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Zapata-Peñasco I, Avelino-Jiménez I, Mendoza-Pérez J, Vázquez Guevara M, Gutiérrez-Ladrón de Guevara M, Valadez- Martínez M, Hernández-Maya L, Garibay-Febles V, Fregoso-Aguilar T, Fonseca-Campos J. Environmental stressor assessment of hydrocarbonoclastic bacteria biofilms from a marine oil spill. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 42:e00834. [PMID: 38948351 PMCID: PMC11211098 DOI: 10.1016/j.btre.2024.e00834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 07/02/2024]
Abstract
The environmental and economic impact of an oil spill can be significant. Biotechnologies applied during a marine oil spill involve bioaugmentation with immobilised or encapsulated indigenous hydrocarbonoclastic species selected under laboratory conditions to improve degradation rates. The environmental factors that act as stressors and impact the effectiveness of hydrocarbon removal are one of the challenges associated with these applications. Understanding how native microbes react to environmental stresses is necessary for effective bioaugmentation. Herein, Micrococcus luteus and M. yunnanensis isolated from a marine oil spill mooring system showed hydrocarbonoclastic activity on Maya crude oil in a short time by means of total petroleum hydrocarbons (TPH) at 144 h: M. luteus up to 98.79 % and M. yunnanensis 97.77 % removal. The assessment of Micrococcus biofilms at different temperature (30 °C and 50 °C), pH (5, 6, 7, 8, 9), salinity (30, 50, 60, 70, 80 g/L), and crude oil concentration (1, 5, 15, 25, 35 %) showed different response to the stressors depending on the strain. According to response surface analysis, the main effect was temperature > salinity > hydrocarbon concentration. The hydrocarbonoclastic biofilm architecture was characterised using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Subtle but significant differences were observed: pili in M. luteus by SEM and the topographical differences measured by AFM Power Spectral Density (PSD) analysis, roughness was higher in M. luteus than in M. yunnanensis. In all three domains of life, the Universal Stress Protein (Usp) is crucial for stress adaptation. Herein, the uspA gene expression was analysed in Micrococcus biofilm under environmental stressors. The uspA expression increased up to 2.5-fold in M. luteus biofilms at 30 °C, and 1.3-fold at 50 °C. The highest uspA expression was recorded in M. yunnanensis biofilms at 50 °C with 2.5 and 3-fold with salinities of 50, 60, and 80 g/L at hydrocarbon concentrations of 15, 25, and 35 %. M. yunnanensis biofilms showed greater resilience than M. luteus biofilms when exposed to harsh environmental stressors. M. yunnanensis biofilms were thicker than M. luteus biofilms. Both biofilm responses to environmental stressors through uspA gene expression were consistent with the behaviours observed in the response surface analyses. The uspA gene is a suitable biomarker for assessing environmental stressors of potential microorganisms for bioremediation of marine oil spills and for biosensing the ecophysiological status of native microbiota in a marine petroleum environment.
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Affiliation(s)
- I. Zapata-Peñasco
- Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas Norte 152, Gustavo A. Madero, Ciudad de México, 07730, Mexico
| | - I.A. Avelino-Jiménez
- Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas Norte 152, Gustavo A. Madero, Ciudad de México, 07730, Mexico
| | - J. Mendoza-Pérez
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu 399, Nueva Industrial Vallejo, Gustavo A. Madero, 07738, Mexico
| | - M. Vázquez Guevara
- Facultad de Química, Universidad de Guanajuato, Noria Alta, Guanajuato, 36050, Mexico
| | - M. Gutiérrez-Ladrón de Guevara
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu 399, Nueva Industrial Vallejo, Gustavo A. Madero, 07738, Mexico
| | - M. Valadez- Martínez
- Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas Norte 152, Gustavo A. Madero, Ciudad de México, 07730, Mexico
| | - L. Hernández-Maya
- Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas Norte 152, Gustavo A. Madero, Ciudad de México, 07730, Mexico
| | - V. Garibay-Febles
- Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas Norte 152, Gustavo A. Madero, Ciudad de México, 07730, Mexico
| | - T. Fregoso-Aguilar
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu 399, Nueva Industrial Vallejo, Gustavo A. Madero, 07738, Mexico
| | - J. Fonseca-Campos
- Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional, Av Instituto Politécnico Nacional, Gustavo A. Madero, 07340, Mexico
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Xin Q, Saborimanesh N, Ridenour C, Farooqi H. Fate, behaviour and microbial response of diluted bitumen and conventional crude spills in a simulated warm freshwater environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 343:123224. [PMID: 38159633 DOI: 10.1016/j.envpol.2023.123224] [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: 11/08/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Diluted bitumen (DB), one of the most transported unconventional crude oils in Canada's pipelines, raises public concerns due to its potential spillage into freshwater environments. This study aimed to compare the fate and behaviour of DB versus conventional crude (CC) in a simulated warm freshwater environment. An equivalent of 10 L of either DB or CC was spilled into 1200 L of North Saskatchewan River (NSR) water containing natural NSR sediment (2.4 kg) in a mesoscale spill tank and its fate and behaviour at air/water temperatures of 18 °C/24 °C were monitored for 56 days. Oil mass distribution analysis showed that 42.3 wt % of CC and 63.6 wt% of DB resided in the oil slicks at the end of 56-day tests, consisting mainly high molecular weight (HMW) compounds (i.e., resins and asphaltenes). The lost oil contained mainly low molecular weight (LMW) compounds (i.e., light saturates and some aromatics) into the atmosphere, water column, and sediment through collective weathering processes. Notably, weathered CC emulsified with water and remained floating until the end, while the weathered DB mat started to lose its buoyancy after 24 days under quiescent conditions and resurfaced once waves were applied. Analysis of the microbial communities of water pre- and post-spills revealed the replacement of indigenous microbial communities with hydrocarbon-degrading species. Exposure to CC reduced the microbial diversity by 12%, while exposure to DB increased the diversity by 10%. During the early stages of the spill (up to Day 21), most dominant species were positively correlated with the benzene, toluene, ethylbenzene, and xylenes (BTEX) content or polycyclic aromatic hydrocarbon (PAH) content of the water column, while the dominant species at the later stages (Days 21-56) of the spill were negatively correlated with BTEX or PAH content and positively correlated with the total organic carbon (TOC) content in waters.
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Affiliation(s)
- Qin Xin
- Natural Resources Canada, CanmetENERGY, 1 Oil Patch Drive, Devon, Alberta, T9G 1A8, Canada.
| | - Nayereh Saborimanesh
- Natural Resources Canada, CanmetENERGY, 1 Oil Patch Drive, Devon, Alberta, T9G 1A8, Canada
| | - Christine Ridenour
- Natural Resources Canada, CanmetENERGY, 1 Oil Patch Drive, Devon, Alberta, T9G 1A8, Canada
| | - Hena Farooqi
- Natural Resources Canada, CanmetENERGY, 1 Oil Patch Drive, Devon, Alberta, T9G 1A8, Canada
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Li J, Luo C, Cai X, Zhang D, Guan G, Li B, Zhang G. Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders. THE ISME JOURNAL 2024; 18:wrae115. [PMID: 38913500 PMCID: PMC11256997 DOI: 10.1093/ismejo/wrae115] [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: 02/14/2024] [Revised: 05/31/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Soil microbial flora constitutes a highly diverse and complex microbiome on Earth, often challenging to cultivation, with unclear metabolic mechanisms in situ. Here, we present a pioneering concept for the in situ construction of functional microbial consortia (FMCs) and introduce an innovative method for creating FMCs by utilizing phenanthrene as a model compound to elucidate their in situ biodegradation mechanisms. Our methodology involves single-cell identification, sorting, and culture of functional microorganisms, resulting in the formation of a precise in situ FMC. Through Raman-activated cell sorting-stable-isotope probing, we identified and isolated phenanthrene-degrading bacterial cells from Achromobacter sp. and Pseudomonas sp., achieving precise and controllable in situ consortia based on genome-guided cultivation. Our in situ FMC outperformed conventionally designed functional flora when tested in real soil, indicating its superior phenanthrene degradation capacity. We revealed that microorganisms with high degradation efficiency isolated through conventional methods may exhibit pollutant tolerance but lack actual degradation ability in natural environments. This finding highlights the potential to construct FMCs based on thorough elucidation of in situ functional degraders, thereby achieving sustained and efficient pollutant degradation. Single-cell sequencing linked degraders with their genes and metabolic pathways, providing insights regarding the construction of in situ FMCs. The consortium in situ comprising microorganisms with diverse phenanthrene metabolic pathways might offer distinct advantages for enhancing phenanthrene degradation efficiency, such as the division of labour and cooperation or communication among microbial species. Our approach underscores the importance of in situ, single-cell precision identification, isolation, and cultivation for comprehensive bacterial functional analysis and resource exploration, which can extend to investigate MFCs in archaea and fungi, clarifying FMC construction methods for element recycling and pollutant transformation in complex real-world ecosystems.
