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Li S, Wang J, Liu J, Zhang H, Bao T, Sun C, Fang J, Cao J. Genomic Analysis of the Deep-Sea Bacterium Shewanella sp. MTB7 Reveals Backgrounds Related to Its Deep-Sea Environment Adaptation. Microorganisms 2023; 11:microorganisms11030798. [PMID: 36985371 PMCID: PMC10059138 DOI: 10.3390/microorganisms11030798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/27/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Shewanella species are widely distributed in various environments, especially deep-sea sediments, due to their remarkable ability to utilize multiple electron receptors and versatile metabolic capabilities. In this study, a novel facultatively anaerobic, psychrophilic, and piezotolerant bacterium, Shewanella sp. MTB7, was isolated from the Mariana Trench at a depth of 5900 m. Here, we report its complete genome sequence and adaptation strategies for survival in deep-sea environments. MTB7 contains what is currently the third-largest genome among all isolated Shewanella strains and shows higher coding density than neighboring strains. Metabolically, MTB7 is predicted to utilize various carbon and nitrogen sources. D-amino acid utilization and HGT-derived purine-degrading genes could contribute to its oligotrophic adaptation. For respiration, the cytochrome o ubiquinol oxidase genes cyoABCDE, typically expressed at high oxygen concentrations, are missing. Conversely, a series of anaerobic respiratory genes are employed, including fumarate reductase, polysulfide reductase, trimethylamine-N-oxide reductase, crotonobetaine reductase, and Mtr subunits. The glycine reductase genes and the triplication of dimethyl sulfoxide reductase genes absent in neighboring strains could also help MTB7 survive in low-oxygen environments. Many genes encoding cold-shock proteins, glycine betaine transporters and biosynthetic enzymes, and reactive oxygen species-scavenging proteins could contribute to its low-temperature adaptation. The genomic analysis of MTB7 will deepen our understanding of microbial adaptation strategies in deep-sea environments.
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Affiliation(s)
- Sicong Li
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Jie Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Hongcai Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Tianqiang Bao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Chengwen Sun
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
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Tamby A, Sinninghe Damsté JS, Villanueva L. Microbial membrane lipid adaptations to high hydrostatic pressure in the marine environment. Front Mol Biosci 2023; 9:1058381. [PMID: 36685280 PMCID: PMC9853057 DOI: 10.3389/fmolb.2022.1058381] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/29/2022] [Indexed: 01/09/2023] Open
Abstract
The deep-sea is characterized by extreme conditions, such as high hydrostatic pressure (HHP) and near-freezing temperature. Piezophiles, microorganisms adapted to high pressure, have developed key strategies to maintain the integrity of their lipid membrane at these conditions. The abundance of specific membrane lipids, such as those containing unsaturated and branched-chain fatty acids, rises with increasing HHP. Nevertheless, this strategy is not universal among piezophiles, highlighting the need to further understand the effects of HHP on microbial lipid membranes. Challenges in the study of lipid membrane adaptations by piezophiles also involve methodological developments, cross-adaptation studies, and insight into slow-growing piezophiles. Moreover, the effects of HHP on piezophiles are often difficult to disentangle from effects caused by low temperature that are often characteristic of the deep sea. Here, we review the knowledge of membrane lipid adaptation strategies of piezophiles, and put it into the perspective of marine systems, highlighting the future challenges of research studying the effects of HHP on the microbial lipid composition.
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Affiliation(s)
- Anandi Tamby
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands,*Correspondence: Anandi Tamby,
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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3
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Sieg J, Sandmeier CC, Lieske J, Meents A, Lemmen C, Streit WR, Rarey M. Analyzing structural features of proteins from deep-sea organisms. Proteins 2022; 90:1521-1537. [PMID: 35313380 DOI: 10.1002/prot.26337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 12/31/2022]
Abstract
Protein adaptations to extreme environmental conditions are drivers in biotechnological process optimization and essential to unravel the molecular limits of life. Most proteins with such desirable adaptations are found in extremophilic organisms inhabiting extreme environments. The deep sea is such an environment and a promising resource that poses multiple extremes on its inhabitants. Conditions like high hydrostatic pressure and high or low temperature are prevalent and many deep-sea organisms tolerate multiple of these extremes. While molecular adaptations to high temperature are comparatively good described, adaptations to other extremes like high pressure are not well-understood yet. To fully unravel the molecular mechanisms of individual adaptations it is probably necessary to disentangle multifactorial adaptations. In this study, we evaluate differences of protein structures from deep-sea organisms and their respective related proteins from nondeep-sea organisms. We created a data collection of 1281 experimental protein structures from 25 deep-sea organisms and paired them with orthologous proteins. We exhaustively evaluate differences between the protein pairs with machine learning and Shapley values to determine characteristic differences in sequence and structure. The results show a reasonable discrimination of deep-sea and nondeep-sea proteins from which we distinguish correlations previously attributed to thermal stability from other signals potentially describing adaptions to high pressure. While some distinct correlations can be observed the overall picture appears intricate.
