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Bao XC, Tang HZ, Li XG, Li AQ, Qi XQ, Li DH, Liu SS, Wu LF, Zhang WJ. Bioluminescence Contributes to the Adaptation of Deep-Sea Bacterium Photobacterium phosphoreum ANT-2200 to High Hydrostatic Pressure. Microorganisms 2023; 11:1362. [PMID: 37374864 DOI: 10.3390/microorganisms11061362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023] Open
Abstract
Bioluminescence is a common phenomenon in nature, especially in the deep ocean. The physiological role of bacterial bioluminescence involves protection against oxidative and UV stresses. Yet, it remains unclear if bioluminescence contributes to deep-sea bacterial adaptation to high hydrostatic pressure (HHP). In this study, we constructed a non-luminescent mutant of ΔluxA and its complementary strain c-ΔluxA of Photobacterium phosphoreum ANT-2200, a deep-sea piezophilic bioluminescent bacterium. The wild-type strain, mutant and complementary strain were compared from aspects of pressure tolerance, intracellular reactive oxygen species (ROS) level and expression of ROS-scavenging enzymes. The results showed that, despite similar growth profiles, HHP induced the accumulation of intracellular ROS and up-regulated the expression of ROS-scavenging enzymes such as dyp, katE and katG, specifically in the non-luminescent mutant. Collectively, our results suggested that bioluminescence functions as the primary antioxidant system in strain ANT-2200, in addition to the well-known ROS-scavenging enzymes. Bioluminescence contributes to bacterial adaptation to the deep-sea environment by coping with oxidative stress generated from HHP. These results further expanded our understanding of the physiological significance of bioluminescence as well as a novel strategy for microbial adaptation to a deep-sea environment.
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Affiliation(s)
- Xu-Chong Bao
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- University of Chinese Academy of Sciences, Beijing 101408, China
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Hong-Zhi Tang
- University of Chinese Academy of Sciences, Beijing 101408, China
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- Hainan Deep-Sea Technology Laboratory, IDSSE-BGI, Institution of Deep-Sea Life Sciences, Sanya 572000, China
| | - An-Qi Li
- University of Chinese Academy of Sciences, Beijing 101408, China
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Xiao-Qing Qi
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- Hainan Deep-Sea Technology Laboratory, IDSSE-BGI, Institution of Deep-Sea Life Sciences, Sanya 572000, China
| | - Deng-Hui Li
- Hainan Deep-Sea Technology Laboratory, IDSSE-BGI, Institution of Deep-Sea Life Sciences, Sanya 572000, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Shan-Shan Liu
- Hainan Deep-Sea Technology Laboratory, IDSSE-BGI, Institution of Deep-Sea Life Sciences, Sanya 572000, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Long-Fei Wu
- LCB, IMM, CNRS, Aix-Marseille University, 13402 Marseille, France
| | - Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- Hainan Deep-Sea Technology Laboratory, IDSSE-BGI, Institution of Deep-Sea Life Sciences, Sanya 572000, China
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2
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Smedile F, Foustoukos DI, Patwardhan S, Mullane K, Schlegel I, Adams MW, Schut GJ, Giovannelli D, Vetriani C. Adaptations to high pressure of Nautilia sp. strain PV-1, a piezophilic Campylobacterium (aka Epsilonproteobacterium) isolated from a deep-sea hydrothermal vent. Environ Microbiol 2022; 24:6164-6183. [PMID: 36271901 PMCID: PMC10092268 DOI: 10.1111/1462-2920.16256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/20/2022] [Indexed: 01/12/2023]
Abstract
Physiological and gene expression studies of deep-sea bacteria under pressure conditions similar to those experienced in their natural habitat are critical for understanding growth kinetics and metabolic adaptations to in situ conditions. The Campylobacterium (aka Epsilonproteobacterium) Nautilia sp. strain PV-1 was isolated from hydrothermal fluids released from an active deep-sea hydrothermal vent at 9° N on the East Pacific Rise. Strain PV-1 is a piezophilic, moderately thermophilic, chemolithoautotrophic anaerobe that conserves energy by coupling the oxidation of hydrogen to the reduction of nitrate or elemental sulfur. Using a high-pressure-high temperature continuous culture system, we established that strain PV-1 has the shortest generation time of all known piezophilic bacteria and we investigated its protein expression pattern in response to different hydrostatic pressure regimes. Proteogenomic analyses of strain PV-1 grown at 20 and 5 MPa showed that pressure adaptation is not restricted to stress response or homeoviscous adaptation but extends to enzymes involved in central metabolic pathways. Protein synthesis, motility, transport, and energy metabolism are all affected by pressure, although to different extents. In strain PV-1, low-pressure conditions induce the synthesis of phage-related proteins and an overexpression of enzymes involved in carbon fixation.
