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Kumar A, Daschakraborty S. Anomalous lateral diffusion of lipids during the fluid/gel phase transition of a lipid membrane. Phys Chem Chem Phys 2023; 25:31431-31443. [PMID: 37962400 DOI: 10.1039/d3cp04081j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
A lipid membrane undergoes a phase transition from fluid to gel phase upon changing external thermodynamic conditions, such as decreasing temperature and increasing pressure. Extremophilic organisms face the challenge of preventing this deleterious phase transition. The main focus of their adaptive strategy is to facilitate effective temperature sensing through sensor proteins, relying on the drastic changes in packing density and membrane fluidity during the phase transition. Although the changes in packing density parameters due to the fluid/gel phase transition are studied in detail, the impact on membrane fluidity is less explored in the literature. Understanding the lateral diffusive dynamics of lipids in response to temperature, particularly during the fluid/gel phase transition, is albeit crucial. Here we have simulated the phase transition of a single component lipid membrane composed of dipalmitoylphosphatidylcholine (DPPC) lipids using a coarse-grained (CG) model and studied the changes of the structural and dynamical properties. It is observed that near the phase transition point, both fluid and gel phase domains coexist together. The dynamics remains highly non-Gaussian for a long time even when the mean square displacement reaches the Fickian regime at a much earlier time. This Fickian yet non-Gaussian diffusion (FnGD) is a characteristic of a highly heterogeneous system, previously observed for the lateral diffusion of lipids in raft mimetic membranes having liquid-ordered and liquid-disordered phases co-existing together. We have analyzed the molecular trajectories and calculated the jump-diffusion of the lipids, stemming from sudden jump translations, using a translational jump-diffusion (TJD) approach. An overwhelming contribution of the jump-diffusion of the lipids is observed suggesting anomalous diffusion of lipids during fluid/gel phase transition of the membrane. These results are important in unravelling the intricate nature of lipid diffusion during the phase transition of the membrane and open up a new possibility of investigating the most significant change of membrane properties during phase transition, which can be effectively sensed by proteins.
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Affiliation(s)
- Abhay Kumar
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India.
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2
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Scheffer G, Gieg LM. The Mystery of Piezophiles: Understudied Microorganisms from the Deep, Dark Subsurface. Microorganisms 2023; 11:1629. [PMID: 37512802 PMCID: PMC10384521 DOI: 10.3390/microorganisms11071629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Microorganisms that can withstand high pressure within an environment are termed piezophiles. These organisms are considered extremophiles and inhabit the deep marine or terrestrial subsurface. Because these microorganisms are not easily accessed and require expensive sampling methods and laboratory instruments, advancements in this field have been limited compared to other extremophiles. This review summarizes the current knowledge on piezophiles, notably the cellular and physiological adaptations that such microorganisms possess to withstand and grow in high-pressure environments. Based on existing studies, organisms from both the deep marine and terrestrial subsurface show similar adaptations to high pressure, including increased motility, an increase of unsaturated bonds within the cell membrane lipids, upregulation of heat shock proteins, and differential gene-regulation systems. Notably, more adaptations have been identified within the deep marine subsurface organisms due to the relative paucity of studies performed on deep terrestrial subsurface environments. Nevertheless, similar adaptations have been found within piezophiles from both systems, and therefore the microbial biogeography concepts used to assess microbial dispersal and explore if similar organisms can be found throughout deep terrestrial environments are also briefly discussed.
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Affiliation(s)
- Gabrielle Scheffer
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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3
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Li J, Xiao X, Zhou M, Zhang Y. Strategy for the Adaptation to Stressful Conditions of the Novel Isolated Conditional Piezophilic Strain Halomonas titanicae ANRCS81. Appl Environ Microbiol 2023; 89:e0130422. [PMID: 36912687 PMCID: PMC10057041 DOI: 10.1128/aem.01304-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2023] Open
Abstract
Microorganisms have successfully predominated deep-sea ecosystems, while we know little about their adaptation strategy to multiple environmental stresses therein, including high hydrostatic pressure (HHP). Here, we focused on the genus Halomonas, one of the most widely distributed halophilic bacterial genera in marine ecosystems and isolated a piezophilic strain Halomonas titanicae ANRCS81 from Antarctic deep-sea sediment. The strain grew under a broad range of temperatures (2 to 45°C), pressures (0.1 to 55 MPa), salinities (NaCl, 0.5 to 17.5%, wt/vol), and chaotropic agent (Mg2+, 0 to 0.9 M) with either oxygen or nitrate as an electron acceptor. Genome annotation revealed that strain ANRCS81 expressed potential antioxidant genes/proteins and possessed versatile energy generation pathways. Based on the transcriptomic analysis, when the strain was incubated at 40 MPa, genes related to antioxidant defenses, anaerobic respiration, and fermentation were upregulated, indicating that HHP induced intracellular oxidative stress. Under HHP, superoxide dismutase (SOD) activity increased, glucose consumption increased with less CO2 generation, and nitrate/nitrite consumption increased with more ammonium generation. The cellular response to HHP represents the common adaptation developed by Halomonas to inhabit and drive geochemical cycling in deep-sea environments. IMPORTANCE Microbial growth and metabolic responses to environmental changes are core aspects of adaptation strategies developed during evolution. In particular, high hydrostatic pressure (HHP) is the most common but least examined environmental factor driving microbial adaptation in the deep sea. According to recent studies, microorganisms developed a common adaptation strategy to multiple stresses, including HHP, with antioxidant defenses and energy regulation as key components, but experimental data are lacking. Meanwhile, cellular SOD activity is elevated under HHP. The significance of this research lies in identifying the HHP adaptation strategy of a Halomonas strain at the genomic, transcriptomic, and metabolic activity levels, which will allow researchers to bridge environmental factors with the ecological function of marine microorganisms.
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Affiliation(s)
- Jiakang Li
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Meng Zhou
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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Chen Z, Chen H, Zhu X, Xia D, Chen Y, Geng M, Bai Z. Physical, chemical, and bio-pretreatments on microbial gas production in Baode Block coal. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:5791-5798. [PMID: 35978250 DOI: 10.1007/s11356-022-22527-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Currently, the exploitation of Baode Block as a biogenic coal-bed gas field has been in the later stage of stable production; hence, exploration and activation of microbial gas production are of great practical significance for the enhancement and stabilization of block production. Pretreatment is the key process to improve anaerobic biodegradation performance and increase yield and production rate of gas. In this study, we examine physical, chemical, and biological pretreatment methods and compare their effectiveness toward microbial gas production in the coal seam. The obtained results indicate that: (1) grinding can enhance contact between the coal sample and bacteria liquid, and coal powder has greater gas-producing performance than the coal lump. (2) Chemical pretreatment of coal samples using acid and base can enhance gas production capacity. NaOH treatment has better gas-producing performance than HCl treatment, and the activity of microbial flora is higher after treatment. (3) Biological pretreatment can greatly enhance the microbial degradation of coal bed. The highest gas yield after white rot fungus pretreatment is 11.65 m3/t, and gas production cycle is shorter than before. This may be due to the white rot fungus effectively degrading macromolecules and, therefore, shortening the duration of methanogenic hydrolysis, which provides more organic matter for methanogens to decompose. During production, in addition to selecting a proper pretreatment method, the treatment cost and balance between energy input of pretreatment and gas energy output must also be considered. The joint pretreatment between different reagents and treatment methods is a possible solution to the problem and a current research trend to realize the large-scale degradation of coal. The simulated microbial methane production of coal seam is feasible for Baode Block in Ordos, where coal samples in this block have great gas-producing potential after treatment, and provides good references for further in-field tests.
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Affiliation(s)
- Zhenhong Chen
- Research Institute of Petroleum Exploration and Development, Beijing, 100083, China
| | - Hao Chen
- Research Institute of Petroleum Exploration and Development, Beijing, 100083, China.
| | - Xinfa Zhu
- CCDC Changqing Downhole Technology Company, Xi'an, 700021, China
| | - Daping Xia
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Yanpeng Chen
- Research Institute of Petroleum Exploration and Development, Beijing, 100083, China
| | - Meng Geng
- Research Institute of Petroleum Exploration and Development, Beijing, 100083, China
| | - Zhihao Bai
- School of Geology and Mining Engineering, Xinjiang University, Urumchi, 830000, China
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5
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Abosamaha A, Williamson MP, Gilmour DJ. Utilization and accumulation of compatible solutes in Halomonas pacifica: a species of moderately halophilic bacteria isolated from a saline lake in South Libya. Access Microbiol 2022; 4:acmi000359. [PMID: 36003353 PMCID: PMC9394535 DOI: 10.1099/acmi.0.000359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
When grown in high salt concentrations, halophilic bacteria often accumulate compatible solutes, which have major applications in biotechnology because they stabilize cells and proteins. Four Gram-negative bacterial strains, belonging to the family Halomonadaceae, were isolated from Qaberoun and Um-Alma lakes in South Libya using high-salinity medium. The strains were identified using 16S rRNA gene sequencing as belonging to Halomonas pacifica (strain ABQ1), Halomonas venusta (ABQ2), Halomonas elongata (ABU1) and Halomonas salifodinae (ABU2). H. pacifica ABQ1 is a moderate halophile (salinity range 0.05 to 2.5 M NaCl), with a broad tolerance to pH (7 to 9) and temperature (25–37 °C). Addition of the compatible solutes glycine betaine (betaine) and ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid) to the medium had a positive effect on growth of H. pacifica at 2 M NaCl. In rich LB medium, betaine was the major compatible solute accumulated, with ectoine only being accumulated at salinities in excess of 1 M NaCl. In minimal M9 medium, betaine was not produced, but increasing amounts of ectoine were synthesized with increasing salinity, and hydroxyectoine [(4S,5S)−5-hydroxy-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid] was also synthesized when the cells were grown in very high salt. We have thus identified H. pacifica as a producer of ectoine and hydroxyectoine, with more being produced at higher salinities. As industrial demand for these compatible solutes continues to increase, this system has biotechnological potential.