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Affiliation(s)
- Jochen Sieg
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
| | | | - Julia Lieske
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | - Alke Meents
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | | | - Wolfgang R Streit
- Universität Hamburg, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
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Microbiomes of Hadal Fishes across Trench Habitats Contain Similar Taxa and Known Piezophiles. mSphere 2022; 7:e0003222. [PMID: 35306867 PMCID: PMC9044967 DOI: 10.1128/msphere.00032-22] [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] [Indexed: 11/29/2022] Open
Abstract
Hadal snailfishes are the deepest-living fishes in the ocean, inhabiting trenches from depths of ∼6,000 to 8,000 m. While the microbial communities in trench environments have begun to be characterized, the microbes associated with hadal megafauna remain relatively unknown. Here, we describe the gut microbiomes of two hadal snailfishes, Pseudoliparis swirei (Mariana Trench) and Notoliparis kermadecensis (Kermadec Trench), using 16S rRNA gene amplicon sequencing. We contextualize these microbiomes with comparisons to the abyssal macrourid Coryphaenoides yaquinae and the continental shelf-dwelling snailfish Careproctus melanurus. The microbial communities of the hadal snailfishes were distinct from their shallower counterparts and were dominated by the same sequences related to the Mycoplasmataceae and Desulfovibrionaceae. These shared taxa indicate that symbiont lineages have remained similar to the ancestral symbiont since their geographic separation or that they are dispersed between geographically distant trenches and subsequently colonize specific hosts. The abyssal and hadal fishes contained sequences related to known, cultured piezophiles, microbes that grow optimally under high hydrostatic pressure, including Psychromonas, Moritella, and Shewanella. These taxa are adept at colonizing nutrient-rich environments present in the deep ocean, such as on particles and in the guts of hosts, and we hypothesize they could make a dietary contribution to deep-sea fishes by degrading chitin and producing fatty acids. We characterize the gut microbiota within some of the deepest fishes to provide new insight into the diversity and distribution of host-associated microbial taxa and the potential of these animals, and the microbes they harbor, for understanding adaptation to deep-sea habitats. IMPORTANCE Hadal trenches, characterized by high hydrostatic pressures and low temperatures, are one of the most extreme environments on our planet. By examining the microbiome of abyssal and hadal fishes, we provide insight into the diversity and distribution of host-associated life at great depth. Our findings show that there are similar microbial populations in fishes geographically separated by thousands of miles, reflecting strong selection for specific microbial lineages. Only a few psychropiezophilic taxa, which do not reflect the diversity of microbial life at great depth, have been successfully isolated in the laboratory. Our examination of deep-sea fish microbiomes shows that typical high-pressure culturing methodologies, which have largely remained unchanged since the pioneering work of Claude ZoBell in the 1950s, may simulate the chemical environment found in animal guts and helps explain why the same deep-sea genera are consistently isolated.
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Shah AM, Yang W, Mohamed H, Zhang Y, Song Y. Microbes: A Hidden Treasure of Polyunsaturated Fatty Acids. Front Nutr 2022; 9:827837. [PMID: 35369055 PMCID: PMC8968027 DOI: 10.3389/fnut.2022.827837] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/21/2022] [Indexed: 12/26/2022] Open
Abstract
Microbes have gained a lot of attention for their potential in producing polyunsaturated fatty acids (PUFAs). PUFAs are gaining scientific interest due to their important health-promoting effects on higher organisms including humans. The current sources of PUFAs (animal and plant) have associated limitations that have led to increased interest in microbial PUFAs as most reliable alternative source. The focus is on increasing the product value of existing oleaginous microbes or discovering new microbes by implementing new biotechnological strategies in order to compete with other sources. The multidisciplinary approaches, including metabolic engineering, high-throughput screening, tapping new microbial sources, genome-mining as well as co-culturing and elicitation for the production of PUFAs, have been considered and discussed in this review. The usage of agro-industrial wastes as alternative low-cost substrates in fermentation for high-value single-cell oil production has also been discussed. Multidisciplinary approaches combined with new technologies may help to uncover new microbial PUFA sources that may have nutraceutical and biotechnological importance.
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Affiliation(s)
- Aabid Manzoor Shah
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
| | - Wu Yang
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
| | - Hassan Mohamed
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut, Egypt
| | - Yingtong Zhang
- Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yuanda Song
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
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Cao WR, Li X, Sun YY, Jiang MY, Xu XD, Li YJ. Shewanella nanhaiensis sp. nov., a marine bacterium isolated from sediment of South China Sea, and emended descriptions of Shewanella woodyi, Shewanella hanedai and Shewanella canadensis. Int J Syst Evol Microbiol 2021; 71. [PMID: 34904941 DOI: 10.1099/ijsem.0.005152] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, motile, facultative anaerobic and rod-shaped bacterium, designated strain NR704-98T, was isolated from marine sediment of the northern South China Sea. Cells were positive for oxidase and catalase activity. Growth was observed at 4-30 °C (optimum 20-25 °C), at pH 6-9 (pH 7) and with 0.5-7 % NaCl (2 %). The 16S rRNA gene-based phylogenetic analysis revealed that the nearest phylogenetic neighbours of strain NR704-98T were Shewanella woodyi MS32T (97.9 %), Shewanella hanedai 281T (97.1 %), Shewanella sediminis HAW-EB3T (96.8 %) and Shewanella canadensis HAW-EB2T (96.7 %). Based on the results of phylogenomic analysis, the average nucleotide identity and the digital DNA-DNA hybridization values between strain NR704-98T and the previously mentioned type strains of species of the genus Shewanella were in the range of 74.9-93.1 % and 20.6-51.4 %, respectively. The respiratory quinones were Q-7 and Q-8. The predominant fatty acids (>10 %) of strain NR704-98T were C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C15 : 0. Phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminophospholipids and five unidentified lipids were detected in strain NR704-98T. Based on the phylogenetic and phenotypic characteristics, strain NR704-98T is considered to represent a novel species of the genus Shewanella, for which the name Shewanella nanhaiensis sp. nov. is proposed. The type strain is NR704-98T (=KCTC 82799T=MCCC 1K06091T).
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Affiliation(s)
- Wen-Rui Cao
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Xue Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Yuan-Yuan Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Ming-Yu Jiang
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Xiao-Dong Xu
- Qingdao Vland Biotech Company Group, Qingdao 266061, PR China
| | - Ying-Jie Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
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7
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Jia YL, Geng SS, Du F, Xu YS, Wang LR, Sun XM, Wang QZ, Li Q. Progress of metabolic engineering for the production of eicosapentaenoic acid. Crit Rev Biotechnol 2021; 42:838-855. [PMID: 34779326 DOI: 10.1080/07388551.2021.1971621] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Eicosapentaenoic Acid (EPA) is an essential ω-3 polyunsaturated fatty acid for human health. Currently, high-quality EPA production is largely dependent on the extraction of fish oil, but this unsustainable approach cannot meet its rising market demand. Biotechnological approaches for EPA production from microorganisms have received increasing attention due to their suitability for large-scale production and independence of the seasonal or climate restrictions. This review summarizes recent research on different microorganisms capable of producing EPA, such as microalgae, bacteria, and fungi, and introduces the different EPA biosynthesis pathways. Notably, some novel engineering strategies have been applied to endow and improve the abilities of microorganisms to synthesize EPA, including the construction and optimization of the EPA biosynthesis pathway, an increase in the acetyl-CoA pool supply, the increase of NADPH and the inhibition of competing pathways. This review aims to provide an updated summary of EPA production.