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Affiliation(s)
- Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xixi Cai
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, China
- College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Guoqing Guan
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Bei Li
- State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China
- Jilin Province Raman Technology Engineering Research Center, HOOKE Instruments Ltd., Changchun 130033, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100039, China
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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Li J, Zhang D, Luo C, Li B, Zhang G. In Situ Discrimination and Cultivation of Active Degraders in Soils by Genome-Directed Cultivation Assisted by SIP-Raman-Activated Cell Sorting. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17087-17098. [PMID: 37823365 DOI: 10.1021/acs.est.3c04247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The identification and in situ cultivation of functional yet uncultivable microorganisms are important to confirm inferences regarding their ecological functions. Here, we developed a new method that couples Raman-activated cell sorting (RACS), stable-isotope probing (SIP), and genome-directed cultivation (GDC)─namely, RACS-SIP-GDC─to identify, sort, and cultivate the active toluene degraders from a complex microbial community in petroleum-contaminated soil. Using SIP, we successfully identified the active toluene degrader Pigmentiphaga, the single cells of which were subsequently sorted and isolated by RACS. We further successfully assembled the genome of Pigmentiphaga based on the metagenomic sequencing of 13C-DNA and genomic sequencing of sorted cells, which was confirmed by gyrB gene comparison and average nucleotide identity determination. Additionally, the genotypes and phenotypes of this degrader were directly linked at the single-cell level, and its complete toluene metabolic pathways in petroleum-contaminated soil were reconstructed. Based on its unique metabolic properties uncovered by genome sequencing, we modified the traditional cultivation medium with antibiotics, amino acids, carbon sources, and growth factors (e.g., vitamins and metals), achieving the successful cultivation of RACS-sorted active degrader Pigmentiphaga sp. Our results implied that RACS-SIP-GDC is a state-of-the-art approach for the precise identification, targeted isolation, and cultivation of functional microbes from complex communities in natural habitats. RACS-SIP-GDC can be used to explore specific and targeted organic-pollution-degrading microorganisms at the single-cell level and provide new insights into their biodegradation mechanisms.
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Affiliation(s)
- Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, China
- College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Bei Li
- State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 130033 Changchun, China
- HOOKE Instruments Ltd., 130033 Changchun, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
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Fitness-Conditional Genes for Soil Adaptation in the Bioaugmentation Agent Pseudomonas veronii 1YdBTEX2. mSystems 2023; 8:e0117422. [PMID: 36786610 PMCID: PMC10134887 DOI: 10.1128/msystems.01174-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Strain inoculation (bioaugmentation) is a potentially useful technology to provide microbiomes with new functionalities. However, there is limited understanding of the genetic factors contributing to successful establishment of inoculants. This work aimed to characterize the genes implicated in proliferation of the monoaromatic compound-degrading Pseudomonas veronii 1YdBTEX2 in nonsterile polluted soils. We generated two independent mutant libraries by random minitransposon-delivered marker insertion followed by deep sequencing (Tn-seq) with a total of 5.0 × 105 unique insertions. Libraries were grown in multiple successive cycles for up to 50 generations either in batch liquid medium or in two types of soil microcosms with different resident microbial content (sand or silt) in the presence of toluene. Analysis of gene insertion abundances at different time points (passed generations of metapopulation growth), in comparison to proportions at start and to in silico generated randomized insertion distributions, allowed to define ~800 essential genes common to both libraries and ~2,700 genes with conditional fitness effects in either liquid or soil (195 of which resulted in fitness gain). Conditional fitness genes largely overlapped among all growth conditions but affected approximately twice as many functions in liquid than in soil. This indicates soil to be a more promiscuous environment for mutant growth, probably because of additional nutrient availability. Commonly depleted genes covered a wide range of biological functions and metabolic pathways, such as inorganic ion transport, fatty acid metabolism, amino acid biosynthesis, or nucleotide and cofactor metabolism. Only sparse gene sets were uncovered whose insertion caused fitness decrease exclusive for soils, which were different between silt and sand. Despite detectable higher resident bacteria and potential protist predatory counts in silt, we were, therefore, unable to detect any immediately obvious candidate genes affecting P. veronii biological competitiveness. In contrast to liquid growth conditions, mutants inactivating flagella biosynthesis and motility consistently gained strong fitness advantage in soils and displayed higher growth rates than wild type. In conclusion, although many gene functions were found to be important for growth in soils, most of these are not specific as they affect growth in liquid minimal medium more in general. This indicates that P. veronii does not need major metabolic reprogramming for proliferation in soil with accessible carbon and generally favorable growth conditions. IMPORTANCE Restoring damaged microbiomes is still a formidable challenge. Classical widely adopted approaches consist of augmenting communities with pure or mixed cultures in the hope that these display their intended selected properties under in situ conditions. Ecological theory, however, dictates that introduction of a nonresident microbe is unlikely to lead to its successful proliferation in a foreign system such as a soil microbiome. In an effort to study this systematically, we used random transposon insertion scanning to identify genes and possibly, metabolic subsystems, that are crucial for growth and survival of a bacterial inoculant (Pseudomonas veronii) for targeted degradation of monoaromatic compounds in contaminated nonsterile soils. Our results indicate that although many gene functions are important for proliferation in soil, they are general factors for growth and not exclusive for soil. In other words, P. veronii is a generalist that is not a priori hindered by the soil for its proliferation and would make a good bioaugmentation candidate.