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Affiliation(s)
- Abdolkader Abosamaha
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Mike P. Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - D. James Gilmour
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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6
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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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Maiti A, Daschakraborty S. How Do Urea and Trimethylamine N-Oxide Influence the Dehydration-Induced Phase Transition of a Lipid Membrane? J Phys Chem B 2021; 125:10149-10165. [PMID: 34486370 DOI: 10.1021/acs.jpcb.1c05852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Living organisms are often exposed to extreme dehydration, which is detrimental to the structure and function of the cell membrane. The lipid membrane undergoes fluid-to-gel phase transition due to dehydration and thus loses fluidity and functionality. To protect the fluid phase of the bilayer these organisms adopt several strategies. Enhanced production of small polar organic solutes (also called osmolytes) is one such strategy. Urea and trimethylamine N-oxide (TMAO) are two osmolytes found in different organisms combating osmotic stress. Previous experiments have found that both these osmolytes have strong effects on lipid membrane under different hydration conditions. Urea prevents the dehydration-induced phase transition of the lipid membrane by directly interacting with the lipids, while TMAO does not inhibit the phase transition. To provide atomistic insights, we have carried out all-atom molecular dynamics (MD) simulation of a lipid membrane under varying hydration levels and studied the effect of these osmolytes on different structural and dynamic properties of the membrane. This study suggests that urea significantly inhibits the dehydration-induced fluid-to-gel phase transition by strongly interacting with the lipid membrane via hydrogen bonds, which balances the reduced lipid hydration due to the decreasing water content. In contrast, TMAO is excluded from the membrane surface due to unfavorable interaction with the lipids. This induces further dehydration of the lipids which reinforces the fluid-to-gel phase transition. We have also studied the counteractive role of TMAO on the effect of urea on lipid membrane when both the osmolytes are present. TMAO draws some urea molecules out of the membrane and thereby reduces the effect of urea on the lipid membrane at lower hydration levels. This is similar to the counteraction of urea's deleterious effects on protein by TMAO. All these observations are consistent with the experimental results and thus provide deep molecular insights into the role of these osmolytes in protecting the fluid phase of the membrane, the key survival strategy against osmotic-stress-induced dehydration.
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Affiliation(s)
- Archita Maiti
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India
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8
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Gault S, Jaworek MW, Winter R, Cockell CS. High pressures increase α-chymotrypsin enzyme activity under perchlorate stress. Commun Biol 2020; 3:550. [PMID: 33009512 PMCID: PMC7532203 DOI: 10.1038/s42003-020-01279-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/10/2020] [Indexed: 11/16/2022] Open
Abstract
Deep subsurface environments can harbour high concentrations of dissolved ions, yet we know little about how this shapes the conditions for life. We know even less about how the combined effects of high pressure influence the way in which ions constrain the possibilities for life. One such ion is perchlorate, which is found in extreme environments on Earth and pervasively on Mars. We investigated the interactions of high pressure and high perchlorate concentrations on enzymatic activity. We demonstrate that high pressures increase α-chymotrypsin enzyme activity even in the presence of high perchlorate concentrations. Perchlorate salts were shown to shift the folded α-chymotrypsin phase space to lower temperatures and pressures. The results presented here may suggest that high pressures increase the habitability of environments under perchlorate stress. Therefore, deep subsurface environments that combine these stressors, potentially including the subsurface of Mars, may be more habitable than previously thought. Gault et al. show that high pressures increase α-chymotrypsin enzyme activity in the presence of high perchlorate concentrations. These perchlorate salts shift the folded enzyme phase space to lower temperatures and pressure and may move the optimum enzyme activity towards lower temperatures in addition to higher pressures, which has implications for Martian habitability.
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Affiliation(s)
- Stewart Gault
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Michel W Jaworek
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, D-44227, Dortmund, Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, D-44227, Dortmund, Germany
| | - Charles S Cockell
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
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Van Landuyt J, Cimmino L, Dumolin C, Chatzigiannidou I, Taveirne F, Mattelin V, Zhang Y, Vandamme P, Scoma A, Williamson A, Boon N. Microbial enrichment, functional characterization and isolation from a cold seep yield piezotolerant obligate hydrocarbon degraders. FEMS Microbiol Ecol 2020; 96:5841521. [PMID: 32436568 DOI: 10.1093/femsec/fiaa097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/20/2020] [Indexed: 11/12/2022] Open
Abstract
Deep-sea environments can become contaminated with petroleum hydrocarbons. The effects of hydrostatic pressure (HP) in the deep sea on microbial oil degradation are poorly understood. Here, we performed long-term enrichments (100 days) from a natural cold seep while providing optimal conditions to sustain high hydrocarbon degradation rates. Through enrichments performed at increased HP and ambient pressure (AP) and by using control enrichments with marine broth, we demonstrated that both pressure and carbon source can have a big impact on the community structure. In contrast to previous studies, hydrocarbonoclastic operational taxonomic units (OTUs) remained dominant at both AP and increased HP, suggesting piezotolerance of these OTUs over the tested pressure range. Twenty-three isolates were obtained after isolation and dereplication. After recultivation at increased HP, an Alcanivorax sp. showed promising piezotolerance in axenic culture. Furthermore, preliminary co-cultivation tests indicated synergistic growth between some isolates, which shows promise for future synthetic community construction. Overall, more insights into the effect of increased HP on oil-degrading communities were obtained as well as several interesting isolates, e.g. a piezotolerant hydrocarbonoclastic bacterium for future deep-sea bioaugmentation investigation.
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Affiliation(s)
- Josefien Van Landuyt
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Lorenzo Cimmino
- Laboratory for Environmental Biotechnology, ENAC-IIE, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Charles Dumolin
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ioanna Chatzigiannidou
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Felix Taveirne
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Valérie Mattelin
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, 800 Dongchuan Rd, 200240 Shanghai, China
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Alberto Scoma
- Engineered Microbial Systems (EMS) Laboratory, Section of Biological and Chemical Engineering (BCE), Department of Engineering, Aarhus University, Hangøvej 2, 8200 Aarhus, Denmark
| | - Adam Williamson
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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10
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Chwastek G, Petrov EP, Sáenz JP. A Method for High-Throughput Measurements of Viscosity in Sub-micrometer-Sized Membrane Systems. Chembiochem 2020; 21:836-844. [PMID: 31566864 PMCID: PMC7154536 DOI: 10.1002/cbic.201900510] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/27/2019] [Indexed: 01/11/2023]
Abstract
To unravel the underlying principles of membrane adaptation in small systems like bacterial cells, robust approaches to characterize membrane fluidity are needed. Currently available relevant methods require advanced instrumentation and are not suitable for high-throughput settings needed to elucidate the biochemical pathways involved in adaptation. We developed a fast, robust, and financially accessible quantitative method to measure the microviscosity of lipid membranes in bulk suspension using a commercially available plate reader. Our approach, which is suitable for high-throughput screening, is based on the simultaneous measurements of absorbance and fluorescence emission of a viscosity-sensitive fluorescent dye, 9-(2,2-dicyanovinyl)julolidine (DCVJ), incorporated into a lipid membrane. We validated our method using artificial membranes with various lipid compositions over a range of temperatures and observed values that were in good agreement with previously published results. Using our approach, we were able to detect a lipid phase transition in the ruminant pathogen Mycoplasma mycoides.