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Affiliation(s)
- Yu-Lei Jia
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Shan-Shan Geng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Fei Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ying-Shuang Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ling-Ru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Qing-Zhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, People's Republic of China
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8
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Yu L, Jian H, Gai Y, Yi Z, Feng Y, Qiu X, Shao Z, Tang X. Characterization of two novel psychrophilic and piezotolerant strains, Shewanella psychropiezotolerans sp. nov. and Shewanella eurypsychrophilus sp. nov, adapted to an extreme deep-sea environment. Syst Appl Microbiol 2021; 44:126266. [PMID: 34653843 DOI: 10.1016/j.syapm.2021.126266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/15/2021] [Accepted: 09/16/2021] [Indexed: 12/20/2022]
Abstract
Three marine bacterial strains designated YLB-06T, YLB-08T and YLB-09 were isolated under high hydrostatic pressure from deep-sea sediment samples collected from the Southwest Indian Ocean. They were Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic and motile. In addition, the strains were capable of growing at 0-20 °C (optimum 4-10 °C) and 0.1-40 MPa (optimum 0.1 MPa), were psychrophiles and piezotolerant, and could use trimethylamine N-oxide (TMAO), DMSO, elemental sulfur and insoluble Fe (III) as terminal electron acceptors during anaerobic growth. Strain YLB-06T could also use nitrate, and strains YLB-08T and YLB-09 could use nitrite as a terminal electron acceptor. Phylogenetic tree analyses based on 16S rRNA gene sequences and 400 optimized universal marker sequences indicated that the strains belonged to the genus Shewanella. The 16S rRNA gene highest similarity, together with the estimated ANI and DDH values for these strains with their related type strains, were below the respective thresholds for species differentiation. The ANI and DDH values between YLB-08T and YLB-09 were 99.9% and 91.8%, respectively, implying that they should belong to the same genospecies. The YLB-06T genome had duplicated genes, and multiple movement modalities, attachment modalities, biofilm synthesis systems, intercellular interactions and a strong antioxidant system, which were all beneficial for survival in an extreme deep-sea environment. The G + C contents of strains YLB-06T, YLB-08T and YLB-09 were 45.1, 43.5 and 43.6 mol%, respectively. Based on polyphasic taxonomic properties, two novel psychropiezotolerant species are proposed, Shewanella psychropiezotolerans sp. nov. with YLB-06T (=MCCC 1A12715T = KCTC 62907T) and S. eurypsychrophilus sp. nov with YLB-08T (=MCCC 1A12718T = KCTC 62909T) as type strains.
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Affiliation(s)
- Libo Yu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; China Ocean Sample Repository (Biology), Xiamen 361005, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yingbao Gai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; China Ocean Sample Repository (Biology), Xiamen 361005, China
| | - Zhiwei Yi
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Ying Feng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xu Qiu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; China Ocean Sample Repository (Biology), Xiamen 361005, China
| | - Xixiang Tang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; China Ocean Sample Repository (Biology), Xiamen 361005, China
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9
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Zhang F, Battaglia-Brunet F, Hellal J, Joulian C, Gautret P, Motelica-Heino M. Impact of Fe(III) (Oxyhydr)oxides Mineralogy on Iron Solubilization and Associated Microbial Communities. Front Microbiol 2020; 11:571244. [PMID: 33329429 PMCID: PMC7715016 DOI: 10.3389/fmicb.2020.571244] [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: 06/10/2020] [Accepted: 11/02/2020] [Indexed: 11/16/2022] Open
Abstract
Iron-reducing bacteria (IRB) are strongly involved in Fe cycling in surface environments. Transformation of Fe and associated trace elements is strongly linked to the reactivity of various iron minerals. Mechanisms of Fe (oxyhydr)oxides bio-reduction have been mostly elucidated with pure bacterial strains belonging to Geobacter or Shewanella genera, whereas studies involving mixed IRB populations remain scarce. The present study aimed to evaluate the iron reducing rates of IRB enriched consortia originating from complex environmental samples, when grown in presence of Fe (oxyhydr)oxides of different mineralogy. The abundances of Geobacter and Shewanella were assessed in order to acquire knowledge about the abundance of these two genera in relation to the effects of mixed IRB populations on kinetic control of mineralogical Fe (oxyhydr)oxides reductive dissolution. Laboratory experiments were carried out with two freshly synthetized Fe (oxyhydr)oxides presenting contrasting specific surfaces, and two defined Fe-oxides, i.e., goethite and hematite. Three IRB consortia were enriched from environmental samples from a riverbank subjected to cyclic redox oscillations related to flooding periods (Decize, France): an unsaturated surface soil, a flooded surface soil and an aquatic sediment, with a mixture of organic compounds provided as electron donors. The consortia could all reduce iron-nitrilotriacetate acid (Fe(III)-NTA) in 1–2 days. When grown on Fe (oxyhydr)oxides, Fe solubilization rates decreased as follows: fresh Fe (oxyhydr)oxides > goethite > hematite. Based on a bacterial rrs gene fingerprinting approach (CE-SSCP), bacterial community structure in presence of Fe(III)-minerals was similar to those of the site sample communities from which they originated but differed from that of the Fe(III)-NTA enrichments. Shewanella was more abundant than Geobacter in all cultures. Its abundance was higher in presence of the most efficiently reduced Fe (oxyhydr)oxide than with other Fe(III)-minerals. Geobacter as a proportion of the total community was highest in the presence of the least easily solubilized Fe (oxyhydr)oxides. This study highlights the influence of Fe mineralogy on the abundance of Geobacter and Shewanella in relation to Fe bio-reduction kinetics in presence of a complex mixture of electron donors.