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Jiang L, Seo J, Peng Y, Jeon D, Lee JH, Kim CY, Lee J. A nostoxanthin-producing bacterium, Sphingomonas nostoxanthinifaciens sp. nov., alleviates the salt stress of Arabidopsis seedlings by scavenging of reactive oxygen species. Front Microbiol 2023; 14:1101150. [PMID: 36846770 PMCID: PMC9950776 DOI: 10.3389/fmicb.2023.1101150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/18/2023] [Indexed: 02/12/2023] Open
Abstract
A novel, nostoxanthin-producing, endophytic bacterium, designated as AK-PDB1-5T, was isolated from the needle-like leaves of the Korean fir (Abies koreana Wilson) collected from Mt. Halla in Jeju, South Korea. A 16S rRNA sequence comparison indicated that the closest phylogenetic neighbors were Sphingomonas crusticola MIMD3T (95.6%) and Sphingomonas jatrophae S5-249T (95.3%) of the family Sphingomonadaceae. Strain AK-PDB1-5T had a genome size of 4,298,284 bp with a 67.8% G + C content, and digital DNA-DNA hybridization and OrthoANI values with the most closely related species of only 19.5-21% and 75.1-76.8%, respectively. Cells of the strain AK-PDB1-5T were Gram-negative, short rods, oxidase- and catalase-positive. Growth occurred at pH 5.0-9.0 (optimum pH 8.0) in the absence of NaCl at 4-37°C (optimum 25-30°C). Strain AK-PDB1-5T contained C14:0 2OH, C16:0 and summed feature 8 as the major cellular fatty acids (> 10%), while sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phospholipids and lipids were found to be the major polar lipids. The strain produces a yellow carotenoid pigment; natural products prediction via AntiSMASH tool found zeaxanthin biosynthesis clusters in the entire genome. Biophysical characterization by ultraviolet-visible absorption spectroscopy and ESI-MS studies confirmed the yellow pigment was nostoxanthin. In addition, strain AK-PDB1-5T was found significantly promote Arabidopsis seedling growth under salt conditions by reducing reactive oxygen species (ROS). Based on the polyphasic taxonomic analysis results, strain AK-PDB1-5T was determined to be a novel species in the genus Sphingomonas with the proposed name Sphingomonas nostoxanthinifaciens sp. nov. The type strain is AK-PDB1-5T (= KCTC 82822T = CCTCC AB 2021150T).
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Affiliation(s)
- Lingmin Jiang
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Jiyoon Seo
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Yuxin Peng
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Doeun Jeon
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Ju Huck Lee
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Cha Young Kim
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
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Yu F, Li Y, Wang H, Peng T, Wu YR, Hu Z. Microbial debromination of hexabromocyclododecanes. Appl Microbiol Biotechnol 2021; 105:4535-4550. [PMID: 34076715 DOI: 10.1007/s00253-021-11095-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/22/2020] [Accepted: 01/03/2021] [Indexed: 11/29/2022]
Abstract
Hexabromocyclododecanes (HBCDs), a new sort of brominated flame retardants (BFRs), are globally prevalent and recalcitrant toxic environmental pollutants. HBCDs have been found in many environmental media and even in the human body, leading to serious health concerns. HBCDs are biodegradable in the environment. By now, dozens of bacteria have been discovered with the ability to transform HBCDs. Microbial debromination of HBCDs is via HBr-elimination, HBr-dihaloelimination, and hydrolytic debromination. Biotic transformation of HBCDs yields many hydroxylated and lower brominated compounds which lack assessment of ecological toxicity. Bioremediation of HBCD pollution has only been applied in the laboratory. Here, we review the current knowledge about microbial debromination of HBCDs, aiming to promote the bioremediation applied in HBCD contaminated sites. KEY POINTS: • Microbial debromination of HBCDs is via hydrolytic debromination, HBr-elimination, and HBr-dihaloelimination. • Newly occurred halogenated contaminants such as HBCDs hitch the degradation pathway tamed by previously discharged anthropogenic organohalides. • Strategy that combines bioaugmentation with phytoremediation for bioremediation of HBCD pollution is promising.
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Affiliation(s)
- Fei Yu
- Department of Biology, Science College, Shantou University, Shantou, 515063, Guangdong Province, People's Republic of China
| | - Yuyang Li
- Department of Biology, Science College, Shantou University, Shantou, 515063, Guangdong Province, People's Republic of China
| | - Hui Wang
- Department of Biology, Science College, Shantou University, Shantou, 515063, Guangdong Province, People's Republic of China
| | - Tao Peng
- Department of Biology, Science College, Shantou University, Shantou, 515063, Guangdong Province, People's Republic of China
| | - Yi-Rui Wu
- Department of Biology, Science College, Shantou University, Shantou, 515063, Guangdong Province, People's Republic of China
| | - Zhong Hu
- Department of Biology, Science College, Shantou University, Shantou, 515063, Guangdong Province, People's Republic of China.
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9
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Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress. THE ISME JOURNAL 2021; 15:1751-1766. [PMID: 33432138 PMCID: PMC8163872 DOI: 10.1038/s41396-020-00884-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023]
Abstract
As a frequent inhabitant of sites polluted with toxic chemicals, the soil bacterium and plant-root colonizer Pseudomonas putida can tolerate high levels of endogenous and exogenous oxidative stress. Yet, the ultimate reason of such phenotypic property remains largely unknown. To shed light on this question, metabolic network-wide routes for NADPH generation-the metabolic currency that fuels redox-stress quenching mechanisms-were inspected when P. putida KT2440 was challenged with a sub-lethal H2O2 dose as a proxy of oxidative conditions. 13C-tracer experiments, metabolomics, and flux analysis, together with the assessment of physiological parameters and measurement of enzymatic activities, revealed a substantial flux reconfiguration in oxidative environments. In particular, periplasmic glucose processing was rerouted to cytoplasmic oxidation, and the cyclic operation of the pentose phosphate pathway led to significant NADPH-forming fluxes, exceeding biosynthetic demands by ~50%. The resulting NADPH surplus, in turn, fueled the glutathione system for H2O2 reduction. These properties not only account for the tolerance of P. putida to environmental insults-some of which end up in the formation of reactive oxygen species-but they also highlight the value of this bacterial host as a platform for environmental bioremediation and metabolic engineering.
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Separate Upper Pathway Ring Cleavage Dioxygenases Are Required for Growth of Sphingomonas wittichii Strain RW1 on Dibenzofuran and Dibenzo- p-Dioxin. Appl Environ Microbiol 2021; 87:AEM.02464-20. [PMID: 33741618 DOI: 10.1128/aem.02464-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/09/2021] [Indexed: 11/20/2022] Open
Abstract
Sphingomonas wittichii RW1 is one of a few strains known to grow on the related compounds dibenzofuran (DBF) and dibenzo-p-dioxin (DXN) as the sole source of carbon. Previous work by others (B. Happe, L. D. Eltis, H. Poth, R. Hedderich, and K. N. Timmis, J Bacteriol 175:7313-7320, 1993, https://doi.org/10.1128/jb.175.22.7313-7320.1993) showed that purified DbfB had significant ring cleavage activity against the DBF metabolite trihydroxybiphenyl but little activity against the DXN metabolite trihydroxybiphenylether. We took a physiological approach to positively identify ring cleavage enzymes involved in the DBF and DXN pathways. Knockout of dbfB on the RW1 megaplasmid pSWIT02 results in a strain that grows slowly on DBF but normally on DXN, confirming that DbfB is not involved in DXN degradation. Knockout of SWIT3046 on the RW1 chromosome results in a strain that grows normally on DBF but that does not grow on DXN, demonstrating that SWIT3046 is required for DXN degradation. A double-knockout strain does not grow on either DBF or DXN, demonstrating that these are the only ring cleavage enzymes involved in RW1 DBF and DXN degradation. The replacement of dbfB by SWIT3046 results in a strain that grows normally (equal to the wild type) on both DBF and DXN, showing that promoter strength is important for SWIT3046 to take the place of DbfB in DBF degradation. Thus, both dbfB- and SWIT3046-encoded enzymes are involved in DBF degradation, but only the SWIT3046-encoded enzyme is involved in DXN degradation.IMPORTANCE S. wittichii RW1 has been the subject of numerous investigations, because it is one of only a few strains known to grow on DXN as the sole carbon and energy source. However, while the genome has been sequenced and several DBF pathway enzymes have been purified, there has been very little research using physiological techniques to precisely identify the genes and enzymes involved in the RW1 DBF and DXN catabolic pathways. Using knockout and gene replacement mutagenesis, our work identifies separate upper pathway ring cleavage enzymes involved in the related catabolic pathways for DBF and DXN degradation. The identification of a new enzyme involved in DXN biodegradation explains why the pathway of DBF degradation on the RW1 megaplasmid pSWIT02 is inefficient for DXN degradation. In addition, our work demonstrates that both plasmid- and chromosomally encoded enzymes are necessary for DXN degradation, suggesting that the DXN pathway has only recently evolved.