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Affiliation(s)
- Grzegorz Chwastek
- B CUBE, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Eugene P Petrov
- Faculty of Physics, Ludwig Maximilian University of Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - James Peter Sáenz
- B CUBE, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
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11
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Ganesh Kumar A, Mathew NC, Sujitha K, Kirubagaran R, Dharani G. Genome analysis of deep sea piezotolerant Nesiotobacter exalbescens COD22 and toluene degradation studies under high pressure condition. Sci Rep 2019; 9:18724. [PMID: 31822790 PMCID: PMC6904484 DOI: 10.1038/s41598-019-55115-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 10/03/2019] [Indexed: 11/09/2022] Open
Abstract
A marine isolate, Nesiotobacter exalbescens COD22, isolated from deep sea sediment (2100 m depth) was capable of degrading aromatic hydrocarbons. The Nesiotobacter sp. grew well in the presence of toluene at 0.1 MPa and 10 MPa at a rate of 0.24 h-1 and 0.12 h-1, respectively, in custom designed high pressure reactors. Percentage of hydrocarbon degradation was found to be 87.5% at ambient pressure and it reached 92% under high pressure condition within a short retention period of 72 h. The biodegradation of hydrocarbon was confirmed by the accumulation of dicarboxylic acid, benzoic acid, benzyl alcohol and benzaldehyde which are key intermediates in toluene catabolism. The complete genome sequence consists of 4,285,402 bp with 53% GC content and contained 3969 total coding genes. The complete genome analysis revealed unique adaptation and degradation capabilities for complex aromatic compounds, biosurfactant synthesis to facilitate hydrocarbon emulsification, advanced mechanisms for chemotaxis and presence of well developed flagellar assembly. The genomic data corroborated with the results of hydrocarbon biodegradation at high pressure growth conditions and confirmed the biotechnological potential of Nesiotobacter sp. towards bioremediation of hydrocarbon polluted deep sea environments.
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Affiliation(s)
- A Ganesh Kumar
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India.
| | - Noelin Chinnu Mathew
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - K Sujitha
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - R Kirubagaran
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - G Dharani
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
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13
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Abstract
The discovery of microbial communities in extreme conditions that would seem hostile to life leads to the question of how the molecules making up these microbes can maintain their structure and function. While microbes that live under extremes of temperature have been heavily studied, those that live under extremes of pressure, or "piezophiles", are now increasingly being studied because of advances in sample collection and high-pressure cells for biochemical and biophysical measurements. Here, adaptations of enzymes in piezophiles against the effects of pressure are discussed in light of recent experimental and computational studies. However, while concepts from studies of enzymes from temperature extremophiles can provide frameworks for understanding adaptations by piezophile enzymes, the effects of temperature and pressure on proteins differ in significant ways. Thus, the state of the knowledge of adaptation in piezophile enzymes is still in its infancy and many more experiments and computational studies on different enzymes from a variety of piezophiles are needed.
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Affiliation(s)
- Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC, 20057, United States
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14
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Perez Calderon LJ, Gontikaki E, Potts LD, Shaw S, Gallego A, Anderson JA, Witte U. Pressure and temperature effects on deep-sea hydrocarbon-degrading microbial communities in subarctic sediments. Microbiologyopen 2018; 8:e00768. [PMID: 30444300 PMCID: PMC6562134 DOI: 10.1002/mbo3.768] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/24/2022] Open
Abstract
The Hatton-Rockall Basin (North-East Atlantic) is an area with potential for deep-sea (2,900 m) hydrocarbon exploration. Following the Deepwater Horizon oil spill, many investigations into the responses of sediment microbial communities to oil pollution have been undertaken. However, hydrostatic pressure is a parameter that is often omitted due to the technical difficulties associated with conducting experiments at high pressure (>10 MPa). In this study, sediments from 2,900 m in the Hatton-Rockall Basin, following a one-week decompression period in a temperature-controlled room at 5°C, were incubated in factorial combinations of 0.1 and 30 MPa, 5 and 20°C, and contamination with a hydrocarbon mixture or uncontaminated controls to evaluate the effect of these environmental variables on the bacterial community composition. Our results revealed varying effects of pressure, temperature, and oil contamination on the composition of the bacterial community within the sediment. Temperature was the strongest determinant of differences in the bacterial community structure between samples followed by pressure. Oil contamination did not exert a strong change in the sediment bacterial community structure when pressure and temperature conditions were held at in situ levels (30 MPa and 5°C). The γ-proteobacteria Pseudomonas and Colwellia, and several Bacteroidetes dominated communities at 30 MPa. In contrast, hydrocarbon degraders such as Halomonas, Alcanivorax, and Marinobacter decreased in relative abundance at the same pressure. This study highlights the importance of considering hydrostatic pressure in ex situ investigations into hydrocarbon-degrading deepwater microbial communities.
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Affiliation(s)
- Luis J Perez Calderon
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK.,Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen, UK.,Marine Laboratory Aberdeen, Marine Scotland Science, Aberdeen, UK
| | - Evangelia Gontikaki
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
| | - Lloyd D Potts
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK.,Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen, UK
| | - Sophie Shaw
- Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
| | | | - James A Anderson
- Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen, UK
| | - Ursula Witte
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
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15
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de Carvalho CCCR, Caramujo MJ. The Various Roles of Fatty Acids. Molecules 2018; 23:molecules23102583. [PMID: 30304860 PMCID: PMC6222795 DOI: 10.3390/molecules23102583] [Citation(s) in RCA: 306] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/01/2018] [Accepted: 10/06/2018] [Indexed: 12/31/2022] Open
Abstract
Lipids comprise a large group of chemically heterogeneous compounds. The majority have fatty acids (FA) as part of their structure, making these compounds suitable tools to examine processes raging from cellular to macroscopic levels of organization. Among the multiple roles of FA, they have structural functions as constituents of phospholipids which are the "building blocks" of cell membranes; as part of neutral lipids FA serve as storage materials in cells; and FA derivatives are involved in cell signalling. Studies on FA and their metabolism are important in numerous research fields, including biology, bacteriology, ecology, human nutrition and health. Specific FA and their ratios in cellular membranes may be used as biomarkers to enable the identification of organisms, to study adaptation of bacterial cells to toxic compounds and environmental conditions and to disclose food web connections. In this review, we discuss the various roles of FA in prokaryotes and eukaryotes and highlight the application of FA analysis to elucidate ecological mechanisms. We briefly describe FA synthesis; analyse the role of FA as modulators of cell membrane properties and FA ability to store and supply energy to cells; and inspect the role of polyunsaturated FA (PUFA) and the suitability of using FA as biomarkers of organisms.
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Affiliation(s)
- Carla C C R de Carvalho
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Maria José Caramujo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2-5º Piso, 1749-016 Lisboa, Portugal.
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16
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Guo N, Wang Y, Tong T, Wang S. The fate of antibiotic resistance genes and their potential hosts during bio-electrochemical treatment of high-salinity pharmaceutical wastewater. WATER RESEARCH 2018; 133:79-86. [PMID: 29367050 DOI: 10.1016/j.watres.2018.01.020] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/23/2017] [Accepted: 01/08/2018] [Indexed: 05/18/2023]
Abstract
Pharmaceutical wastewaters containing antibiotics and high salinity can damage traditional biological treatment and result in the proliferation of antibiotic resistance genes (ARGs). Bioelectrochemical system (BES) is a promising approach for treating pharmaceutical wastewater. However, the fate of ARGs in BES and their correlations with microbial communities and horizontal genes transfer are unknown. In this study, we investigated the response of ARGs to bio-electrochemical treatment of chloramphenicol wastewater and their potential hosts under different salinities. Three ARGs encoding efflux pump (cmlA, floR and tetC), one class 1 integron integrase encoding gene (intI1), and sul1 gene (associate with intI1) were analyzed. Correlation analysis between microbial community and ARGs revealed that the abundances of potential hosts of ARGs were strongly affected by salinity, which further determined the alteration in ARGs abundances under different salinities. There were no significant correlations between ARGs and intI1, indicating that horizontal gene transfer was not related to the important changes in ARGs. Moreover, the chloramphenicol removal efficiency was enhanced under a moderate salinity, attributed to the altered microbial community driven by salinity. Therefore, microbial community shift is the major factor for the changes of ARGs and chloramphenicol removal efficiency in BES under different salinities. This study provides new insights on the mechanisms underlying the alteration of ARGs in BES treating high-salinity pharmaceutical wastewater.
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Affiliation(s)
- Ning Guo
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Yunkun Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan 250100, China.
| | - Tiezheng Tong
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO 80523, United States
| | - Shuguang Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan 250100, China.
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17
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Peoples LM, Donaldson S, Osuntokun O, Xia Q, Nelson A, Blanton J, Allen EE, Church MJ, Bartlett DH. Vertically distinct microbial communities in the Mariana and Kermadec trenches. PLoS One 2018; 13:e0195102. [PMID: 29621268 PMCID: PMC5886532 DOI: 10.1371/journal.pone.0195102] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/17/2018] [Indexed: 01/13/2023] Open
Abstract
Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct microbial communities compared to those at shallower depths due to high hydrostatic pressures, topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of the communities present in the bottom waters of the Kermadec and Mariana trenches. Estimates of microbial protein production indicate active populations under in situ hydrostatic pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and size fraction are important drivers of microbial community structure. Many putative hadal bathytypes, such as members related to the Marinimicrobia, Rhodobacteraceae, Rhodospirilliceae, and Aquibacter, are similar to members identified in other trenches. Most of the differences between the two trench microbiomes consists of taxa belonging to the Gammaproteobacteria whose distributions extend throughout the water column. Growth and survival estimates of representative isolates of these taxa under deep-sea conditions suggest that some members may descend from shallower depths and exist as a potentially inactive fraction of the hadal zone. We conclude that the distinct pelagic communities residing in these two trenches, and perhaps by extension other trenches, reflect both cosmopolitan hadal bathytypes and ubiquitous genera found throughout the water column.