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Affiliation(s)
- Francesco Smedile
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Institute of Polar Science (ISP-CNR), Messina, Italy
| | - Dionysis I Foustoukos
- Earth and Planets Laboratory, Carnegie Institution of Washington, Washington, District of Columbia, USA
| | - Sushmita Patwardhan
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Kelli Mullane
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Ian Schlegel
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Michael W Adams
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Gerrit J Schut
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Donato Giovannelli
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
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3
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Wu JH, McGenity TJ, Rettberg P, Simões MF, Li WJ, Antunes A. The archaeal class Halobacteria and astrobiology: Knowledge gaps and research opportunities. Front Microbiol 2022; 13:1023625. [PMID: 36312929 PMCID: PMC9608585 DOI: 10.3389/fmicb.2022.1023625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/07/2022] [Indexed: 09/19/2023] Open
Abstract
Water bodies on Mars and the icy moons of the outer solar system are now recognized as likely being associated with high levels of salt. Therefore, the study of high salinity environments and their inhabitants has become increasingly relevant for Astrobiology. Members of the archaeal class Halobacteria are the most successful microbial group living in hypersaline conditions and are recognized as key model organisms for exposure experiments. Despite this, data for the class is uneven across taxa and widely dispersed across the literature, which has made it difficult to properly assess the potential for species of Halobacteria to survive under the polyextreme conditions found beyond Earth. Here we provide an overview of published data on astrobiology-linked exposure experiments performed with members of the Halobacteria, identifying clear knowledge gaps and research opportunities.
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Affiliation(s)
- Jia-Hui Wu
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Taipa, Macau SAR, China
| | - Terry J. McGenity
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Petra Rettberg
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | - Marta F. Simões
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Taipa, Macau SAR, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Taipa, Macau SAR, China
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Ceron-Chafla P, García-Timermans C, de Vrieze J, Ganigué R, Boon N, Rabaey K, van Lier JB, Lindeboom REF. Pre-incubation conditions determine the fermentation pattern and microbial community structure in fermenters at mild hydrostatic pressure. Biotechnol Bioeng 2022; 119:1792-1807. [PMID: 35312065 PMCID: PMC9325544 DOI: 10.1002/bit.28085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 02/08/2022] [Accepted: 03/05/2022] [Indexed: 11/11/2022]
Abstract
Fermentation at elevated hydrostatic pressure is a novel strategy targeting product selectivity. However, the role of inoculum history and cross-resistance, that is, acquired tolerance from incubation under distinctive environmental stress, remains unclear in high-pressure operation. In our here presented work, we studied fermentation and microbial community responses of halotolerant marine sediment inoculum (MSI) and anaerobic digester inoculum (ADI), pre-incubated in serum bottles at different temperatures and subsequently exposed to mild hydrostatic pressure (MHP; < 10 MPa) in stainless steel reactors. Results showed that MHP effects on microbial growth, activity, and community structure were strongly temperature-dependent. At moderate temperature (20°C), biomass yield and fermentation were not limited by MHP; suggesting a cross-resistance effect from incubation temperature and halotolerance. Low temperatures (10°C) and MHP imposed kinetic and bioenergetic limitations, constraining growth and product formation. Fermentation remained favorable in MSI at 28°C and ADI at 37°C, despite reduced biomass yield resulting from maintenance and decay proportionally increasing with temperature. Microbial community structure was modified by temperature during the enrichment, and slight differences observed after MHP-exposure did not compromise functionality. Results showed that the relation incubation temperature-halotolerance proved to be a modifier of microbial responses to MHP and could be potentially exploited in fermentations to modulate product/biomass ratio.