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Affiliation(s)
- Fengfeng Zhang
- Univ. Orléans, CNRS, BRGM, ISTO, UMR 7327, Orléans, France.,BRGM, Orléans, France
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10
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Tang X, Yu L, Yi Y, Wang J, Wang S, Meng C, Liu S, Hao Y, Zhang Y, Cao X, Jian H, Xiao X. Phylogenomic analysis reveals a two-stage process of the evolutionary transition of Shewanella from the upper ocean to the hadal zone. Environ Microbiol 2020; 23:744-756. [PMID: 32657519 DOI: 10.1111/1462-2920.15162] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/21/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022]
Abstract
Shewanella strains are characterized by versatile metabolic capabilities, resulting in their wide distribution in the ocean at different depths. Considering that particle sedimentation is an important dynamic process in the ocean, we hypothesized that hadal Shewanella species evolved from the upper ocean. In this study, we isolated three novel Shewanella strains from deep-sea sediments in the Southwest Indian Ocean. Genome sequencing indicated that strains YLB-06 and YLB-08 represent two novel species in the genus Shewanella. Through phylogenomic analysis, we showed that speciation and genomic changes in marine Shewanella strains are related to water depth. We further confirmed the aforementioned hypothesis and revealed a two-stage process of the evolutionary transition of Shewanella from the upper ocean to the hadal zone by comparative genomics and gene gain/loss analysis. Finally, the transcriptomic analysis demonstrated that recently obtained genes are strictly repressed and may thus play a minor role in the response to environmental changes.
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Affiliation(s)
- Xixiang Tang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.,China Ocean Sample Repository (Biology), Xiamen, 361005, China
| | - Libo Yu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.,China Ocean Sample Repository (Biology), Xiamen, 361005, China
| | - Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiahua Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Siyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Canxing Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yue Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaorong Cao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.,China Ocean Sample Repository (Biology), Xiamen, 361005, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
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11
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Minich JJ, Petrus S, Michael JD, Michael TP, Knight R, Allen EE. Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus. mSphere 2020; 5:e00401-20. [PMID: 32434844 PMCID: PMC7380571 DOI: 10.1128/msphere.00401-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], and pyloric ceca) from 229 Pacific chub mackerel, Scomber japonicus, collected across 38 time points spanning 1 year from the Scripps Institution of Oceanography Pier (La Jolla, CA). Mucosal sites had unique microbial communities significantly different from the surrounding seawater and sediment communities with over 10 times more total diversity than seawater. The external surfaces of skin and gill were more similar to seawater, while digesta was more similar to sediment. Alpha and beta diversity of the skin and gill was explained by environmental and biological factors, specifically, sea surface temperature, chlorophyll a, and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by regional migration of chub mackerel subpopulations by nanopore sequencing a 14,769-bp region of the 16,568-bp mitochondria across all temporal fish specimens. A cosmopolitan pathogen, Photobacterium damselae, was prevalent across multiple body sites all year but highest in the skin, GI, and digesta between June and September, when the ocean is warmest. The longitudinal fish microbiome study evaluates the extent to which the environment and host biology drives mucosal microbial ecology and establishes a baseline for long-term surveys linking environment stressors to mucosal health of wild marine fish.IMPORTANCE Pacific chub mackerel, Scomber japonicus, are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean.
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Affiliation(s)
- Jeremiah J Minich
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Semar Petrus
- J. Craig Venter Institute, La Jolla, California, USA
| | | | - Todd P Michael
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- J. Craig Venter Institute, La Jolla, California, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
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12
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Thorell K, Meier-Kolthoff JP, Sjöling Å, Martín-Rodríguez AJ. Whole-Genome Sequencing Redefines Shewanella Taxonomy. Front Microbiol 2019; 10:1861. [PMID: 31555221 PMCID: PMC6722870 DOI: 10.3389/fmicb.2019.01861] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/29/2019] [Indexed: 12/30/2022] Open
Abstract
The genus Shewanella encompasses a diverse group of Gram negative, primarily aquatic bacteria with a remarkable ecological relevance, an outstanding set of metabolic features and an emergent clinical importance. The rapid expansion of the genus over the 2000 s has prompted questions on the real taxonomic position of some isolates and species. Recent work by us and others identified inconsistencies in the existing species classification. In this study we aimed to clarify such issues across the entire genus, making use of the genomic information publicly available worldwide. Phylogenomic analyses, including comparisons based on genome-wide identity indexes (digital DNA-DNA hybridization and Average Nucleotide Identity) combined with core and accessory genome content evaluation suggested that the taxonomic position of 64 of the 131 analyzed strains should be revisited. Based on the genomic information currently available, emended descriptions for some Shewanella species are proposed. Our study establishes for the first time a whole-genome based phylogeny for Shewanella spp. including a classification at the subspecific level.
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Affiliation(s)
- Kaisa Thorell
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany
| | - Åsa Sjöling
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alberto J. Martín-Rodríguez
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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13
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Peoples LM, Grammatopoulou E, Pombrol M, Xu X, Osuntokun O, Blanton J, Allen EE, Nunnally CC, Drazen JC, Mayor DJ, Bartlett DH. Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches. Front Microbiol 2019; 10:347. [PMID: 30930856 PMCID: PMC6428765 DOI: 10.3389/fmicb.2019.00347] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/11/2019] [Indexed: 11/13/2022] Open
Abstract
Hadal ocean sediments, found at sites deeper than 6,000 m water depth, are thought to contain microbial communities distinct from those at shallower depths due to high hydrostatic pressures and higher abundances of organic matter. These communities may also differ from one other as a result of geographical isolation. Here we compare microbial community composition in surficial sediments of two hadal environments—the Mariana and Kermadec trenches—to evaluate microbial biogeography at hadal depths. Sediment microbial consortia were distinct between trenches, with higher relative sequence abundances of taxa previously correlated with organic matter degradation present in the Kermadec Trench. In contrast, the Mariana Trench, and deeper sediments in both trenches, were enriched in taxa predicted to break down recalcitrant material and contained other uncharacterized lineages. At the 97% similarity level, sequence-abundant taxa were not trench-specific and were related to those found in other hadal and abyssal habitats, indicating potential connectivity between geographically isolated sediments. Despite the diversity of microorganisms identified using culture-independent techniques, most isolates obtained under in situ pressures were related to previously identified piezophiles. Members related to these same taxa also became dominant community members when native sediments were incubated under static, long-term, unamended high-pressure conditions. Our results support the hypothesis that there is connectivity between sediment microbial populations inhabiting the Mariana and Kermadec trenches while showing that both whole communities and specific microbial lineages vary between trench of collection and sediment horizon depth. This in situ biodiversity is largely missed when incubating samples within pressure vessels and highlights the need for revised protocols for high-pressure incubations.