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Affiliation(s)
- Logan M. Peoples
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Sierra Donaldson
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Oladayo Osuntokun
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Qing Xia
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
- Department of Soil Science, North Carolina State University, Raleigh, NC, United States of America
| | - Alex Nelson
- Center for Microbial Oceanography: Research and Education, C-MORE Hale, University of Hawaiʻi at Mānoa, Honolulu, HI, United States of America
| | - Jessica Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Matthew J. Church
- Center for Microbial Oceanography: Research and Education, C-MORE Hale, University of Hawaiʻi at Mānoa, Honolulu, HI, United States of America
- Flathead Lake Biological Station, University of Montana, Polson, MT, United States of America
| | - Douglas H. Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
- * E-mail:
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18
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Schwendner P, Bohmeier M, Rettberg P, Beblo-Vranesevic K, Gaboyer F, Moissl-Eichinger C, Perras AK, Vannier P, Marteinsson VT, Garcia-Descalzo L, Gómez F, Malki M, Amils R, Westall F, Riedo A, Monaghan EP, Ehrenfreund P, Cabezas P, Walter N, Cockell C. Beyond Chloride Brines: Variable Metabolomic Responses in the Anaerobic Organism Yersinia intermedia MASE-LG-1 to NaCl and MgSO 4 at Identical Water Activity. Front Microbiol 2018; 9:335. [PMID: 29535699 PMCID: PMC5835128 DOI: 10.3389/fmicb.2018.00335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/12/2018] [Indexed: 11/18/2022] Open
Abstract
Growth in sodium chloride (NaCl) is known to induce stress in non-halophilic microorganisms leading to effects on the microbial metabolism and cell structure. Microorganisms have evolved a number of adaptations, both structural and metabolic, to counteract osmotic stress. These strategies are well-understood for organisms in NaCl-rich brines such as the accumulation of certain organic solutes (known as either compatible solutes or osmolytes). Less well studied are responses to ionic environments such as sulfate-rich brines which are prevalent on Earth but can also be found on Mars. In this paper, we investigated the global metabolic response of the anaerobic bacterium Yersinia intermedia MASE-LG-1 to osmotic salt stress induced by either magnesium sulfate (MgSO4) or NaCl at the same water activity (0.975). Using a non-targeted mass spectrometry approach, the intensity of hundreds of metabolites was measured. The compatible solutes L-asparagine and sucrose were found to be increased in both MgSO4 and NaCl compared to the control sample, suggesting a similar osmotic response to different ionic environments. We were able to demonstrate that Yersinia intermedia MASE-LG-1 accumulated a range of other compatible solutes. However, we also found the global metabolic responses, especially with regard to amino acid metabolism and carbohydrate metabolism, to be salt-specific, thus, suggesting ion-specific regulation of specific metabolic pathways.
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Affiliation(s)
- Petra Schwendner
- School of Physics and Astronomy, UK Center for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria Bohmeier
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Petra Rettberg
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Kristina Beblo-Vranesevic
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Frédéric Gaboyer
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, Orléans, France
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Alexandra K. Perras
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Department of Microbiology and Archaea, University of Regensburg, Regensburg, Germany
| | | | - Viggó T. Marteinsson
- MATIS - Prokaria, Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Reykjavik, Iceland
| | | | - Felipe Gómez
- Instituto Nacional de Técnica Aeroespacial - Centro de Astrobiología, Madrid, Spain
| | - Moustafa Malki
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Frances Westall
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, Orléans, France
| | - Andreas Riedo
- Leiden Observatory, Universiteit Leiden, Leiden, Netherlands
| | | | - Pascale Ehrenfreund
- Leiden Observatory, Universiteit Leiden, Leiden, Netherlands
- Space Policy Institute, George Washington University, Washington, DC, United States
| | - Patricia Cabezas
- Space Policy Institute, George Washington University, Washington, DC, United States
- European Science Foundation, Strasbourg, France
| | - Nicolas Walter
- Space Policy Institute, George Washington University, Washington, DC, United States
- European Science Foundation, Strasbourg, France
| | - Charles Cockell
- School of Physics and Astronomy, UK Center for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
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19
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Harrison JP, Angel R, Cockell CS. Astrobiology as a framework for investigating antibiotic susceptibility: a study of Halomonas hydrothermalis. J R Soc Interface 2017; 14:20160942. [PMID: 28123098 PMCID: PMC5310740 DOI: 10.1098/rsif.2016.0942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/14/2016] [Indexed: 01/19/2023] Open
Abstract
Physical and chemical boundaries for microbial multiplication on Earth are strongly influenced by interactions between environmental extremes. However, little is known about how interactions between multiple stress parameters affect the sensitivity of microorganisms to antibiotics. Here, we assessed how 12 distinct permutations of salinity, availability of an essential nutrient (iron) and atmospheric composition (aerobic or microaerobic) affect the susceptibility of a polyextremotolerant bacterium, Halomonas hydrothermalis, to ampicillin, kanamycin and ofloxacin. While salinity had a significant impact on sensitivity to all three antibiotics (as shown by turbidimetric analyses), the nature of this impact was modified by iron availability and the ambient gas composition, with differing effects observed for each compound. These two parameters were found to be of particular importance when considered in combination and, in the case of ampicillin, had a stronger combined influence on antibiotic tolerance than salinity. Our data show how investigating microbial responses to multiple extremes, which are more representative of natural habitats than single extremes, can improve our understanding of the effects of antimicrobial compounds and suggest how studies of habitability, motivated by the desire to map the limits of life, can be used to systematically assess the effectiveness of antibiotics.
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Affiliation(s)
- Jesse P Harrison
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, UK
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry Meets Microbiology', University of Vienna, Vienna 1090, Austria
| | - Roey Angel
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry Meets Microbiology', University of Vienna, Vienna 1090, Austria
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, UK
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20
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Moissl-Eichinger C, Cockell C, Rettberg P. Venturing into new realms? Microorganisms in space. FEMS Microbiol Rev 2016; 40:722-37. [PMID: 27354346 DOI: 10.1093/femsre/fuw015] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 12/15/2022] Open
Abstract
One of the biggest challenges of science is the determination of whether extraterrestrial life exists. Although potential habitable areas might be available for complex life, it is more likely that microbial life could exist in space. Many extremotolerant and extremophilic microbes have been found to be able to withstand numerous, combined environmental factors, such as high or low temperatures and pressures, high-salt conditions, high doses of radiation, desiccation or nutrient limitations. They may even survive the transit from one planet to another. Terrestrial Mars-analogue sites are one focus of researchers, in order to understand the microbial diversity in preparation for upcoming space missions aimed at the detection of life. However, such missions could also pose a risk with respect to contamination of the extraterrestrial environment by accidentally transferred terrestrial microorganisms. Closer to the Earth, the International Space Station is the most enclosed habitat, where humans work and live-and with them numerous microorganisms. It is still unknown how microbes adapt to this environment, possibly even creating a risk for the crew. Information on the microbiology of the ISS will have an impact on the planning and implementation of long-term human spaceflights in order to ensure a safe, stable and balanced microbiome on board.