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Affiliation(s)
- Pamela Ceron-Chafla
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, the Netherlands
| | - Cristina García-Timermans
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Jo de Vrieze
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium.,Division of Soil and Water Management, Department of Earth and Environmental Sciences, KU Leuven, Leuven, Belgium.,Bio- and Chemical Systems Technology, Reactor Engineering and Safety (CREaS), Department of Chemical Engineering, KU Leuven, Leuven, Belgium
| | - Ramon Ganigué
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Nico Boon
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Korneel Rabaey
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium.,Center for Advanced Process Technology for Urban Resource Recovery, Ghent, Belgium
| | - Jules B van Lier
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, the Netherlands
| | - Ralph E F Lindeboom
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, the Netherlands
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5
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Ceron-Chafla P, Chang YT, Rabaey K, van Lier JB, Lindeboom REF. Directional Selection of Microbial Community Reduces Propionate Accumulation in Glycerol and Glucose Anaerobic Bioconversion Under Elevated pCO 2. Front Microbiol 2021; 12:675763. [PMID: 34220760 PMCID: PMC8242345 DOI: 10.3389/fmicb.2021.675763] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/24/2021] [Indexed: 11/30/2022] Open
Abstract
Volatile fatty acid accumulation is a sign of digester perturbation. Previous work showed the thermodynamic limitations of hydrogen and CO2 in syntrophic propionate oxidation under elevated partial pressure of CO2 (pCO2). Here we study the effect of directional selection under increasing substrate load as a strategy to restructure the microbial community and induce cross-protection mechanisms to improve glucose and glycerol conversion performance under elevated pCO2. After an adaptive laboratory evolution (ALE) process, viable cell density increased and predominant microbial groups were modified: an increase in Methanosaeta and syntrophic propionate oxidizing bacteria (SPOB) associated with the Smithella genus was found with glycerol as the substrate. A modest increase in SPOB along with a shift in the predominance of Methanobacterium toward Methanosaeta was observed with glucose as the substrate. The evolved inoculum showed affected diversity within archaeal spp. under 5 bar initial pCO2; however, higher CH4 yield resulted from enhanced propionate conversion linked to the community shifts and biomass adaptation during the ALE process. Moreover, the evolved inoculum attained increased cell viability with glucose and a marginal decrease with glycerol as the substrate. Results showed differences in terms of carbon flux distribution using the evolved inoculum under elevated pCO2: glucose conversion resulted in a higher cell density and viability, whereas glycerol conversion led to higher propionate production whose enabled conversion reflected in increased CH4 yield. Our results highlight that limited propionate conversion at elevated pCO2 resulted from decreased cell viability and low abundance of syntrophic partners. This limitation can be mitigated by promoting alternative and more resilient SPOB and building up biomass adaptation to environmental conditions via directional selection of microbial community.