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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
| | - Eleanna Grammatopoulou
- Oceanlab, The Institute of Biological and Environmental Sciences, King's College, The University of Aberdeen, Aberdeen, United Kingdom
| | - Michelle Pombrol
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Xiaoxiong Xu
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Oladayo Osuntokun
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Jessica Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Clifton C Nunnally
- Louisiana Universities Marine Consortium (LUMCON), Chauvin, LA, United States
| | - Jeffrey C Drazen
- Department of Oceanography, University of Hawai'i at Ma-noa, Honolulu, HI, United States
| | - Daniel J Mayor
- Oceanlab, The Institute of Biological and Environmental Sciences, King's College, The University of Aberdeen, Aberdeen, United Kingdom.,National Oceanography Centre, University of Southampton Waterfront Campus European Way, Southampton, United Kingdom
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
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14
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Response of neutrophilic Shewanella violacea to acid stress: growth rate, organic acid production, and gene expression. Extremophiles 2019; 23:319-326. [DOI: 10.1007/s00792-019-01083-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/15/2019] [Indexed: 12/20/2022]
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15
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Fujimori K, Fujii S, Lisdiana L, Wakai S, Yagi H, Sambongi Y. Differences in biochemical properties of two 5'-nucleotidases from deep- and shallow-sea Shewanella species under various harsh conditions. Biosci Biotechnol Biochem 2019; 83:1085-1093. [PMID: 30764715 DOI: 10.1080/09168451.2019.1578641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Deep-sea Shewanella violacea 5'-nucleotidase (SVNTase) activity exhibited higher NaCl tolerance than that of a shallow-sea Shewanella amazonensis homologue (SANTase), the sequence identity between them being 70.4%. Here, SVNTase exhibited higher activity than SANTase with various inorganic salts, similar to the difference in their NaCl tolerance. In contrast, SVNTase activity decreased with various organic solvents, while SANTase activity was retained with the same concentrations of the solvents. Therefore, SVNTase is more robust than SANTase with inorganic salts, but more vulnerable with organic solvents. As to protein stability, SANTase was more stable against organic solvents and heat than SVNTase, which correlated with the differences in their enzymatic activities. We also found that SANTase retained higher activity for three weeks than SVNTase did in the presence of glycerol. These findings will facilitate further application of these enzymes as appropriate biological catalysts under various harsh conditions. Abbreviations: NTase: 5'-nucleotidase; SANTase: Shewanella amazonensis 5'-nucleotidase; SVNTase: Shewanella violacea 5'-nucleotidase; CD: circular dichroism.
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Affiliation(s)
- Kiko Fujimori
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
| | - Sotaro Fujii
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
| | - Lisa Lisdiana
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan.,b Department of Biology , Universitas Negeri Surabaya, Kampus Unesa Ketintang , Surabaya , Indonesia
| | - Satoshi Wakai
- c Graduate School of Science, Technology, and Innovation , Kobe University , Kobe , Japan
| | - Hisashi Yagi
- d Department of Chemistry and Biotechnology, Graduate School of Sustainability Science , Tottori University , Tottori , Japan.,e Center for Research on Green Sustainable Chemistry , Tottori University , Tottori , Japan
| | - Yoshihiro Sambongi
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
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16
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Wakai S. Biochemical and thermodynamic analyses of energy conversion in extremophiles. Biosci Biotechnol Biochem 2018; 83:49-64. [PMID: 30381012 DOI: 10.1080/09168451.2018.1538769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A variety of extreme environments, characterized by extreme values of various physicochemical parameters (temperature, pressure, salinity, pH, and so on), are found on Earth. Organisms that favorably live in such extreme environments are called extremophiles. All living organisms, including extremophiles, must acquire energy to maintain cellular homeostasis, including extremophiles. For energy conversion in harsh environments, thermodynamically useful reactions and stable biomolecules are essential. In this review, I briefly summarize recent studies of extreme environments and extremophiles living in these environments and describe energy conversion processes in various extremophiles based on my previous research. Furthermore, I discuss the correlation between the biological system of electrotrophy, a third biological energy acquisition system, and the mechanism underlying microbiologically influenced corrosion. These insights into energy conversion in extremophiles may improve our understanding of the "limits of life". Abbreviations: PPi: pyrophosphate; PPase: pyrophosphatase; ITC: isothermal titration microcalorimetry; SVNTase: Shewanella violacea 5'-nucleotidase; SANTase: Shewanella amazonensis 5'-nucleotidase.
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Affiliation(s)
- Satoshi Wakai
- a Graduate School of Science, Technology and Innovation , Kobe University , Kobe , Japan
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17
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Palma Esposito F, Ingham CJ, Hurtado-Ortiz R, Bizet C, Tasdemir D, de Pascale D. Isolation by Miniaturized Culture Chip of an Antarctic bacterium Aequorivita sp. with antimicrobial and anthelmintic activity. ACTA ACUST UNITED AC 2018; 20:e00281. [PMID: 30225207 PMCID: PMC6139392 DOI: 10.1016/j.btre.2018.e00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 01/28/2023]
Abstract
Novel microbial isolation approach allowed the identification of a Gram-negative Antarctic bacterium belonging to the genus Aequorivita. Aequorivita sp. showed antimicrobial and anthelmintic activity without toxic effect towards eukaryotic cells. The whole genome of Aequorivita sp. was sequenced and compared with other strains to identify biosynthetic gene clusters. This novel approach represents a promising strategy to isolate rare or novel strains useful for biotechnological applications.