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Affiliation(s)
- Christine Moissl-Eichinger
- Department for Internal Medicine, Medical University of Graz, 8036 Graz, Austria BioTechMed Graz, 8010 Graz, Austria
| | - Charles Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH10 4EP, UK
| | - Petra Rettberg
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
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21
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Kleist S, Ulbrich M, Bill N, Schmidt-Hohagen K, Geffers R, Schomburg D. Dealing with salinity extremes and nitrogen limitation - an unexpected strategy of the marine bacteriumDinoroseobacter shibae. Environ Microbiol 2016; 19:894-908. [DOI: 10.1111/1462-2920.13266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/12/2016] [Accepted: 02/12/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Sarah Kleist
- Department of Bioinformatics and Biochemistry, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig; Langer Kamp 19 b D-38106 Braunschweig Germany
| | - Marcus Ulbrich
- Department of Bioinformatics and Biochemistry, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig; Langer Kamp 19 b D-38106 Braunschweig Germany
| | - Nelli Bill
- Department of Bioinformatics and Biochemistry, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig; Langer Kamp 19 b D-38106 Braunschweig Germany
| | - Kerstin Schmidt-Hohagen
- Department of Bioinformatics and Biochemistry, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig; Langer Kamp 19 b D-38106 Braunschweig Germany
| | - Robert Geffers
- Department of Molecular Bacteriology; Helmholtz-Centre for Infection Research (HZI); D-38124 Braunschweig
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig; Langer Kamp 19 b D-38106 Braunschweig Germany
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22
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Scoma A, Boon N. Osmotic Stress Confers Enhanced Cell Integrity to Hydrostatic Pressure but Impairs Growth in Alcanivorax borkumensis SK2. Front Microbiol 2016; 7:729. [PMID: 27242746 PMCID: PMC4870253 DOI: 10.3389/fmicb.2016.00729] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/02/2016] [Indexed: 01/13/2023] Open
Abstract
Alcanivorax is a hydrocarbonoclastic genus dominating oil spills worldwide. While its presence has been detected in oil-polluted seawaters, marine sediment and salt marshes under ambient pressure, its presence in deep-sea oil-contaminated environments is negligible. Recent laboratory studies highlighted the piezosensitive nature of some Alcanivorax species, whose growth yields are highly impacted by mild hydrostatic pressures (HPs). In the present study, osmotic stress was used as a tool to increase HP resistance in the type strain Alcanivorax borkumensis SK2. Control cultures grown under standard conditions of salinity and osmotic pressure with respect to seawater (35.6 ppt or 1136 mOsm kg-1, respectively) were compared with cultures subjected to hypo- and hyperosmosis (330 and 1720 mOsm kg-1, or 18 and 62 ppt in salinity, equivalent to brackish and brine waters, respectively), under atmospheric or increased HP (0.1 and 10 MPa). Osmotic stress had a remarkably positive impact on cell metabolic activity in terms of CO2 production (thus, oil bioremediation) and O2 respiration under hyperosmosis, as acclimation to high salinity enhanced cell activity under 10 MPa by a factor of 10. Both osmotic shocks significantly enhanced cell protection by reducing membrane damage under HP, with cell integrities close to 100% under hyposmosis. The latter was likely due to intracellular water-reclamation as no trace of the piezolyte ectoine was found, contrary to hyperosmosis. Notably, ectoine production was equivalent at 0.1 MPa in hyperosmosis-acclimated cells and at 10 MPa under isosmotic conditions. While stimulating cell metabolism and enhancing cell integrity, osmotic stress had always a negative impact on culture growth and performance. No net growth was observed during 4-days incubation tests, and CO2:O2 ratios and pH values indicated that culture performance in terms of hydrocarbon degradation was lowered by the effects of osmotic stress alone or combined with increased HP. These findings confirm the piezosensitive nature of A. borkumensis, which lacks proper resistance mechanisms to improve its metabolic efficiency under increased HP, thus explaining its limited role in oil-polluted deep-sea environments.
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Affiliation(s)
- Alberto Scoma
- Center for Microbial Ecology and Technology, Department of Biochemical and Microbial Technology, University of Ghent Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Department of Biochemical and Microbial Technology, University of Ghent Ghent, Belgium
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23
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Fichtel K, Logemann J, Fichtel J, Rullkötter J, Cypionka H, Engelen B. Temperature and pressure adaptation of a sulfate reducer from the deep subsurface. Front Microbiol 2015; 6:1078. [PMID: 26500624 PMCID: PMC4594026 DOI: 10.3389/fmicb.2015.01078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/21/2015] [Indexed: 11/13/2022] Open
Abstract
Microbial life in deep marine subsurface faces increasing temperatures and hydrostatic pressure with depth. In this study, we have examined growth characteristics and temperature-related adaptation of the Desulfovibrio indonesiensis strain P23 to the in situ pressure of 30 MPa. The strain originates from the deep subsurface of the eastern flank of the Juan de Fuca Ridge (IODP Site U1301). The organism was isolated at 20°C and atmospheric pressure from ~61°C-warm sediments approximately 5 m above the sediment-basement interface. In comparison to standard laboratory conditions (20°C and 0.1 MPa), faster growth was recorded when incubated at in situ pressure and high temperature (45°C), while cell filamentation was induced by further compression. The maximum growth temperature shifted from 48°C at atmospheric pressure to 50°C under high-pressure conditions. Complementary cellular lipid analyses revealed a two-step response of membrane viscosity to increasing temperature with an exchange of unsaturated by saturated fatty acids and subsequent change from branched to unbranched alkyl moieties. While temperature had a stronger effect on the degree of fatty acid saturation and restructuring of main phospholipids, pressure mainly affected branching and length of side chains. The simultaneous decrease of temperature and pressure to ambient laboratory conditions allowed the cultivation of our moderately thermophilic strain. This may in turn be one key to a successful isolation of microorganisms from the deep subsurface adapted to high temperature and pressure.
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Affiliation(s)
- Katja Fichtel
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Jörn Logemann
- Organic Geochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Jörg Fichtel
- Organic Geochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Jürgen Rullkötter
- Organic Geochemistry Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Heribert Cypionka
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, OldenburgGermany
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24
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Reduction of the temperature sensitivity of Halomonas hydrothermalis by iron starvation combined with microaerobic conditions. Appl Environ Microbiol 2015; 81:2156-62. [PMID: 25595757 DOI: 10.1128/aem.03639-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The limits to biological processes on Earth are determined by physicochemical parameters, such as extremes of temperature and low water availability. Research into microbial extremophiles has enhanced our understanding of the biophysical boundaries which define the biosphere. However, there remains a paucity of information on the degree to which rates of microbial multiplication within extreme environments are determined by the availability of specific chemical elements. Here, we show that iron availability and the composition of the gaseous phase (aerobic versus microaerobic) determine the susceptibility of a marine bacterium, Halomonas hydrothermalis, to suboptimal and elevated temperature and salinity by impacting rates of cell division (but not viability). In particular, iron starvation combined with microaerobic conditions (5% [vol/vol] O2, 10% [vol/vol] CO2, reduced pH) reduced sensitivity to temperature across the 13°C range tested. These data demonstrate that nutrient limitation interacts with physicochemical parameters to determine biological permissiveness for extreme environments. The interplay between resource availability and stress tolerance, therefore, may shape the distribution and ecology of microorganisms within Earth's biosphere.
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25
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Pond DW, Tarling GA, Mayor DJ. Hydrostatic pressure and temperature effects on the membranes of a seasonally migrating marine copepod. PLoS One 2014; 9:e111043. [PMID: 25338196 PMCID: PMC4206463 DOI: 10.1371/journal.pone.0111043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/23/2014] [Indexed: 02/03/2023] Open
Abstract
Marine planktonic copepods of the order Calanoida are central to the ecology and productivity of high latitude ecosystems, representing the interface between primary producers and fish. These animals typically undertake a seasonal vertical migration into the deep sea, where they remain dormant for periods of between three and nine months. Descending copepods are subject to low temperatures and increased hydrostatic pressures. Nothing is known about how these organisms adapt their membranes to these environmental stressors. We collected copepods (Calanoides acutus) from the Southern Ocean at depth horizons ranging from surface waters down to 1000 m. Temperature and/or pressure both had significant, additive effects on the overall composition of the membrane phospholipid fatty acids (PLFAs) in C. acutus. The most prominent constituent of the PLFAs, the polyunsaturated fatty acid docosahexanoic acid [DHA - 22:6(n-3)], was affected by a significant interaction between temperature and pressure. This moiety increased with pressure, with the rate of increase being greater at colder temperatures. We suggest that DHA is key to the physiological adaptations of vertically migrating zooplankton, most likely because the biophysical properties of this compound are suited to maintaining membrane order in the cold, high pressure conditions that persist in the deep sea. As copepods cannot synthesise DHA and do not feed during dormancy, sufficient DHA must be accumulated through ingestion before migration is initiated. Climate-driven changes in the timing and abundance of the flagellated microplankton that supply DHA to copepods have major implications for the capacity of these animals to undertake their seasonal life cycle successfully.
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Affiliation(s)
- David W. Pond
- Scottish Association for Marine Science, Oban, Argyll, United Kingdom
| | - Geraint A. Tarling
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Daniel J. Mayor
- Institute of Biological and Environmental Sciences, Oceanlab, University of Aberdeen, Newburgh, Aberdeenshire, United Kingdom
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Physiological features of Halomonas lionensis sp. nov., a novel bacterium isolated from a Mediterranean Sea sediment. Res Microbiol 2014; 165:490-500. [PMID: 25086262 DOI: 10.1016/j.resmic.2014.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 07/22/2014] [Indexed: 11/19/2022]
Abstract
A novel halophilic bacterium, strain RHS90(T), was isolated from marine sediments from the Gulf of Lions, in the Mediterranean Sea. Its metabolic and physiological characteristics were examined under various cultural conditions, including exposure to stressful ones (oligotrophy, high pressure and high concentrations of metals). Based on phylogenetic analysis of the 16S rRNA gene, the strain was found to belong to the genus Halomonas in the class Gammaproteobacteria. Its closest relatives are Halomonas axialensis and Halomonas meridiana (98% similarity). DNA-DNA hybridizations indicated that the novel isolate is genotypically distinct from these species. The DNA G + C content of the strain is 54.4 mol%. The main fatty acids (C18:1ω7c, 2-OH iso-C15:0, C16:0 and/or C19:0 cyclo ω8c), main polar lipids (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified phosphoglycolipid) and major respiratory quinone (ubiquinone Q9) were determined. The novel isolate is heterotrophic, mesophilic, euryhaline (growth optimum ranging from 2 to 8% w/v NaCl) and is able to grow under stressful conditions. The strain accumulates poly-β-hydroxyalkanoates granules and compatible solutes. Based on genotypic, chemotaxonomic and phenotypic distinctiveness, this isolate is likely to represent a novel species, for which the name Halomonas lionensis is proposed. The type strain of H. lionensis is RHS90(T) (DSM 25632(T) = CIP 110370(T) = UBOCC 3186(T)).
