124, Germany
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