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11
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Morales M, Sentchilo V, Hadadi N, van der Meer JR. Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils. ENVIRONMENTAL MICROBIOME 2021; 16:8. [PMID: 33926576 PMCID: PMC8082905 DOI: 10.1186/s40793-021-00378-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Bioaugmentation aims to use the capacities of specific bacterial strains inoculated into sites to enhance pollutant biodegradation. Bioaugmentation results have been mixed, which has been attributed to poor inoculant growth and survival in the field, and, consequently, moderate catalytic performance. However, our understanding of biodegradation activity mostly comes from experiments conducted under laboratory conditions, and the processes occurring during adaptation and invasion of inoculants into complex environmental microbiomes remain poorly known. The main aim of this work was thus to study the specific and different cellular reactions of an inoculant for bioaugmentation during adaptation, growth and survival in natural clean and contaminated non-sterile soils, in order to better understand factors limiting bioaugmentation. RESULTS As inoculant we focused on the monoaromatic compound-degrading bacterium Pseudomonas veronii 1YdBTEX2. The strain proliferated in all but one soil types in presence and in absence of exogenously added toluene. RNAseq and differential genome-wide gene expression analysis illustrated both a range of common soil responses such as increased nutrient scavenging and recycling, expression of defense mechanisms, as well as environment-specific reactions, notably osmoprotection and metal homeostasis. The core metabolism of P. veronii remained remarkably constant during exponential growth irrespective of the environment, with slight changes in cofactor regeneration pathways, possibly needed for balancing defense reactions. CONCLUSIONS P. veronii displayed a versatile global program, enabling it to adapt to a variety of soil environments in the presence and even in absence of its target pollutant toluene. Our results thus challenge the widely perceived dogma of poor survival and growth of exogenous inoculants in complex microbial ecosystems such as soil and provide a further basis to developing successful bioaugmentation strategies.
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Affiliation(s)
- Marian Morales
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Noushin Hadadi
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
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12
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Dubey M, Hadadi N, Pelet S, Carraro N, Johnson DR, van der Meer JR. Environmental connectivity controls diversity in soil microbial communities. Commun Biol 2021; 4:492. [PMID: 33888858 PMCID: PMC8062517 DOI: 10.1038/s42003-021-02023-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/24/2021] [Indexed: 01/03/2023] Open
Abstract
Interspecific interactions are thought to govern the stability and functioning of microbial communities, but the influence of the spatial environment and its structural connectivity on the potential of such interactions to unfold remain largely unknown. Here we studied the effects on community growth and microbial diversity as a function of environmental connectivity, where we define environmental connectivity as the degree of habitat fragmentation preventing microbial cells from living together. We quantitatively compared growth of a naturally-derived high microbial diversity community from soil in a completely mixed liquid suspension (high connectivity) to growth in a massively fragmented and poorly connected environment (low connectivity). The low connectivity environment consisted of homogenously-sized miniature agarose beads containing random single or paired founder cells. We found that overall community growth was the same in both environments, but the low connectivity environment dramatically reduced global community-level diversity compared to the high connectivity environment. Experimental observations were supported by community growth modeling. The model predicts a loss of diversity in the low connectivity environment as a result of negative interspecific interactions becoming more dominant at small founder species numbers. Counterintuitively for the low connectivity environment, growth of isolated single genotypes was less productive than that of random founder genotype cell pairs, suggesting that the community as a whole profited from emerging positive interspecific interactions. Our work demonstrates the importance of environmental connectivity for growth of natural soil microbial communities, which aids future efforts to intervene in or restore community composition to achieve engineering and biotechnological objectives. Manupriyam Dubey et al. use experimental systems with naturally derived soil microbiomes in liquid suspensions and encapsulated beads to compare community dynamics in well-connected and poorly connected environments. While their results show that microbial growth does not vary between conditions, they report that low connectivity led to reduced microbial diversity and suggest that these reductions in microbial diversity may be due to increased negative interspecific interactions.
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Affiliation(s)
- Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Noushin Hadadi
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Dübendorf, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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13
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Rojas-Jaimes J, Lindo-Seminario D, Correa-Núñez G, Diringer B. Characterization of the bacterial microbiome of Rhipicephalus (Boophilus) microplus collected from Pecari tajacu "Sajino" Madre de Dios, Peru. Sci Rep 2021; 11:6661. [PMID: 33758359 PMCID: PMC7988070 DOI: 10.1038/s41598-021-86177-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/08/2021] [Indexed: 01/05/2023] Open
Abstract
Ticks are arthropods that can host and transmit pathogens to wild animals, domestic animals, and even humans. The bacterial microbiome of adult (males and females) and nymph Rhipicephalus microplus ticks collected from a collared peccary, Pecari tajacu, captured in the rural area of Botijón Village in the Amazon region of Madre de Dios, Peru, was evaluated using metagenomics. The Chao1 and Shannon-Weaver analyses indicated greater bacterial richness and diversity in female ticks (GARH; 375-4.15) and nymph ticks (GARN; 332-4.75) compared to that in male ticks (GARM; 215-3.20). Taxonomic analyses identified 185 operational taxonomic units representing 147 bacterial genera. Of the 25 most prevalent genera, Salmonella (17.5%) and Vibrio (15.0%) showed the highest relative abundance followed by several other potentially pathogenic genera, such as Paracoccus (7.8%), Staphylococcus (6.8%), Pseudomonas (6.6%), Corynebacterium (5.0%), Cloacibacterium (3.6%), and Acinetobacter (2.5%). In total, 19.7% of the detected genera are shared by GARH, GARM, and GARN, and they can be considered as the core microbiome of R. microplus. To the best of our knowledge, this study is the first to characterize the microbiome of ticks collected from P. tajacu and to report the presence of Salmonella and Vibrio in R. microplus. The pathogenic potential and the role of these bacteria in the physiology of R. microplus should be further investigated due to the possible implications for public health and animal health in populations neighboring the habitat of P. tajacu.
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Affiliation(s)
- Jesús Rojas-Jaimes
- Facultad de Ciencias de la Salud, Universidad Privada del Norte, Av. El Sol 461, San Juan de Lurigancho, 15434, Lima, Peru.
| | | | - Germán Correa-Núñez
- Departamento Académico de Ciencias Básicas, Universidad Nacional Amazónica de Madre de Dios, Puerto Maldonado, Peru
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14
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Rocha-Arriaga C, Espinal-Centeno A, Martinez-Sánchez S, Caballero-Pérez J, Alcaraz LD, Cruz-Ramírez A. Deep microbial community profiling along the fermentation process of pulque, a biocultural resource of Mexico. Microbiol Res 2020; 241:126593. [DOI: 10.1016/j.micres.2020.126593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/26/2022]
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15
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Park C, Kim M, Lee BH, Lee KE, Park W. Sphingomonas changnyeongensis sp. nov. isolated from the Hapcheon–Changnyeong barrage area in the Nakdong river. Int J Syst Evol Microbiol 2020; 70:6091-6097. [DOI: 10.1099/ijsem.0.004503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The novel bacterial strain C33T was isolated from a freshwater sample collected from the Hapcheon–Changnyeong barrage. The Gram-negative, motile, yellow-pigmented strain C33T was characterized as a rod-shaped and strictly aerobic bacterium. A 16S-rRNA phylogenetic analysis revealed that this strain was most closely related to
Sphingomonas changbaiensis
V2M44T,
Sphingomonas tabacisoli
X1-8T, and
Sphingomonas flavalba
ZLT-5T with 97.1, 97.0, and 95.0 % 16S-rRNA sequence similarities, respectively. The genomic DNA GC content of strain C33T was estimated at 65.0 mol%. The average nucleotide identity of strain C33T relative to
S. changbaiensis
V2M44T and
S. flavalba
ZLT-5T was found to be 77.0 and 75.6%, with average amino-acid identities of 69.9, and 66.7%, and the digital DNA–DNA hybridization values of 21.3 and 17.7 %, respectively. The cells grew at 19–37 °C and pH 6–9 with 0–0.5 % (w/v) NaCl (optimum: 28 °C, pH 6.5, and 0 % NaCl). The major component identified in the polyamine pattern was sym-homospermidine, and the main ubiquinone was Q-10. The predominant polar lipids characterized were diphophatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, and sphingoglycolipid. Iso-C15 : 0, C15 : 0 anteiso, and summed feature 3 (C16 : 1
ω6c and/or C16 : 1
ω7c) were found to be the primary cellular fatty acids in strain C33T. Based on these genotypic and phenotypic characteristics, strain C33T was classified as a novel species of the genus
Sphingomonas
; and the name Sphingomonas changnyeongensis sp. nov. is proposed (=KACC 21511T=JCM 33880T).