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da Silva MAC, Cavalett A, Spinner A, Rosa DC, Jasper RB, Quecine MC, Bonatelli ML, Pizzirani-Kleiner A, Corção G, Lima AODS. Phylogenetic identification of marine bacteria isolated from deep-sea sediments of the eastern South Atlantic Ocean. SPRINGERPLUS 2013; 2:127. [PMID: 23565357 PMCID: PMC3616218 DOI: 10.1186/2193-1801-2-127] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 03/08/2013] [Indexed: 11/26/2022]
Abstract
The deep-sea environments of the South Atlantic Ocean are less studied in comparison to the North Atlantic and Pacific Oceans. With the aim of identifying the deep-sea bacteria in this less known ocean, 70 strains were isolated from eight sediment samples (depth range between 1905 to 5560 m) collected in the eastern part of the South Atlantic, from the equatorial region to the Cape Abyssal Plain, using three different culture media. The strains were classified into three phylogenetic groups, Gammaproteobacteria, Firmicutes and Actinobacteria, by the analysis of 16s rRNA gene sequences. Gammaproteobacteria and Firmicutes were the most frequently identified groups, with Halomonas the most frequent genus among the strains. Microorganisms belonging to Firmicutes were the only ones observed in all samples. Sixteen of the 41 identified operational taxonomic units probably represent new species. The presence of potentially new species reinforces the need for new studies in the deep-sea environments of the South Atlantic.
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Affiliation(s)
- Marcus Adonai Castro da Silva
- Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Itajaí, SC, CEP 88302202 Brazil
| | - Angélica Cavalett
- Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Itajaí, SC, CEP 88302202 Brazil
| | - Ananda Spinner
- Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Itajaí, SC, CEP 88302202 Brazil
| | - Daniele Cristina Rosa
- Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Itajaí, SC, CEP 88302202 Brazil
| | - Regina Beltrame Jasper
- Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Itajaí, SC, CEP 88302202 Brazil
| | - Maria Carolina Quecine
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Av. Padua Dias, 11, Piracicaba, SP, CEP 13418-260 Brasil
| | - Maria Letícia Bonatelli
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Av. Padua Dias, 11, Piracicaba, SP, CEP 13418-260 Brasil
| | - Aline Pizzirani-Kleiner
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Av. Padua Dias, 11, Piracicaba, SP, CEP 13418-260 Brasil
| | - Gertrudes Corção
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Sarmento Leite 500, Cidade Baixa, Porto Alegre-RS, CEP 90050-170 Brazil
| | - André Oliveira de Souza Lima
- Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí (UNIVALI), Rua Uruguai, 458, Itajaí, SC, CEP 88302202 Brazil
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Coyne KJ, Countway PD, Pilditch CA, Lee CK, Caron DA, Cary SC. Diversity and Distributional Patterns of Ciliates in Guaymas Basin Hydrothermal Vent Sediments. J Eukaryot Microbiol 2013; 60:433-47. [DOI: 10.1111/jeu.12051] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 03/18/2013] [Accepted: 03/18/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Kathryn J. Coyne
- College of Earth, Ocean, and Environment; University of Delaware; 700 Pilottown Road Lewes Delaware 19958 USA
| | - Peter D. Countway
- Department of Biological Sciences; University of Southern California; Los Angeles California 90089-0371 USA
| | - Conrad A. Pilditch
- Department of Biological Sciences; University of Waikato; Private Bag 3105 Hamilton 3240 New Zealand
| | - Charles K. Lee
- Department of Biological Sciences; University of Waikato; Private Bag 3105 Hamilton 3240 New Zealand
| | - David A. Caron
- Department of Biological Sciences; University of Southern California; Los Angeles California 90089-0371 USA
| | - Stephen C. Cary
- College of Earth, Ocean, and Environment; University of Delaware; 700 Pilottown Road Lewes Delaware 19958 USA
- Department of Biological Sciences; University of Waikato; Private Bag 3105 Hamilton 3240 New Zealand
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Dick GJ, Anantharaman K, Baker BJ, Li M, Reed DC, Sheik CS. The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Front Microbiol 2013; 4:124. [PMID: 23720658 PMCID: PMC3659317 DOI: 10.3389/fmicb.2013.00124] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/30/2013] [Indexed: 11/24/2022] Open
Abstract
Hydrothermal plumes are an important yet understudied component of deep-sea vent microbial ecosystems. The significance of plume microbial processes can be appreciated from three perspectives: (1) mediation of plume biogeochemistry, (2) dispersal of seafloor hydrothermal vent microbes between vents sites, (3) as natural laboratories for understanding the ecology, physiology, and function of microbial groups that are distributed throughout the pelagic deep sea. Plume microbiology has been largely neglected in recent years, especially relative to the extensive research conducted on seafloor and subseafloor systems. Rapidly advancing technologies for investigating microbial communities provide new motivation and opportunities to characterize this important microbial habitat. Here we briefly highlight microbial contributions to plume and broader ocean (bio)geochemistry and review recent work to illustrate the ecological and biogeographic linkages between plumes, seafloor vent habitats, and other marine habitats such as oxygen minimum zones (OMZs), cold seeps, and oil spills. 16S rRNA gene surveys and metagenomic/-transcriptomic data from plumes point to dominant microbial populations, genes, and functions that are also operative in OMZs (SUP05, ammonia-oxidizing Archaea, and SAR324 Deltaproteobacteria) and hydrocarbon-rich environments (methanotrophs). Plume microbial communities are distinct from those on the seafloor or in the subsurface but contain some signatures of these habitats, consistent with the notion that plumes are potential vectors for dispersal of microorganisms between seafloor vent sites. Finally, we put forward three pressing questions for the future of deep-sea hydrothermal plume research and consider interactions between vents and oceans on global scales.
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Affiliation(s)
- Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA ; Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA ; Center for Computational Medicine and Bioinformatics, University of Michigan Ann Arbor, MI, USA
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30
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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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31
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Thermal effects on microbial composition and microbiologically induced corrosion and mineral precipitation affecting operation of a geothermal plant in a deep saline aquifer. Extremophiles 2013; 17:311-27. [DOI: 10.1007/s00792-013-0518-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/10/2013] [Indexed: 11/26/2022]
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32
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Sutherland R, Viljoen A, Myburg AA, van den Berg N. Pathogenicity associated genes in Fusarium oxysporum f. sp. cubense race 4. S AFR J SCI 2013. [DOI: 10.1590/sajs.2013/20120023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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33
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Bazylinski DA, Williams TJ, Lefèvre CT, Trubitsyn D, Fang J, Beveridge TJ, Moskowitz BM, Ward B, Schübbe S, Dubbels BL, Simpson B. Magnetovibrio blakemorei gen. nov., sp. nov., a magnetotactic bacterium (Alphaproteobacteria: Rhodospirillaceae) isolated from a salt marsh. Int J Syst Evol Microbiol 2012; 63:1824-1833. [PMID: 22984137 DOI: 10.1099/ijs.0.044453-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A magnetotactic bacterium, designated strain MV-1(T), was isolated from sulfide-rich sediments in a salt marsh near Boston, MA, USA. Cells of strain MV-1(T) were Gram-negative, and vibrioid to helicoid in morphology. Cells were motile by means of a single polar flagellum. The cells appeared to display a transitional state between axial and polar magnetotaxis: cells swam in both directions, but generally had longer excursions in one direction than the other. Cells possessed a single chain of magnetosomes containing truncated hexaoctahedral crystals of magnetite, positioned along the long axis of the cell. Strain MV-1(T) was a microaerophile that was also capable of anaerobic growth on some nitrogen oxides. Salinities greater than 10 % seawater were required for growth. Strain MV-1(T) exhibited chemolithoautotrophic growth on thiosulfate and sulfide with oxygen as the terminal electron acceptor (microaerobic growth) and on thiosulfate using nitrous oxide (N2O) as the terminal electron acceptor (anaerobic growth). Chemo-organoautotrophic and methylotrophic growth was supported by formate under microaerobic conditions. Autotrophic growth occurred via the Calvin-Benson-Bassham cycle. Chemo-organoheterotrophic growth was supported by various organic acids and amino acids, under microaerobic and anaerobic conditions. Optimal growth occurred at pH 7.0 and 26-28 °C. The genome of strain MV-1(T) consisted of a single, circular chromosome, about 3.7 Mb in size, with a G+C content of 52.9-53.5 mol%.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MV-1(T) belongs to the family Rhodospirillaceae within the Alphaproteobacteria, but is not closely related to the genus Magnetospirillum. The name Magnetovibrio blakemorei gen. nov., sp. nov. is proposed for strain MV-1(T). The type strain of Magnetovibrio blakemorei is MV-1(T) ( = ATCC BAA-1436(T) = DSM 18854(T)).