Microbes are prolific sources of bioactive molecules; however, the cultivability issue has severely hampered access to microbial diversity. Novel secondary metabolites from as-yet-unknown or atypical microorganisms from extreme environments have realistic potential to lead to new drugs with benefits for human health. Here, we used a novel approach that mimics the natural environment by using a Miniaturized Culture Chip allowing the isolation of several bacterial strains from Antarctic shallow water sediments under near natural conditions. A Gram-negative Antarctic bacterium belonging to the genus Aequorivita was subjected to further analyses. The Aequorivita sp. genome was sequenced and a bioinformatic approach was applied to identify biosynthetic gene clusters. The extract of the Aequorivita sp. showed antimicrobial and anthelmintic activity towards Multidrug resistant bacteria and the nematode Caenorhabditis elegans. This is the first multi-approach study exploring the genomics and biotechnological potential of the genus Aequorivita that is a promising candidate for pharmaceutical applications.
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Affiliation(s)
- Fortunato Palma Esposito
- Institute of Protein Biochemistry, National Research Council, Naples, 80131, Italy.,Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | | | - Raquel Hurtado-Ortiz
- CIP-Collection of Institut Pasteur, Department of Microbiology, Institut Pasteur, Paris, 75015, France.,CRBIP-Biological Resource Centre, Department of Microbiology, Institut Pasteur, Paris, 75015, France
| | - Chantal Bizet
- CIP-Collection of Institut Pasteur, Department of Microbiology, Institut Pasteur, Paris, 75015, France.,CRBIP-Biological Resource Centre, Department of Microbiology, Institut Pasteur, Paris, 75015, France
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, 24106, Germany
| | - Donatella de Pascale
- Institute of Protein Biochemistry, National Research Council, Naples, 80131, Italy.,Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
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18
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Using metabolic charge production in the tricarboxylic acid cycle (Q TCA) to evaluate the extracellular-electron-transfer performances of Shewanella spp. Bioelectrochemistry 2018; 124:119-126. [PMID: 30015268 DOI: 10.1016/j.bioelechem.2018.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/24/2018] [Accepted: 07/03/2018] [Indexed: 01/13/2023]
Abstract
Using an electrochemical cell equipped with carbon felt electrodes (poised at +0.63 V vs. SHE), the current production capabilities of two Shewanella strains-NTOU1 and KR-12-were examined under various conditions with lactate as an electron donor. The metabolic charge produced in the tricarboxylic acid cycle (QTCA) was calculated by mass-balance. The data showed a linear relation between the electric coulomb production (QEL) and QTCA with an R2 of 0.65. In addition, a large amount of pyruvate accumulation was observed at pH = 6, rendering QTCA negative. The results indicate an occurrence of an undesired cataplerotic reaction. It was also found that QTCA provides important information showing the oxygen-boosting TCA cycle and anodic-current generation of Shewanella spp. Linear dependence of the change in charge for biomass growth (4.52FΔnCell) on QTCA was also found as expressed by 4.52FΔnCell = 1.0428 QTCA + 0.0442, indicating that these two charge quantities are inherently identical under most of the experimental conditions. In the mediator-spiked experiments, the external addition of the mediators (ferricyanide, anthraquinone-2, 6-disulfonate, and riboflavin) beyond certain concentrations inhibited the activity of the TCA cycle, indicating that the oxidative phosphorylation is deactivated by excessive amounts of mediators, yet Shewanella spp. are constrained with regard to carrying out the substrate-level phosphorylation.
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19
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Polyunsaturated fatty acids in marine bacteria and strategies to enhance their production. Appl Microbiol Biotechnol 2018; 102:5811-5826. [PMID: 29749565 DOI: 10.1007/s00253-018-9063-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 10/16/2022]
Abstract
Polyunsaturated fatty acids (PUFAs) play an important role in human diet. Despite the wide-ranging importance and benefits from heart health to brain functions, humans and mammals cannot synthesize PUFAs de novo. The primary sources of PUFA are fish and plants. Due to the increasing concerns associated with food security as well as issues of environmental contaminants in fish oil, there has been considerable interest in the production of polyunsaturated fatty acids from alternative resources which are more sustainable, safer, and economical. For instance, marine bacteria, particularly the genus of Shewanella, Photobacterium, Colwellia, Moritella, Psychromonas, Vibrio, and Alteromonas, are found to be one among the major microbial producers of polyunsaturated fatty acids. Recent developments in the area with a focus on the production of polyunsaturated fatty acids from marine bacteria as well as the metabolic engineering strategies for the improvement of PUFA production are discussed.
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20
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Ohmae E, Hamajima Y, Nagae T, Watanabe N, Kato C. Similar structural stabilities of 3-isopropylmalate dehydrogenases from the obligatory piezophilic bacterium Shewanella benthica strain DB21MT-2 and its atmospheric congener S. oneidensis strain MR-1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:680-691. [PMID: 29630970 DOI: 10.1016/j.bbapap.2018.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/01/2018] [Accepted: 04/05/2018] [Indexed: 11/30/2022]
Abstract
We previously found that the enzymatic activity of 3-isopropylmalate dehydrogenase from the obligatory piezophilic bacterium Shewanella benthica strain DB21MT-2 (SbIPMDH) was pressure-tolerant up to 100 MPa, but that from its atmospheric congener S. oneidensis strain MR-1 (SoIPMDH) was pressure-sensitive. Such characteristics were determined by only one amino acid residue at position 266, serine (SoIPMDH) or alanine (SbIPMDH) [Y. Hamajima et al. Extremophiles 20: 177, 2016]. In this study, we investigated the structural stability of these enzymes. At pH 7.6, SoIPMDH was slightly more stable against hydrostatic pressure than SbIPMDH, contrary to the physiological pressures of their normal environments. Pressure unfolding of these IPMDHs followed a two-state unfolding model between a native dimer and two unfolded monomers, and the dimer structure was pressure-tolerant up to 200 MPa, employing a midpoint pressure of 245.3 ± 0.1 MPa and a volume change of -225 ± 24 mL mol-1 for the most unstable mutant, SbIPMDH A266S. Thus, their pressure-dependent activity did not originate from structural perturbations such as unfolding or dimer dissociation. Conversely, urea-induced unfolding of these IPMDHs followed a three-state unfolding model, including a dimer intermediate. Interestingly, the first transition was strongly pH-dependent but pressure-independent; however, the second transition showed the opposite pattern. Obtained volume changes due to urea-induced unfolding were almost equal for both IPMDHs, approximately +10 and -30 mL mol-1 for intermediate formation and dimer dissociation, respectively. These results indicated that both IPMDHs have similar structural stability, and a pressure-adaptation mechanism was provided for only the enzymatic activity of SbIPMDH.