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Affiliation(s)
- Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Byoung-Hee Lee
- National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Ki-Eun Lee
- National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
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16
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Gran-Scheuch A, Ramos-Zuñiga J, Fuentes E, Bravo D, Pérez-Donoso JM. Effect of Co-contamination by PAHs and Heavy Metals on Bacterial Communities of Diesel Contaminated Soils of South Shetland Islands, Antarctica. Microorganisms 2020; 8:microorganisms8111749. [PMID: 33171767 PMCID: PMC7695015 DOI: 10.3390/microorganisms8111749] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/26/2020] [Accepted: 10/31/2020] [Indexed: 01/04/2023] Open
Abstract
Diesel oil is the main source of energy used in Antarctica. Since diesel is composed of toxic compounds such as polycyclic aromatic hydrocarbons (PAHs) and heavy metals, it represents a constant threat to the organisms inhabiting this continent. In the present study, we characterized the chemical and biological parameters of diesel-exposed soils obtained from King George Island in Antarctica. Contaminated soils present PAH concentrations 1000 times higher than non-exposed soils. Some contaminated soil samples also exhibited high concentrations of cadmium and lead. A 16S metagenome analysis revealed the effect of co-contamination on bacterial communities. An increase in the relative abundance of bacteria known as PAH degraders or metal resistant was determined in co-contaminated soils. Accordingly, the soil containing higher amounts of PAHs exhibited increased dehydrogenase activity than control soils, suggesting that the microorganisms present can metabolize diesel. The inhibitory effect on soil metabolism produced by cadmium was lower in diesel-contaminated soils. Moreover, diesel-contaminated soils contain higher amounts of cultivable heterotrophic, cadmium-tolerant, and PAH-degrading bacteria than control soils. Obtained results indicate that diesel contamination at King George island has affected microbial communities, favoring the presence of microorganisms capable of utilizing PAHs as a carbon source, even in the presence of heavy metals.
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Affiliation(s)
- Alejandro Gran-Scheuch
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica # 330, Santiago 8370146, Chile; (A.G.-S.); (J.R.-Z.)
- Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone Pohlhammer # 1007, Santiago 8380000, Chile;
| | - Javiera Ramos-Zuñiga
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica # 330, Santiago 8370146, Chile; (A.G.-S.); (J.R.-Z.)
| | - Edwar Fuentes
- Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone Pohlhammer # 1007, Santiago 8380000, Chile;
| | - Denisse Bravo
- Laboratorio de Microbiología Oral, Facultad de Odontología, Universidad de Chile, Sergio Livingstone Pohlhammer # 943, Santiago 8380453, Chile;
| | - José M. Pérez-Donoso
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica # 330, Santiago 8370146, Chile; (A.G.-S.); (J.R.-Z.)
- Correspondence:
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17
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Chai B, Tsoi T, Sallach JB, Liu C, Landgraf J, Bezdek M, Zylstra G, Li H, Johnston CT, Teppen BJ, Cole JR, Boyd SA, Tiedje JM. Bioavailability of clay-adsorbed dioxin to Sphingomonas wittichii RW1 and its associated genome-wide shifts in gene expression. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 712:135525. [PMID: 32050392 DOI: 10.1016/j.scitotenv.2019.135525] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/10/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Polychlorinated dibenzo-p-dioxins and dibenzofurans are a group of chemically-related pollutants categorically known as dioxins. Some of their chlorinated congeners are among the most hazardous pollutants that persist in the environment. This persistence is due in part to the limited number of bacteria capable of metabolizing these compounds, but also to their limited bioavailability in soil. We used Sphingomonas wittichii strain RW1 (RW1), one of the few strains able to grow on dioxin, to characterize its ability to respond to and degrade clay-bound dioxin. We found that RW1 grew on and completely degraded dibenzo-p-dioxin (DD) intercalated into the smectite clay saponite (SAP). To characterize the effects of DD sorption on RW1 gene expression, we compared transcriptomes of RW1 grown with either free crystalline DD or DD intercalated clay, i.e. sandwiched between the clay interlayers (DDSAP). Free crystalline DD appeared to cause greater expression of toxicity and stress related functions. Genes coding for heat shock proteins, chaperones, as well as genes involved in DNA repair, and efflux were up-regulated during growth on crystalline dioxin compared to growth on intercalated dioxin. In contrast, growth on intercalated dioxin up-regulated genes that might be important in recognition and uptake mechanisms, as well as surface interaction/attachment/biofilm formation such as extracellular solute-binding protein and LuxR. These differences in gene expression may reflect the underlying adaptive mechanisms by which RW1 cells sense and deploy pathways to access dioxin intercalated into clay. These data show that intercalated DD remains bioavailable to the degrading bacterium with implications for bioremediation alternatives.
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Affiliation(s)
- Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Tamara Tsoi
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - J Brett Sallach
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Cun Liu
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Jeff Landgraf
- Research Technology Support Facility, Michigan State University, East Lansing, MI, USA
| | - Mark Bezdek
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Gerben Zylstra
- Department of Biochemistry & Microbiology, Rutgers University, New Brunswick, NJ, USA
| | - Hui Li
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Cliff T Johnston
- Department of Crop, Soil and Environmental Sciences, Purdue University, West Lafayette, IN, USA
| | - Brian J Teppen
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Stephen A Boyd
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA; Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
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18
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Samantarrai D, Lakshman Sagar A, Gudla R, Siddavattam D. TonB-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation. Microorganisms 2020; 8:microorganisms8030359. [PMID: 32138166 PMCID: PMC7142613 DOI: 10.3390/microorganisms8030359] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/24/2019] [Accepted: 01/07/2020] [Indexed: 12/19/2022] Open
Abstract
TonB-dependent transport system plays a critical role in the transport of nutrients across the energy-deprived outer membrane of Gram-negative bacteria. It contains a specialized outer membrane TonB-dependent transporter (TBDT) and energy generating (ExbB/ExbD) and transducing (TonB) inner membrane multi-protein complex, called TonB complex. Very few TonB complex protein-coding sequences exist in the genomes of Gram-negative bacteria. Interestingly, the TBDT coding alleles are phenomenally high, especially in the genomes of bacteria surviving in complex and stressful environments. Sphingomonads are known to survive in highly polluted environments using rare, recalcitrant, and toxic substances as their sole source of carbon. Naturally, they also contain a huge number of TBDTs in the outer membrane. Out of them, only a few align with the well-characterized TBDTs. The functions of the remaining TBDTs are not known. Predictions made based on genome context and expression pattern suggest their involvement in the transport of xenobiotic compounds across the outer membrane.