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Affiliation(s)
- Pamela Ceron-Chafla
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, Netherlands
| | - Yu-Ting Chang
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, Netherlands
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium.,Center for Advanced Process Technology for Urban Resource Recovery, Ghent, Belgium
| | - Jules B van Lier
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, Netherlands
| | - Ralph E F Lindeboom
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Delft, Netherlands
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6
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Booker AE, Hoyt DW, Meulia T, Eder E, Nicora CD, Purvine SO, Daly RA, Moore JD, Wunch K, Pfiffner SM, Lipton MS, Mouser PJ, Wrighton KC, Wilkins MJ. Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp. Appl Environ Microbiol 2019; 85:e00018-19. [PMID: 30979840 PMCID: PMC6544827 DOI: 10.1128/aem.00018-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/10/2019] [Indexed: 01/12/2023] Open
Abstract
Bacterial Halanaerobium strains become the dominant persisting microbial community member in produced fluids across geographically distinct hydraulically fractured shales. Halanaerobium is believed to be inadvertently introduced into this environment during the drilling and fracturing process and must therefore tolerate large changes in pressure, temperature, and salinity. Here, we used a Halanaerobium strain isolated from a natural gas well in the Utica Point Pleasant formation to investigate metabolic and physiological responses to growth under high-pressure subsurface conditions. Laboratory incubations confirmed the ability of Halanaerobium congolense strain WG8 to grow under pressures representative of deep shale formations (21 to 48 MPa). Under these conditions, broad metabolic and physiological shifts were identified, including higher abundances of proteins associated with the production of extracellular polymeric substances. Confocal laser scanning microscopy indicated that extracellular polymeric substance (EPS) production was associated with greater cell aggregation when biomass was cultured at high pressure. Changes in Halanaerobium central carbon metabolism under the same conditions were inferred from nuclear magnetic resonance (NMR) and gas chromatography measurements, revealing large per-cell increases in production of ethanol, acetate, and propanol and cessation of hydrogen production. These metabolic shifts were associated with carbon flux through 1,2-propanediol in response to slower fluxes of carbon through stage 3 of glycolysis. Together, these results reveal the potential for bioclogging and corrosion (via organic acid fermentation products) associated with persistent Halanaerobium growth in deep, hydraulically fractured shale ecosystems, and offer new insights into cellular mechanisms that enable these strains to dominate deep-shale microbiomes.IMPORTANCE The hydraulic fracturing of deep-shale formations for hydrocarbon recovery accounts for approximately 60% of U.S. natural gas production. Microbial activity associated with this process is generally considered deleterious due to issues associated with sulfide production, microbially induced corrosion, and bioclogging in the subsurface. Here we demonstrate that a representative Halanaerobium species, frequently the dominant microbial taxon in hydraulically fractured shales, responds to pressures characteristic of the deep subsurface by shifting its metabolism to generate more corrosive organic acids and produce more polymeric substances that cause "clumping" of biomass. While the potential for increased corrosion of steel infrastructure and clogging of pores and fractures in the subsurface may significantly impact hydrocarbon recovery, these data also offer new insights for microbial control in these ecosystems.
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Affiliation(s)
- Anne E Booker
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - David W Hoyt
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tea Meulia
- College of Food, Agricultural, and Environmental Sciences, Ohio State University, Columbus, Ohio, USA
| | - Elizabeth Eder
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Rebecca A Daly
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - Joseph D Moore
- DowDuPont Industrial Biosciences, Wilmington, Delaware, USA
| | - Kenneth Wunch
- DowDuPont Industrial Biosciences, Wilmington, Delaware, USA
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Mary S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Paula J Mouser
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, New Hampshire, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
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7
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Czech L, Hermann L, Stöveken N, Richter AA, Höppner A, Smits SHJ, Heider J, Bremer E. Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis. Genes (Basel) 2018; 9:genes9040177. [PMID: 29565833 PMCID: PMC5924519 DOI: 10.3390/genes9040177] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 01/26/2023] Open
Abstract
Fluctuations in environmental osmolarity are ubiquitous stress factors in many natural habitats of microorganisms, as they inevitably trigger osmotically instigated fluxes of water across the semi-permeable cytoplasmic membrane. Under hyperosmotic conditions, many microorganisms fend off the detrimental effects of water efflux and the ensuing dehydration of the cytoplasm and drop in turgor through the accumulation of a restricted class of organic osmolytes, the compatible solutes. Ectoine and its derivative 5-hydroxyectoine are prominent members of these compounds and are synthesized widely by members of the Bacteria and a few Archaea and Eukarya in response to high salinity/osmolarity and/or growth temperature extremes. Ectoines have excellent function-preserving properties, attributes that have led to their description as chemical chaperones and fostered the development of an industrial-scale biotechnological production process for their exploitation in biotechnology, skin care, and medicine. We review, here, the current knowledge on the biochemistry of the ectoine/hydroxyectoine biosynthetic enzymes and the available crystal structures of some of them, explore the genetics of the underlying biosynthetic genes and their transcriptional regulation, and present an extensive phylogenomic analysis of the ectoine/hydroxyectoine biosynthetic genes. In addition, we address the biochemistry, phylogenomics, and genetic regulation for the alternative use of ectoines as nutrients.