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Affiliation(s)
- Eiji Ohmae
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
| | - Yuki Hamajima
- Department of Life Science, College of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Takayuki Nagae
- Synchrotron Radiation Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Nobuhisa Watanabe
- Synchrotron Radiation Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan; Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Aichi 464-8603, Japan
| | - Chiaki Kato
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
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21
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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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22
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Fujii S, Masanari-Fujii M, Kobayashi S, Kato C, Nishiyama M, Harada Y, Wakai S, Sambongi Y. Commonly stabilized cytochromes c from deep-sea Shewanella and Pseudomonas. Biosci Biotechnol Biochem 2018; 82:1-8. [PMID: 29540113 DOI: 10.1080/09168451.2018.1448255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/23/2018] [Indexed: 10/17/2022]
Abstract
Two cytochromes c5 (SBcytc and SVcytc) have been derived from Shewanella living in the deep-sea, which is a high pressure environment, so it could be that these proteins are more stable at high pressure than at atmospheric pressure, 0.1 MPa. This study, however, revealed that SBcytc and SVcytc were more stable at 0.1 MPa than at higher pressure. In addition, at 0.1-150 MPa, the stability of SBcytc and SVcytc was higher than that of homologues from atmospheric-pressure Shewanella, which was due to hydrogen bond formation with the heme in the former two proteins. This study further revealed that cytochrome c551 (PMcytc) of deep-sea Pseudomonas was more stable than a homologue of atmospheric-pressure Pseudomonas aeruginosa, and that specific hydrogen bond formation with the heme also occurred in the former. Although SBcytc and SVcytc, and PMcytc are phylogenetically very distant, these deep-sea cytochromes c are commonly stabilized through hydrogen bond formation.
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Affiliation(s)
- Sotaro Fujii
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
- b Global Career Design Center , Hiroshima University , Higashi-Hiroshima , Japan
| | - Misa Masanari-Fujii
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
| | - Shinya Kobayashi
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
| | - Chiaki Kato
- c Japan Agency for Marine-Earth Science and Technology , Yokosuka , Japan
| | - Masayoshi Nishiyama
- d The HAKUBI Center for Advanced Research , Kyoto University , Kyoto , Japan
| | - Yoshie Harada
- e Institute for Integrated Cell-Material Sciences (WPI-iCeMS) , Kyoto University , Kyoto , Japan
| | - Satoshi Wakai
- f Graduate School of Science Technology and Innovation , Kobe University , Kobe , Japan
| | - Yoshihiro Sambongi
- a Graduate School of Biosphere Science , Hiroshima University , Higashi-Hiroshima , Japan
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Kusube M, Kyaw TS, Tanikawa K, Chastain RA, Hardy KM, Cameron J, Bartlett DH. Colwellia marinimaniae sp. nov., a hyperpiezophilic species isolated from an amphipod within the Challenger Deep, Mariana Trench. Int J Syst Evol Microbiol 2017; 67:824-831. [DOI: 10.1099/ijsem.0.001671] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Masataka Kusube
- Department of Material Science, National Institute of Technology, Wakayama College, 77 Noshima, Nada-cho, Gobo, Wakayama 644-0023, Japan
| | - Than S. Kyaw
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USA
| | - Kumiko Tanikawa
- Department of Material Science, National Institute of Technology, Wakayama College, 77 Noshima, Nada-cho, Gobo, Wakayama 644-0023, Japan
| | - Roger A. Chastain
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USA
| | - Kevin M. Hardy
- Global Ocean Dynamics. Global Ocean Design, 7955 Silverton Ave., Suite 1208, San Diego, CA 92126, USA
| | - James Cameron
- Avatar Alliance Foundation, 16255 Ventura Blvd. Suite 525, Encino, CA 91436, USA
| | - Douglas H. Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USA
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24
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Yousfi K, Bekal S, Usongo V, Touati A. Current trends of human infections and antibiotic resistance of the genus Shewanella. Eur J Clin Microbiol Infect Dis 2017; 36:1353-1362. [PMID: 28299457 DOI: 10.1007/s10096-017-2962-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/05/2017] [Indexed: 10/20/2022]
Abstract
Shewanella spp. are commonly known as environmental bacteria and are most frequently isolated from aquatic areas. Currently, diseases syndromes and multidrug resistance have increasingly been reported in the genus Shewanella. Some species are associated with various infections, such as skin and soft tissue infections, as well as bacteremia. Generally, these bacteria are opportunistic and mostly affect people with an impaired immune system. This genus is also a probable vehicle and progenitor of antibiotic resistance genes. In fact, several resistance genes and mobile genetic elements have been identified in some resistant species isolated from environmental or clinical settings. These genes confer resistance to different antibiotic classes, including those used in therapies such as β-lactams and quinolones, and are generally located on the chromosome. Recently, a multidrug-resistant (MDR) plasmid harboring several drug resistance genes associated with transposons and integrons has been identified in Shewanella xiamenensis. These antibiotic resistance genes can circulate in the environment and contribute to the emergence of antibiotic resistance. This review describes different aspects of Shewanella, focusing on the infections caused by this genus, as well as their role in the propagation of antibiotic resistance via mobile genetic elements.
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Affiliation(s)
- K Yousfi
- Laboratoire d'Écologie Microbienne, FSNV, Université de Bejaia, Bejaia, 06000, Algeria.,Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - S Bekal
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - V Usongo
- Laboratoire d'Écologie Microbienne, FSNV, Université de Bejaia, Bejaia, 06000, Algeria.,Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC, Canada
| | - A Touati
- Laboratoire d'Écologie Microbienne, FSNV, Université de Bejaia, Bejaia, 06000, Algeria.