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19
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Saibu S, Adebusoye SA, Oyetibo GO. Aerobic bacterial transformation and biodegradation of dioxins: a review. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-0294-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractWaste generation tends to surge in quantum as the population and living conditions grow. A group of structurally related chemicals of dibenzofurans and dibenzo-p-dioxins including their chlorinated congeners collectively known as dioxins are among the most lethal environmental pollutants formed during different anthropogenic activities. Removal of dioxins from the environment is challenging due to their persistence, recalcitrance to biodegradation, and prevalent nature. Dioxin elimination through the biological approach is considered both economically and environmentally as a better substitute to physicochemical conventional approaches. Bacterial aerobic degradation of these compounds is through two major catabolic routes: lateral and angular dioxygenation pathways. Information on the diversity of bacteria with aerobic dioxin degradation capability has accumulated over the years and efforts have been made to harness this fundamental knowledge to cleanup dioxin-polluted soils. This paper covers the previous decades and recent developments on bacterial diversity and aerobic bacterial transformation, degradation, and bioremediation of dioxins in contaminated systems.
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20
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Fanesi A, Zegeye A, Mustin C, Cébron A. Soil Particles and Phenanthrene Interact in Defining the Metabolic Profile of Pseudomonas putida G7: A Vibrational Spectroscopy Approach. Front Microbiol 2018; 9:2999. [PMID: 30564224 PMCID: PMC6288191 DOI: 10.3389/fmicb.2018.02999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/20/2018] [Indexed: 01/21/2023] Open
Abstract
In soil, organic matter and mineral particles (soil particles; SPs) strongly influence the bio-available fraction of organic pollutants, such as polycyclic aromatic hydrocarbons (PAHs), and the metabolic activity of bacteria. However, the effect of SPs as well as comparative approaches to discriminate the metabolic responses to PAHs from those to simple carbon sources are seldom considered in mineralization experiments, limiting our knowledge concerning the dynamics of contaminants in soil. In this study, the metabolic profile of a model PAH-degrading bacterium, Pseudomonas putida G7, grown in the absence and presence of different SPs (i.e., sand, clays and humic acids), using either phenanthrene or glucose as the sole carbon and energy source, was characterized using vibrational spectroscopy (i.e., FT-Raman and FT-IR spectroscopy) and multivariate classification analysis (i.e., PLS-DA). The different type of SPs specifically altered the metabolic profile of P. putida, especially in combination with phenanthrene. In comparison to the cells grown in the absence of SPs, sand induced no remarkable change in the metabolic profile of the cells, whereas clays and humic acids affected it the most, as revealed by the higher discriminative accuracy (R2, RMSEP and sensitivity) of the PLS-DA for those conditions. With respect to the carbon-source (phenanthrene vs. glucose), no effect on the metabolic profile was evident in the absence of SPs or in the presence of sand. On the other hand, with clays and humic acids, more pronounced spectral clusters between cells grown on glucose or on phenanthrene were evident, suggesting that these SPs modify the way cells access and metabolize PAHs. The macromolecular changes regarded mainly protein secondary structures (a shift from α-helices to β-sheets), amino acid levels, nucleic acid conformation and cell wall carbohydrates. Our results provide new interesting evidences that SPs specifically interact with PAHs in defining bacteria metabolic profiles and further emphasize the importance of studying the interaction of bacteria with their surrounding matrix to deeply understand PAHs degradation in soils.
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Affiliation(s)
- Andrea Fanesi
- Laboratoire Interdisciplinaire des Environnements Continentaux, CNRS, Université de Lorraine, Nancy, France
| | - Asfaw Zegeye
- Laboratoire Interdisciplinaire des Environnements Continentaux, CNRS, Université de Lorraine, Nancy, France
| | - Christian Mustin
- Laboratoire Interdisciplinaire des Environnements Continentaux, CNRS, Université de Lorraine, Nancy, France
| | - Aurélie Cébron
- Laboratoire Interdisciplinaire des Environnements Continentaux, CNRS, Université de Lorraine, Nancy, France
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Atashgahi S, Sánchez-Andrea I, Heipieper HJ, van der Meer JR, Stams AJM, Smidt H. Prospects for harnessing biocide resistance for bioremediation and detoxification. Science 2018; 360:743-746. [DOI: 10.1126/science.aar3778] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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22
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Lu ZM, Wang ZM, Zhang XJ, Mao J, Shi JS, Xu ZH. Microbial ecology of cereal vinegar fermentation: insights for driving the ecosystem function. Curr Opin Biotechnol 2017; 49:88-93. [PMID: 28843369 DOI: 10.1016/j.copbio.2017.07.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/07/2017] [Accepted: 07/12/2017] [Indexed: 01/08/2023]
Abstract
Over thousands of years, humans have mastered the natural vinegar fermentation technique of cultivating functional microbiota on different raw materials. Functional microbial communities that form reproducibly on non-autoclaved raw materials through repeated batch acetic acid fermentation underpin the flavour development of traditional cereal vinegars. However, how to modulate rationally and optimise the metabolic function of these naturally engineered acidic ecosystems remains unclear. Exploring two key minorities in a vinegar ecosystem, including microbial functions (e.g., flavour and aroma synthesis) and microbial strains, is a crucial step for the vinegar industry to modulate the metabolic function of vinegar microbiota, to monitor the fermentation process, and to maintain the flavour quality of final product.
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Affiliation(s)
- Zhen-Ming Lu
- National Engineering Laboratory for Cereal Fermentation Technology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, PR China
| | - Zong-Min Wang
- National Engineering Laboratory for Cereal Fermentation Technology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, PR China
| | - Xiao-Juan Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, PR China
| | - Jian Mao
- National Engineering Laboratory for Cereal Fermentation Technology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Shi
- National Engineering Laboratory for Cereal Fermentation Technology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, PR China; National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China.
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23
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Morales M, Sentchilo V, Bertelli C, Komljenovic A, Kryuchkova-Mostacci N, Bourdilloud A, Linke B, Goesmann A, Harshman K, Segers F, Delapierre F, Fiorucci D, Seppey M, Trofimenco E, Berra P, El Taher A, Loiseau C, Roggero D, Sulfiotti M, Etienne A, Ruiz Buendia G, Pillard L, Escoriza A, Moritz R, Schneider C, Alfonso E, Ben Jeddou F, Selmoni O, Resch G, Greub G, Emery O, Dubey M, Pillonel T, Robinson-Rechavi M, van der Meer JR. The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand. PLoS One 2016; 11:e0165850. [PMID: 27812150 PMCID: PMC5094676 DOI: 10.1371/journal.pone.0165850] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/18/2016] [Indexed: 12/31/2022] Open
Abstract
The natural restoration of soils polluted by aromatic hydrocarbons such as benzene, toluene, ethylbenzene and m- and p-xylene (BTEX) may be accelerated by inoculation of specific biodegraders (bioaugmentation). Bioaugmentation mainly involves introducing bacteria that deploy their metabolic properties and adaptation potential to survive and propagate in the contaminated environment by degrading the pollutant. In order to better understand the adaptive response of cells during a transition to contaminated material, we analyzed here the genome and short-term (1 h) changes in genome-wide gene expression of the BTEX-degrading bacterium Pseudomonas veronii 1YdBTEX2 in non-sterile soil and liquid medium, both in presence or absence of toluene. We obtained a gapless genome sequence of P. veronii 1YdBTEX2 covering three individual replicons with a total size of 8 Mb, two of which are largely unrelated to current known bacterial replicons. One-hour exposure to toluene, both in soil and liquid, triggered massive transcription (up to 208-fold induction) of multiple gene clusters, such as toluene degradation pathway(s), chemotaxis and toluene efflux pumps. This clearly underlines their key role in the adaptive response to toluene. In comparison to liquid medium, cells in soil drastically changed expression of genes involved in membrane functioning (e.g., lipid composition, lipid metabolism, cell fatty acid synthesis), osmotic stress response (e.g., polyamine or trehalose synthesis, uptake of potassium) and putrescine metabolism, highlighting the immediate response mechanisms of P. veronii 1YdBTEX2 for successful establishment in polluted soil.