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Affiliation(s)
- Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Lucas Hermann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Nadine Stöveken
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
| | - Alexandra A Richter
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Astrid Höppner
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
| | - Johann Heider
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
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Enhancing the Adaptability of the Deep-Sea Bacterium Shewanella piezotolerans WP3 to High Pressure and Low Temperature by Experimental Evolution under H 2O 2 Stress. Appl Environ Microbiol 2018; 84:AEM.02342-17. [PMID: 29269502 DOI: 10.1128/aem.02342-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/10/2017] [Indexed: 11/20/2022] Open
Abstract
Oxidative stresses commonly exist in natural environments, and microbes have developed a variety of defensive systems to counteract such events. Although increasing evidence has shown that high hydrostatic pressure (HHP) and low temperature (LT) induce antioxidant defense responses in cells, there is no direct evidence to prove the connection between antioxidant defense mechanisms and the adaptation of bacteria to HHP and LT. In this study, using the wild-type (WT) strain of a deep-sea bacterium, Shewanella piezotolerans WP3, as an ancestor, we obtained a mutant, OE100, with an enhanced antioxidant defense capacity by experimental evolution under H2O2 stress. Notably, OE100 exhibited better tolerance not only to H2O2 stress but also to HHP and LT (20 MPa and 4°C, respectively). Whole-genome sequencing identified a deletion mutation in the oxyR gene, which encodes the transcription factor that controls the oxidative stress response. Comparative transcriptome analysis showed that the genes associated with oxidative stress defense, anaerobic respiration, DNA repair, and the synthesis of flagella and bacteriophage were differentially expressed in OE100 compared with the WT at 20 MPa and 4°C. Genetic analysis of oxyR and ccpA2 indicated that the OxyR-regulated cytochrome c peroxidase CcpA2 significantly contributed to the adaptation of WP3 to HHP and LT. Taken together, these results confirmed the inherent relationship between antioxidant defense mechanisms and the adaptation of a benthic microorganism to HHP and LT.IMPORTANCE Oxidative stress exists in various niches, including the deep-sea ecosystem, which is an extreme environment with conditions of HHP and predominantly LT. Although previous studies have shown that HHP and LT induce antioxidant defense responses in cells, direct evidence to prove the connection between antioxidant defense mechanisms and the adaptation of bacteria to HHP and LT is lacking. In this work, using the deep-sea bacterium Shewanella piezotolerans WP3 as a model, we proved that enhancement of the adaptability of WP3 to HHP and LT can benefit from its antioxidant defense mechanism, which provided useful insight into the ecological roles of antioxidant genes in a benthic microorganism and contributed to an improved understanding of microbial adaptation strategies in deep-sea environments.
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9
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An impaired metabolic response to hydrostatic pressure explains Alcanivorax borkumensis recorded distribution in the deep marine water column. Sci Rep 2016; 6:31316. [PMID: 27515484 PMCID: PMC4981847 DOI: 10.1038/srep31316] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/18/2016] [Indexed: 01/11/2023] Open
Abstract
Alcanivorax borkumensis is an ubiquitous model organism for hydrocarbonoclastic bacteria, which dominates polluted surface waters. Its negligible presence in oil-contaminated deep waters (as observed during the Deepwater Horizon accident) raises the hypothesis that it may lack adaptive mechanisms to hydrostatic pressure (HP). The type strain SK2 was tested under 0.1, 5 and 10 MPa (corresponding to surface water, 500 and 1000 m depth, respectively). While 5 MPa essentially inactivated SK2, further increase to 10 MPa triggered some resistance mechanism, as indicated by higher total and intact cell numbers. Under 10 MPa, SK2 upregulated the synthetic pathway of the osmolyte ectoine, whose concentration increased from 0.45 to 4.71 fmoles cell−1. Central biosynthetic pathways such as cell replication, glyoxylate and Krebs cycles, amino acids metabolism and fatty acids biosynthesis, but not β-oxidation, were upregulated or unaffected at 10 MPa, although total cell number was remarkably lower with respect to 0.1 MPa. Concomitantly, expression of more than 50% of SK2 genes was downregulated, including genes related to ATP generation, respiration and protein translation. Thus, A. borkumensis lacks proper adaptation to HP but activates resistance mechanisms. These consist in poorly efficient biosynthetic rather than energy-yielding degradation-related pathways, and suggest that HP does represent a major driver for its distribution at deep-sea.