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Affiliation(s)
- Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154, USA
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Christopher T Lefèvre
- CEA Cadarache/CNRS/Aix-Marseille Université, UMR7265 Service de Biologie Végétale et de Microbiologie Environnementale, Laboratoire de Bioénergétique Cellulaire, 13108 Saint Paul lez Durance, France
| | - Denis Trubitsyn
- School of Life Sciences, University of Nevada at Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154, USA
| | - Jiasong Fang
- Department of Natural Sciences, Hawaii Pacific University, 45-045 Kamehameha Highway, Kaneohe, HI 96744, USA
| | - Terrence J Beveridge
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Bruce M Moskowitz
- Institute for Rock Magnetism, Department of Earth Sciences, University of Minnesota-Twin Cities, 310 Pillsbury Dr., SE, Minneapolis, MN 55455, USA
| | - Bruce Ward
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JR, UK
| | - Sabrina Schübbe
- School of Life Sciences, University of Nevada at Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154, USA
| | - Bradley L Dubbels
- Life Technologies Corporation, 29851 Willow Creek Road, Eugene, OR 97402, USA
| | - Brian Simpson
- United States Navy, Helseacombatron Two Three, San Diego, CA 92135, USA
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Zhao L, Ma T, Gao M, Gao P, Cao M, Zhu X, Li G. Characterization of microbial diversity and community in water flooding oil reservoirs in China. World J Microbiol Biotechnol 2012; 28:3039-52. [PMID: 22806743 DOI: 10.1007/s11274-012-1114-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 06/15/2012] [Indexed: 12/01/2022]
Abstract
The diversity and distribution of bacterial and archaeal communities in four different water flooding oil reservoirs with different geological properties were investigated using 16S rDNA clone library construction method. Canonical correspondence analysis was used to analyze microbial community clustering and the correlation with environmental factors. The results indicated that the diversity and abundance in the bacterial communities were significantly higher than the archaeal communities, while both of them had high similarity within the communities respectively. Phylogenetic analysis showed that of compositions of bacterial communities were distinctly different both at phylum and genus level. Proteobacteria dominated in each bacterial community, ranging from 61.35 to 75.83 %, in which α-proteobacteria and γ-proteobacteria were the main groups. In comparison to bacterial communities, the compositions of archaeal communities were similar at phylum level, while varied at genus level, and the dominant population was Methanomicrobia, ranging from 65.91 to 92.74 % in the single oil reservoir. The factor that most significantly influenced the microbial communities in these reservoirs was found to be temperature. Other environmental factors also influenced the microbial communities but not significantly. It is therefore assumed that microbial communities are formed by an accumulated effect of several factors. These results are essential for understanding ecological environment of the water flooding oil reservoirs and providing scientific guidance to the performance of MEOR technology.
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Affiliation(s)
- Lingxia Zhao
- Key Laboratory of Molecular Microbiology Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
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Kish A, Griffin PL, Rogers KL, Fogel ML, Hemley RJ, Steele A. High-pressure tolerance in Halobacterium salinarum NRC-1 and other non-piezophilic prokaryotes. Extremophiles 2012; 16:355-61. [PMID: 22212652 DOI: 10.1007/s00792-011-0418-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 12/13/2011] [Indexed: 01/23/2023]
Abstract
In this study, we examined the high-pressure survival of a range of prokaryotes not found in high-pressure environments to determine the effects of adaptations to osmotic and oxidative stresses on piezo-resistance. The pressure survivals of Halobacterium salinarum NRC-1, Deinococcus radiodurans R1, and Chromohalobacter salexigens were compared to that of Escherichia coli MG1655. C. salexigens, which uses the compatible solute ectoine as an osmolyte, was as piezo-sensitive as E. coli MG1655, suggesting that ectoine is not a piezolyte. D. radiodurans R1 and H. salinarum NRC-1, both resistant to oxidative stress, were found to be highly piezo-resistant. H. salinarum NRC-1 showed nearly full survival after pressurization up to 400 MPa; a survival 3.5 log units higher than E. coli MG1655. This piezo-resistance was maintained in H. salinarum NRC-1 for pressurizations up to 1 h. We hypothesize that the high-pressure resistance of H. salinarum NRC-1 is due to a combination of factors including cell envelope structure and the presence of intracellular salts.
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Affiliation(s)
- Adrienne Kish
- Geophysical Laboratory, Carnegie Institution of Washington, 5251 Broad Branch Rd., NW, Washington, DC, 20015, USA.
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36
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Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir. Appl Microbiol Biotechnol 2011; 95:811-21. [DOI: 10.1007/s00253-011-3717-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 10/23/2011] [Accepted: 11/06/2011] [Indexed: 11/26/2022]
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37
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Microbiological food safety assessment of high hydrostatic pressure processing: A review. Lebensm Wiss Technol 2011. [DOI: 10.1016/j.lwt.2010.11.001] [Citation(s) in RCA: 259] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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38
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Specific dynamic action affects the hydrostatic pressure tolerance of the shallow-water spider crab Maja brachydactyla. Naturwissenschaften 2011; 98:299-313. [DOI: 10.1007/s00114-011-0768-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 01/18/2011] [Accepted: 01/21/2011] [Indexed: 10/18/2022]
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Kaye JZ, Sylvan JB, Edwards KJ, Baross JA. Halomonas and Marinobacter ecotypes from hydrothermal vent, subseafloor and deep-sea environments. FEMS Microbiol Ecol 2010; 75:123-33. [DOI: 10.1111/j.1574-6941.2010.00984.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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40
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Response of microbial community structure to microbial plugging in a mesothermic petroleum reservoir in China. Appl Microbiol Biotechnol 2010; 88:1413-22. [DOI: 10.1007/s00253-010-2841-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 08/11/2010] [Accepted: 08/12/2010] [Indexed: 10/19/2022]
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41
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Vevers WF, Dixon DR, Dixon LRJ. The role of hydrostatic pressure on developmental stages of Pomatoceros lamarcki (Polychaeta: Serpulidae) exposed to water accommodated fractions of crude oil and positive genotoxins at simulated depths of 1000-3000 m. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2010; 158:1702-1709. [PMID: 20022152 DOI: 10.1016/j.envpol.2009.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 11/22/2009] [Accepted: 11/25/2009] [Indexed: 05/28/2023]
Abstract
The effect of high hydrostatic pressures on the ecotoxicological profile of pollutants is an unexplored research area. Using Pomatoceros lamarcki as a surrogate organism for this eco-barotoxicological study, it was found that in a 48 h larval bioassay with water accommodated fractions (WAF) of crude oil of up to 15.1 mg L(-1) (total hydrocarbon content) and hydrostatic pressures up to 300 bar (3000 m), an additive response was found (p < 0.001) rather than any synergism (p = 0.881). Comprehensive cytogenetic analysis of 6-h (15 degrees C) embryos exposed to WAF (0.19 mg L(-1)) at 100 bar showed no effects on mitotic fidelity or cell division rate over the 1 bar treatment. However, embryo's treated with the clastogen mitomycin-c at 100 bar exhibited a significant increase in mitotic aberrations over 1 bar treated as was the case with hypo/hypersaline treatments (p < 0.05). Conversely, an increase in hydrostatic pressure actually reduced the effects of spindle inhibition by the aneugen colchicine (p < 0.05).
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Affiliation(s)
- William F Vevers
- The Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.
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42
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Giordano A, Vella FM, Romano I, Gambacorta A. Structural elucidation of a novel phosphoglycolipid isolated from six species of Halomonas. J Lipid Res 2007; 48:1825-31. [PMID: 17519342 DOI: 10.1194/jlr.m700152-jlr200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structure of a new phosphoglycolipid from the halophilic Gram-negative bacteria Halomonas elongata ATCC 33173(T), Halomonas eurihalina ATCC 49336(T), Halomonas almeriensis CECT 7050(T), strain Sharm (AM238662), Halomonas halophila DSM 4770(T), and Halomonas salina ATCC 49509(T) was elucidated by NMR and mass spectroscopy studies. In all of the species examined, the polar lipid composition consisted of 1,2-diacylglycero-3-phosphorylethanolamine, 1,2-diacylglycero-3-phosphoryl-glycerol, bisphosphatidyl glycerol, and the new phosphoglycolipid PGL1. The structure of PGL1 was established to be (2-(alpha-D-glucopyranosyloxy)-3-hydroxy-propyl)-phosphatidyl diacylglycerol. C16:0;C18:1 and C16:0;C19:cyclopropane are the most abundant acyl chains linked to the phosphatidylglycerol moiety of each isolated PGL1. All of the species presenting the lipid PGL1 belong to Halomonas rRNA group 1, suggesting that the new phosphoglycolipid could be a chemotaxonomic marker of this phylogenetic group.