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Affiliation(s)
- Marian Morales
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Andrea Komljenovic
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Nadezda Kryuchkova-Mostacci
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Audrey Bourdilloud
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Burkhard Linke
- Bioinformatics and Systems Biology, Justus-Liebig-University, Gießen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University, Gießen, Germany
| | - Keith Harshman
- Lausanne Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Francisca Segers
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Fabien Delapierre
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Damien Fiorucci
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Mathieu Seppey
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Evgeniya Trofimenco
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Pauline Berra
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Athimed El Taher
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Chloé Loiseau
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Dejan Roggero
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Madeleine Sulfiotti
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Angela Etienne
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Gustavo Ruiz Buendia
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Loïc Pillard
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Angelique Escoriza
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Roxane Moritz
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Cedric Schneider
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Esteban Alfonso
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Fatma Ben Jeddou
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Oliver Selmoni
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Gregory Resch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Olivier Emery
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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Morimoto H, Kadoya R, Takahashi K, Kasahara Y. Proteome analysis of Pseudomonas putida F1 genes induced in soil environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:825-832. [PMID: 27452675 DOI: 10.1111/1758-2229.12445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Knowledge of the gene expression dynamics of a single soil bacterial strain contributes to the understanding of its behaviour, physiological state and surrounding microenvironment. Genes expressed in soil environments rather than in laboratory media are considered to particularly relevant. Here, we compared genome-wide gene expression profiles of the bacterium Pseudomonas putida F1 inoculated in three different types of nonsterile soils deduced using proteome analysis via sodium dodecyl sulfate-polyacrylamide gel electrophoresis combined with liquid chromatography-tandem mass spectrometry. Proteins commonly detected in all three samples and involved with bacterial growth and fundamental metabolism were excluded. Nine proteins were identified as specifically expressed in soil including an aldehyde dehydrogenase, a nitric oxide dioxygenase and five proteins encoded by a cluster of metabolism-associated genes. Expression factor analysis revealed that the nitric oxide dioxygenase-coding gene was induced by nitric oxide and the five clustered genes were induced under phosphate starvation. The expression of these genes can be attributed to response to soil environmental stimuli surrounding the F1 cells. These results strongly suggest that our soil metaproteome approach is useful for understanding the autecology and lifestyle of a single bacterial strain in soil environments and allows the prediction of the microenvironment surrounding the bacterial cells.
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Affiliation(s)
- Hajime Morimoto
- Institute of Low Temperature Science, Hokkaido University, Kita 19, Nishi 8, Kita-ku, Sapporo 060-0819, Japan
| | - Ryosuke Kadoya
- Institute of Low Temperature Science, Hokkaido University, Kita 19, Nishi 8, Kita-ku, Sapporo 060-0819, Japan
| | - Kazuhiro Takahashi
- Institute of Low Temperature Science, Hokkaido University, Kita 19, Nishi 8, Kita-ku, Sapporo 060-0819, Japan
| | - Yasuhiro Kasahara
- Institute of Low Temperature Science, Hokkaido University, Kita 19, Nishi 8, Kita-ku, Sapporo 060-0819, Japan
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25
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Chai B, Tsoi TV, Iwai S, Liu C, Fish JA, Gu C, Johnson TA, Zylstra G, Teppen BJ, Li H, Hashsham SA, Boyd SA, Cole JR, Tiedje JM. Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay. PLoS One 2016; 11:e0157008. [PMID: 27309357 PMCID: PMC4911050 DOI: 10.1371/journal.pone.0157008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 05/23/2016] [Indexed: 12/23/2022] Open
Abstract
Sphingomonas wittichii strain RW1 (RW1) is one of the few strains that can grow on dibenzo-p-dioxin (DD). We conducted a transcriptomic study of RW1 using RNA-Seq to outline transcriptional responses to DD, dibenzofuran (DF), and the smectite clay mineral saponite with succinate as carbon source. The ability to grow on DD is rare compared to growth on the chemically similar DF even though the same initial dioxygenase may be involved in oxidation of both substrates. Therefore, we hypothesized the reason for this lies beyond catabolic pathways and may concern genes involved in processes for cell-substrate interactions such as substrate recognition, transport, and detoxification. Compared to succinate (SUC) as control carbon source, DF caused over 240 protein-coding genes to be differentially expressed, whereas more than 300 were differentially expressed with DD. Stress response genes were up-regulated in response to both DD and DF. This effect was stronger with DD than DF, suggesting a higher toxicity of DD compared to DF. Both DD and DF caused changes in expression of genes involved in active cross-membrane transport such as TonB-dependent receptor proteins, but the patterns of change differed between the two substrates. Multiple transcription factor genes also displayed expression patterns distinct to DD and DF growth. DD and DF induced the catechol ortho- and the salicylate/gentisate pathways, respectively. Both DD and DF induced the shared down-stream aliphatic intermediate compound pathway. Clay caused category-wide down-regulation of genes for cell motility and chemotaxis, particularly those involved in the synthesis, assembly and functioning of flagella. This is an environmentally important finding because clay is a major component of soil microbes’ microenvironment influencing local chemistry and may serve as a geosorbent for toxic pollutants. Similar to clay, DD and DF also affected expression of genes involved in motility and chemotaxis.
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Affiliation(s)
- Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America
| | - Tamara V. Tsoi
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America
| | - Shoko Iwai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America
| | - Cun Liu
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America
| | - Jordan A. Fish
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America
| | - Cheng Gu
- School of the Environment, Nanjing University, Nanjing, China
| | - Timothy A. Johnson
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America
| | - Gerben Zylstra
- Department of Biochemistry & Microbiology, Rutgers University, New Brunswick, NJ, United States of America
| | - Brian J. Teppen
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America
| | - Hui Li
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America
| | - Syed A. Hashsham
- Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States of America
| | - Stephen A. Boyd
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America
| | - James R. Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America
- * E-mail:
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26
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Festa S, Macchi M, Cortés F, Morelli IS, Coppotelli BM. Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing. FEMS Microbiol Ecol 2016; 92:fiw125. [PMID: 27279417 DOI: 10.1093/femsec/fiw125] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2016] [Indexed: 11/15/2022] Open
Abstract
The effect of bioaugmentation with Sphingobium sp. AM strain on different soils microbiomes, pristine soil (PS), chronically contaminated soil (IPK) and recently contaminated soil (Phe) and their implications in bioremediation efficiency was studied by focusing on the ecology that drives bacterial communities in response to inoculation. AM strain draft genome codifies genes for metabolism of aromatic and aliphatic hydrocarbons. In Phe, the inoculation improved the elimination of phenanthrene during the whole treatment, whereas in IPK no improvement of degradation of any PAH was observed. Through the pyrosequencing analysis, we observed that inoculation managed to increase the richness and diversity in both contaminated microbiomes, therefore, independently of PAH degradation improvement, we observed clues of inoculant establishment, suggesting it may use other resources to survive. On the other hand, the inoculation did not influence the bacterial community of PS. On both contaminated microbiomes, incubation conditions produced a sharp increase on Actinomycetales and Sphingomonadales orders, while inoculation caused a relative decline of Actinomycetales. Inoculation of most diverse microbiomes, PS and Phe, produced a coupled increase of Sphingomonadales, Burkholderiales and Rhizobiales orders, although it may exist a synergy between those genera; our results suggest that this would not be directly related to PAH degradation.