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10
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Jorge AB, Hazael R. Use ofShewanella oneidensisfor Energy Conversion in Microbial Fuel Cells. MACROMOL CHEM PHYS 2016. [DOI: 10.1002/macp.201500477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- A. Belen Jorge
- Materials Research Institute; School of Engineering and Materials Sciences; Queen Mary University of London; Mile End Rd E1 4NS United Kingdom
| | - Rachael Hazael
- Christopher Ingold Building; Department of Chemistry; University College London; 20 Gordon Street WC1H 0AJ United Kingdom
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11
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Hazael R, Foglia F, Kardzhaliyska L, Daniel I, Meersman F, McMillan P. Laboratory investigation of high pressure survival in Shewanella oneidensis MR-1 into the gigapascal pressure range. Front Microbiol 2014; 5:612. [PMID: 25452750 PMCID: PMC4233909 DOI: 10.3389/fmicb.2014.00612] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/28/2014] [Indexed: 11/13/2022] Open
Abstract
The survival of Shewanella oneidensis MR-1 at up to 1500 MPa was investigated by laboratory studies involving exposure to high pressure followed by evaluation of survivors as the number (N) of colony forming units (CFU) that could be cultured following recovery to ambient conditions. Exposing the wild type (WT) bacteria to 250 MPa resulted in only a minor (0.7 log N units) drop in survival compared with the initial concentration of 108 cells/ml. Raising the pressure to above 500 MPa caused a large reduction in the number of viable cells observed following recovery to ambient pressure. Additional pressure increase caused a further decrease in survivability, with approximately 102 CFU/ml recorded following exposure to 1000 MPa (1 GPa) and 1.5 GPa. Pressurizing samples from colonies resuscitated from survivors that had been previously exposed to high pressure resulted in substantially greater survivor counts. Experiments were carried out to examine potential interactions between pressure and temperature variables in determining bacterial survival. One generation of survivors previously exposed to 1 GPa was compared with WT samples to investigate survival between 37 and 8°C. The results did not reveal any coupling between acquired high pressure resistance and temperature effects on growth.
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Affiliation(s)
- Rachael Hazael
- Christopher Ingold Laboratories, Department of Chemistry, University College London London, UK
| | - Fabrizia Foglia
- Christopher Ingold Laboratories, Department of Chemistry, University College London London, UK
| | - Liya Kardzhaliyska
- Christopher Ingold Laboratories, Department of Chemistry, University College London London, UK
| | - Isabelle Daniel
- Laboratoire de Géologie de Lyon, UMR 5276 CNRS, ENS de Lyon and Université Claude Bernard Lyon 1 - Université de Lyon Lyon, France
| | - Filip Meersman
- Christopher Ingold Laboratories, Department of Chemistry, University College London London, UK ; Biomolecular and Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp Antwerpen, Belgium
| | - Paul McMillan
- Christopher Ingold Laboratories, Department of Chemistry, University College London London, UK
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Meersman F, McMillan PF. High hydrostatic pressure: a probing tool and a necessary parameter in biophysical chemistry. Chem Commun (Camb) 2014; 50:766-75. [PMID: 24286104 DOI: 10.1039/c3cc45844j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High pressures extending up to several thousands of atmospheres provide extreme conditions for biological organisms to survive. Recent studies are investigating the survival mechanisms and biological function of microorganisms under natural and laboratory conditions extending into the GigaPascal range, with applications to understanding the Earth's deep biosphere and food technology. High pressure has also emerged as a useful tool and physical parameter for probing changes in the structure and functional properties of biologically important macromolecules and polymers encountered in soft matter science. Here we highlight some areas of current interest in high pressure biophysics and physical chemistry that are emerging at the frontier of this cross-disciplinary field.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, University College London, 20 Gordon St., London WC1H 0AJ, UK.