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Affiliation(s)
- Assunta Giordano
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, 34 80078 Pozzuoli, Italy.
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Odić D, Turk V, Stopar D. Environmental stress determines the quality of bacterial lysate and its utilization efficiency in a simple microbial loop. MICROBIAL ECOLOGY 2007; 53:639-49. [PMID: 17406773 DOI: 10.1007/s00248-006-9143-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 06/12/2006] [Indexed: 05/14/2023]
Abstract
Heterotrophic bacteria provide the critical link in the microbial loop by converting dissolved organic matter (DOM) into particulate form. In this study, DOM was prepared from recently isolated estuarine bacterial strain Vibrio sp. (DSM14379) grown at different salinities [0.2%, 0.5%, 3%, 5%, or 10% (w/v)], washed, concentrated, and lysed by autoclaving. The corresponding lysate-containing media were designated LM(0.2), LM(0.5), LM(3), LM(5), and LM(10). Vibrio sp. cells grown at different salinities had similar C/N/P ratios, but different C/S ratios, different trace element composition, and different 2D gel electrophoresis protein profiles. Pseudoalteromonas sp. (DSM06238) isolated from a similar environment was able to grow on all lysates, and its biomass production was dependent on lysate type. The highest growth rate and biomass production of Pseudoalteromonas sp. at saturation lysate concentrations were observed in LM(3). The biomass production at saturation lysate concentrations was about 3-fold higher as compared to LM(0.2) and LM(10). The initial respiration rate, intracellular adenosine triphosphate (ATP) levels, and (3)H-Leu and (3)H-TdR incorporation rates were lowest in LM(3). On the other hand, in LM(0.2) or LM(10) lysates the situation was reversed, the growth rates and biomass production were lowest, whereas (3)H-Leu and (3)H-TdR incorporation, respiration rates, as well as ATP levels, were highest. These results imply uncoupling of catabolism from growth in either high- or low-salinity lysates. The results also suggest that differences in organic carbon quality generated during Vibrio sp. growth at different NaCl concentrations were propagated through the simple microbial loop, which may have important ecological implications for higher trophic levels that depend on microbial grazing.
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Affiliation(s)
- Dusko Odić
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Lauro FM, Chastain RA, Blankenship LE, Yayanos AA, Bartlett DH. The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Appl Environ Microbiol 2006; 73:838-45. [PMID: 17158629 PMCID: PMC1800765 DOI: 10.1128/aem.01726-06] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the ocean's most extreme depths, pressures of 70 to 110 megapascals prevent the growth of all but the most hyperpiezophilic (pressure-loving) organisms. The physiological adaptations required for growth under these conditions are considered to be substantial. Efforts to determine specific adaptations permitting growth at extreme pressures have thus far focused on relatively few gamma-proteobacteria, in part due to the technical difficulties of obtaining piezophilic bacteria in pure culture. Here, we present the molecular phylogenies of several new piezophiles of widely differing geographic origins. Included are results from an analysis of the first deep-trench bacterial isolates recovered from the southern hemisphere (9.9-km depth) and of the first gram-positive piezophilic strains. These new data allowed both phylogenetic and structural 16S rRNA comparisons among deep-ocean trench piezophiles and closely related strains not adapted to high pressure. Our results suggest that (i) the Circumpolar Deep Water acts as repository for hyperpiezophiles and drives their dissemination to deep trenches in the Pacific Ocean and (ii) the occurrence of elongated helices in the 16S rRNA genes increases with the extent of adaptation to growth at elevated pressure. These helix changes are believed to improve ribosome function under deep-sea conditions.
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Affiliation(s)
- Federico M Lauro
- Center for Marine Biotechnology and Biomedicine, Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA
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Xiong H, Song L, Xu Y, Tsoi MY, Dobretsov S, Qian PY. Characterization of proteolytic bacteria from the Aleutian deep-sea and their proteases. J Ind Microbiol Biotechnol 2006; 34:63-71. [PMID: 16932887 DOI: 10.1007/s10295-006-0165-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Accepted: 07/22/2006] [Indexed: 10/24/2022]
Abstract
Six deep-sea proteolytic bacteria taken from Aleutian margin sediments were screened; one of them produced a cold-adapted neutral halophilic protease. These bacteria belong to Pseudoalteromonas spp., which were identified by the 16S rDNA sequence. Of the six proteases produced, two were neutral cold-adapted proteases that showed their optimal activity at pH 7-8 and at temperature close to 35 degrees C, and the other four were alkaline proteases that showed their optimal activity at pH 9 and at temperature of 40-45 degrees C. The neutral cold-adapted protease E1 showed its optimal activity at a sodium chloride concentration of 2 M, whereas the activity of the other five proteases decreased at elevated sodium chloride concentrations. Protease E1 was purified to electrophoretic homogeneity and its molecular mass was 34 kDa, as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The molecular weight of protease E1 was determined to be 32,411 Da by mass spectrometric analysis. Phenylmethyl sulfonylfluoride (PMSF) did not inhibit the activity of this protease, whereas it was partially inhibited by ethylenediaminetetra-acetic acid sodium salt (EDTA-Na). De novo amino acid sequencing proved protease E1 to be a novel protein.
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Affiliation(s)
- Hairong Xiong
- Coastal Marine Laboratory, Department of Biology, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
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Mitchell JG, Kogure K. Bacterial motility: links to the environment and a driving force for microbial physics. FEMS Microbiol Ecol 2006; 55:3-16. [PMID: 16420610 DOI: 10.1111/j.1574-6941.2005.00003.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial motility was recognized 300 years ago. Throughout this history, research into motility has led to advances in microbiology and physics. Thirty years ago, this union helped to make run and tumble chemotaxis the paradigm for bacterial movement. This review highlights how this paradigm has expanded and changed, and emphasizes the following points. The absolute magnitude of swimming speed is ecologically important because it helps determine vulnerability to Brownian motion, sensitivity to gradients, the type of receptors used and the cost of moving, with some bacteria moving at 1 mm s(-1). High costs for high speeds are offset by the benefit of resource translocation across submillimetre redox and other environmental gradients. Much of environmental chemotaxis appears adapted to respond to gradients of micrometres, rather than migrations of centimetres. In such gradients, control of ion pumps is particularly important. Motility, at least in the ocean, is highly intermittent and the speed is variable within a run. Subtleties in flagellar physics provide a variety of reorientation mechanisms. Finally, while careful physical analysis has contributed to our current understanding of bacterial movement, tactic bacteria are increasingly widely used as experimental and theoretical model systems in physics.
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Affiliation(s)
- James G Mitchell
- Marine Microbiology, Ocean Research Institute, University of Tokyo, Tokyo, Japan.
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Takai K, Nakagawa S, Reysenbach AL, Hoek J. Microbial ecology of mid-ocean ridges and back-arc basins. ACTA ACUST UNITED AC 2006. [DOI: 10.1029/166gm10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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Yancey PH. Organic osmolytes as compatible, metabolic and counteracting cytoprotectants in high osmolarity and other stresses. J Exp Biol 2005; 208:2819-30. [PMID: 16043587 DOI: 10.1242/jeb.01730] [Citation(s) in RCA: 1102] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
SUMMARYOrganic osmolytes are small solutes used by cells of numerous water-stressed organisms and tissues to maintain cell volume. Similar compounds are accumulated by some organisms in anhydrobiotic, thermal and possibly pressure stresses. These solutes are amino acids and derivatives,polyols and sugars, methylamines, methylsulfonium compounds and urea. Except for urea, they are often called `compatible solutes', a term indicating lack of perturbing effects on cellular macromolecules and implying interchangeability. However, these features may not always exist, for three reasons. First, some of these solutes may have unique protective metabolic roles, such as acting as antioxidants (e.g. polyols, taurine, hypotaurine),providing redox balance (e.g. glycerol) and detoxifying sulfide (hypotaurine in animals at hydrothermal vents and seeps). Second, some of these solutes stabilize macromolecules and counteract perturbants in non-interchangeable ways. Methylamines [e.g. trimethylamine N-oxide (TMAO)] can enhance protein folding and ligand binding and counteract perturbations by urea (e.g. in elasmobranchs and mammalian kidney), inorganic ions, and hydrostatic pressure in deep-sea animals. Trehalose and proline in overwintering insects stabilize membranes at subzero temperatures. Trehalose in insects and yeast,and anionic polyols in microorganisms around hydrothermal vents, can protect proteins from denaturation by high temperatures. Third, stabilizing solutes appear to be used in nature only to counteract perturbants of macromolecules,perhaps because stabilization is detrimental in the absence of perturbation. Some of these solutes have applications in biotechnology, agriculture and medicine, including in vitro rescue of the misfolded protein of cystic fibrosis. However, caution is warranted if high levels cause overstabilization of proteins.
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Affiliation(s)
- Paul H Yancey
- Biology Department, Whitman College, Walla Walla, WA 99362, USA.
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