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Affiliation(s)
- Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata1900, Buenos Aires, Argentina
| | - Marianela Macchi
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata1900, Buenos Aires, Argentina
| | - Federico Cortés
- Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), Mar del Plata 7600, Argentina
| | - Irma S Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata1900, Buenos Aires, Argentina Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata 1900, Argentina
| | - Bibiana M Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata1900, Buenos Aires, Argentina
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27
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Jin HM, Jeong HI, Kim KH, Hahn Y, Madsen EL, Jeon CO. Genome-wide transcriptional responses of Alteromonas naphthalenivorans SN2 to contaminated seawater and marine tidal flat sediment. Sci Rep 2016; 6:21796. [PMID: 26887987 PMCID: PMC4757865 DOI: 10.1038/srep21796] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/01/2016] [Indexed: 11/09/2022] Open
Abstract
A genome-wide transcriptional analysis of Alteromonas naphthalenivorans SN2 was performed to investigate its ecophysiological behavior in contaminated tidal flats and seawater. The experimental design mimicked these habitats that either added naphthalene or pyruvate; tidal flat-naphthalene (TF-N), tidal flat-pyruvate (TF-P), seawater-naphthalene (SW-N), and seawater-pyruvate (SW-P). The transcriptional profiles clustered by habitat (TF-N/TF-P and SW-N/SW-P), rather than carbon source, suggesting that the former may exert a greater influence on genome-wide expression in strain SN2 than the latter. Metabolic mapping of cDNA reads from strain SN2 based on KEGG pathway showed that metabolic and regulatory genes associated with energy metabolism, translation, and cell motility were highly expressed in all four test conditions, probably highlighting the copiotrophic properties of strain SN2 as an opportunistic marine r-strategist. Differential gene expression analysis revealed that strain SN2 displayed specific cellular responses to environmental variables (tidal flat, seawater, naphthalene, and pyruvate) and exhibited certain ecological fitness traits -- its notable PAH degradation capability in seasonally cold tidal flat might be reflected in elevated expression of stress response and chaperone proteins, while fast growth in nitrogen-deficient and aerobic seawater probably correlated with high expression of glutamine synthetase, enzymes utilizing nitrite/nitrate, and those involved in the removal of reactive oxygen species.
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Affiliation(s)
- Hyun Mi Jin
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.,Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hye Im Jeong
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Eugene L Madsen
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Moreno-Forero SK, Rojas E, Beggah S, van der Meer JR. Comparison of differential gene expression to water stress among bacteria with relevant pollutant-degradation properties. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:91-102. [PMID: 26616826 DOI: 10.1111/1758-2229.12356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 11/15/2015] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
Resistance to semi-dry environments has been considered a crucial trait for superior growth and survival of strains used for bioaugmentation in contaminated soils. In order to compare water stress programmes, we analyse differential gene expression among three phylogenetically different strains capable of aromatic compound degradation: Arthrobacter chlorophenolicus A6, Sphingomonas wittichii RW1 and Pseudomonas veronii 1YdBTEX2. Standardized laboratory-induced water stress was imposed by shock exposure of liquid cultures to water potential decrease, induced either by addition of solutes (NaCl, solute stress) or by addition of polyethylene glycol (matric stress), both at absolute similar stress magnitudes and at those causing approximately similar decrease of growth rates. Genome-wide differential gene expression was recorded by micro-array hybridizations. Growth of P. veronii 1YdBTEX2 was the most sensitive to water potential decrease, followed by S. wittichii RW1 and A. chlorophenolicus A6. The number of genes differentially expressed under decreasing water potential was lowest for A. chlorophenolicus A6, increasing with increasing magnitude of the stress, followed by S. wittichii RW1 and P. veronii 1YdBTEX2. Gene inspection and gene ontology analysis under stress conditions causing similar growth rate reduction indicated that common reactions among the three strains included diminished expression of flagellar motility and increased expression of compatible solutes (which were strain-specific). Furthermore, a set of common genes with ill-defined function was found between all strains, including ABC transporters and aldehyde dehydrogenases, which may constitute a core conserved response to water stress. The data further suggest that stronger reduction of growth rate of P. veronii 1YdBTEX2 under water stress may be an indirect result of the response demanding heavy NADPH investment, rather than the presence or absence of a suitable stress defence mechanism per se.
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Affiliation(s)
- Silvia K Moreno-Forero
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Edward Rojas
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Siham Beggah
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
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29
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Coronado E, Valtat A, van der Meer JR. Sphingomonas wittichii RW1 gene reporters interrogating the dibenzofuran metabolic network highlight conditions for early successful development in contaminated microcosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:480-488. [PMID: 25683238 DOI: 10.1111/1758-2229.12276] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/31/2015] [Indexed: 06/04/2023]
Abstract
In order to better understand the fate and activity of bacteria introduced into contaminated material for the purpose of enhancing biodegradation rates, we constructed Sphingomonas wittichii RW1 variants with gene reporters interrogating dibenzofuran metabolic activity. Three potential promoters from the dibenzofuran metabolic network were selected and fused to the gene for enhanced green fluorescent protein (EGFP). The stability of the resulting genetic constructions in RW1 was examined, with plasmids based on the broad-host range vector pME6012 being the most reliable. One of the selected promoters, upstream of the gene Swit_4925 for a putative 2-hydroxy-2,4-pentadienoate hydratase, was inducible by growth on dibenzofuran. Sphingomonas wittichii RW1 equipped with the Swit_4925 promoter egfp fusion grew in a variety of non-sterile sandy microcosms contaminated with dibenzofuran and material from a former gasification site. The strain also grew in microcosms without added dibenzofuran but to a very limited extent, and EGFP expression indicated the formation of consistent small subpopulations of cells with an active inferred dibenzofuran metabolic network. Evidence was obtained for competition for dibenzofuran metabolites scavenged by resident bacteria in the gasification site material, which resulted in a more rapid decline of the RW1 population. Our results show the importance of low inoculation densities in order to observe the population development of the introduced bacteria and further illustrate that the limited availability of unique carbon substrate may be the most important factor impinging growth.
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Affiliation(s)
- Edith Coronado
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, 1015, Switzerland
| | - Annabelle Valtat
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, 1015, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, 1015, Switzerland
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30
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Coronado E, Roggo C, van der Meer JR. Identification of genes potentially involved in solute stress response in Sphingomonas wittichii RW1 by transposon mutant recovery. Front Microbiol 2014; 5:585. [PMID: 25408691 PMCID: PMC4219479 DOI: 10.3389/fmicb.2014.00585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/17/2014] [Indexed: 11/13/2022] Open
Abstract
The term water stress refers to the effects of low water availability on microbial growth and physiology. Water availability has been proposed as a major constraint for the use of microorganisms in contaminated sites with the purpose of bioremediation. Sphingomonas wittichii RW1 is a bacterium capable of degrading the xenobiotic compounds dibenzofuran and dibenzo-p-dioxin, and has potential to be used for targeted bioremediation. The aim of the current work was to identify genes implicated in water stress in RW1 by means of transposon mutagenesis and mutant growth experiments. Conditions of low water potential were mimicked by adding NaCl to the growth media. Three different mutant selection or separation method were tested which, however recovered different mutants. Recovered transposon mutants with poorer growth under salt-induced water stress carried insertions in genes involved in proline and glutamate biosynthesis, and further in a gene putatively involved in aromatic compound catabolism. Transposon mutants growing poorer on medium with lowered water potential also included ones that had insertions in genes involved in more general functions such as transcriptional regulation, elongation factor, cell division protein, RNA polymerase β or an aconitase.
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Affiliation(s)
- Edith Coronado
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| | - Clémence Roggo
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
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