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13
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Picard A, Daniel I. Pressure as an environmental parameter for microbial life--a review. Biophys Chem 2013; 183:30-41. [PMID: 23891571 DOI: 10.1016/j.bpc.2013.06.019] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/18/2013] [Accepted: 06/22/2013] [Indexed: 01/18/2023]
Abstract
Microbial life has been prevailing in the biosphere for the last 3.8 Ga at least. Throughout most of the Earth's history it has experienced a range of pressures; both dynamic pressure when the young Earth was heavily bombarded, and static pressure in subsurface environments that could have served as a refuge and where microbial life nowadays flourishes. In this review, we discuss the extent of high-pressure habitats in early and modern times and provide a short overview of microbial survival under dynamic pressures. We summarize the current knowledge about the impact of microbial activity on biogeochemical cycles under pressures characteristic of the deep subsurface. We evaluate the possibility that pressure can be a limiting parameter for life at depth. Finally, we discuss the open questions and knowledge gaps that exist in the field of high-pressure geomicrobiology.
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Affiliation(s)
- Aude Picard
- Center for Applied Geoscience, Eberhard Karls University Tübingen, Sigwartstrasse 10, 72076 Tübingen, Germany.
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The limits for life under multiple extremes. Trends Microbiol 2013; 21:204-12. [DOI: 10.1016/j.tim.2013.01.006] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/28/2013] [Accepted: 01/31/2013] [Indexed: 12/19/2022]
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15
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Effects of intracellular Mn on the radiation resistance of the halophilic archaeon Halobacterium salinarum. Extremophiles 2013; 17:485-97. [DOI: 10.1007/s00792-013-0533-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 03/07/2013] [Indexed: 02/01/2023]
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Radiation Resistance in Extremophiles: Fending Off Multiple Attacks. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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17
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Role of Mn2+ and compatible solutes in the radiation resistance of thermophilic bacteria and archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2012; 2012:845756. [PMID: 23209374 PMCID: PMC3505630 DOI: 10.1155/2012/845756] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/18/2012] [Accepted: 10/13/2012] [Indexed: 01/28/2023]
Abstract
Radiation-resistant bacteria have garnered a great deal of attention from scientists seeking to expose the mechanisms underlying their incredible survival abilities. Recent analyses showed that the resistance to ionizing radiation (IR) in the archaeon Halobacterium salinarum is dependent upon Mn-antioxidant complexes responsible for the scavenging of reactive oxygen species (ROS) generated by radiation. Here we examined the role of the compatible solutes trehalose, mannosylglycerate, and di-myo-inositol phosphate in the radiation resistance of aerobic and anaerobic thermophiles. We found that the IR resistance of the thermophilic bacteria Rubrobacter xylanophilus and Rubrobacter radiotolerans was highly correlated to the accumulation of high intracellular concentration of trehalose in association with Mn, supporting the model of Mn2+-dependent ROS scavenging in the aerobes. In contrast, the hyperthermophilic archaea Thermococcus gammatolerans and Pyrococcus furiosus did not contain significant amounts of intracellular Mn, and we found no significant antioxidant activity from mannosylglycerate and di-myo-inositol phosphate in vitro. We therefore propose that the low levels of IR-generated ROS under anaerobic conditions combined with highly constitutively expressed detoxification systems in these anaerobes are key to their radiation resistance and circumvent the need for the accumulation of Mn-antioxidant complexes in the cell.
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