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25
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Fang J, Kato C, Runko GM, Nogi Y, Hori T, Li J, Morono Y, Inagaki F. Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor. Front Microbiol 2017; 8:137. [PMID: 28220112 PMCID: PMC5292414 DOI: 10.3389/fmicb.2017.00137] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/19/2017] [Indexed: 11/13/2022] Open
Abstract
Phylogenetically diverse microorganisms have been observed in marine subsurface sediments down to ~2.5 km below the seafloor (kmbsf). However, very little is known about the pressure-adapted and/or pressure-loving microorganisms, the so called piezophiles, in the deep subseafloor biosphere, despite that pressure directly affects microbial physiology, metabolism, and biogeochemical processes of carbon and other elements in situ. In this study, we studied taxonomic compositions of microbial communities in high-pressure incubated sediment, obtained during the Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula, Japan. Analysis of 16S rRNA gene-tagged sequences showed that members of spore-forming bacteria within Firmicutes and Actinobacteria were predominantly detected in all enrichment cultures from ~1.5 to 2.4 km-deep sediment samples, followed by members of Proteobacteria, Acidobacteria, and Bacteroidetes according to the sequence frequency. To further study the physiology of the deep subseafloor sedimentary piezophilic bacteria, we isolated and characterized two bacterial strains, 19R1-5 and 29R7-12, from 1.9 and 2.4 km-deep sediment samples, respectively. The isolates were both low G+C content, gram-positive, endospore-forming and facultative anaerobic piezophilic bacteria, closely related to Virgibacillus pantothenticus and Bacillus subtilis within the phylum Firmicutes, respectively. The optimal pressure and temperature conditions for growth were 20 MPa and 42°C for strain 19R1-5, and 10 MPa and 43°C for strain 29R7-12. Bacterial (endo)spores were observed in both the enrichment and pure cultures examined, suggesting that these piezophilic members were derived from microbial communities buried in the ~20 million-year-old coal-bearing sediments after the long-term survival as spores and that the deep biosphere may host more abundant gram-positive spore-forming bacteria and their spores than hitherto recognized.
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Affiliation(s)
- Jiasong Fang
- Hadal Science and Technology Research Center, Shanghai Ocean UniversityShanghai, China; Department of Natural Sciences, Hawaii Pacific University, HonoluluHI, USA
| | - Chiaki Kato
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Gabriella M Runko
- Department of Natural Sciences, Hawaii Pacific University, Honolulu HI, USA
| | - Yuichi Nogi
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Ibaraki, Japan
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University Shanghai, China
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology Kochi, Japan
| | - Fumio Inagaki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and TechnologyKochi, Japan; Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science and TechnologyYokohama, Japan; Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and TechnologyYokosuka, Japan
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26
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Difference in NaCl tolerance of membrane-bound 5'-nucleotidases purified from deep-sea and brackish water Shewanella species. Extremophiles 2017; 21:357-368. [PMID: 28050644 DOI: 10.1007/s00792-016-0909-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022]
Abstract
Shewanella species are widely distributed in sea, brackish, and fresh water areas, growing psychrophilically or mesophilically, and piezophilically or piezo-sensitively. Here, membrane-bound 5'-nucleotidases (NTases) from deep-sea Shewanella violacea and brackish water Shewanella amazonensis were examined from the aspect of NaCl tolerance to gain an insight into protein stability against salt. Both NTases were single polypeptides with molecular masses of ~59 kDa, as determined on mass spectroscopy. They similarly required 10 mM MgCl2 for their activities, and they exhibited the same pH dependency and substrate specificity for 5'-nucleotides. However, S. violacea 5'-nucleotidase (SVNTase) was active enough in the presence of 2.5 M NaCl, whereas S. amazonensis 5'-nucleotidase (SANTase) exhibited significantly reduced activity with the same concentration of the salt. Although SVNTase and SANTase exhibited high sequence identity (69.7%), differences in the ratio of acidic to basic amino acid residues and the number of potential salt bridges maybe being responsible for the difference in the protein stability against salt. 5'-Nucleotidases from these Shewanella species will provide useful information regarding NaCl tolerance, which may be fundamental for understanding bacterial adaptation to growth environments.
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27
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Domagal-Goldman SD, Wright KE, Adamala K, Arina de la Rubia L, Bond J, Dartnell LR, Goldman AD, Lynch K, Naud ME, Paulino-Lima IG, Singer K, Walther-Antonio M, Abrevaya XC, Anderson R, Arney G, Atri D, Azúa-Bustos A, Bowman JS, Brazelton WJ, Brennecka GA, Carns R, Chopra A, Colangelo-Lillis J, Crockett CJ, DeMarines J, Frank EA, Frantz C, de la Fuente E, Galante D, Glass J, Gleeson D, Glein CR, Goldblatt C, Horak R, Horodyskyj L, Kaçar B, Kereszturi A, Knowles E, Mayeur P, McGlynn S, Miguel Y, Montgomery M, Neish C, Noack L, Rugheimer S, Stüeken EE, Tamez-Hidalgo P, Imari Walker S, Wong T. The Astrobiology Primer v2.0. ASTROBIOLOGY 2016; 16:561-653. [PMID: 27532777 PMCID: PMC5008114 DOI: 10.1089/ast.2015.1460] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 06/06/2016] [Indexed: 05/09/2023]
Affiliation(s)
- Shawn D Domagal-Goldman
- 1 NASA Goddard Space Flight Center , Greenbelt, Maryland, USA
- 2 Virtual Planetary Laboratory , Seattle, Washington, USA
| | - Katherine E Wright
- 3 University of Colorado at Boulder , Colorado, USA
- 4 Present address: UK Space Agency, UK
| | - Katarzyna Adamala
- 5 Department of Genetics, Cell Biology and Development, University of Minnesota , Minneapolis, Minnesota, USA
| | | | - Jade Bond
- 7 Department of Physics, University of New South Wales , Sydney, Australia
| | | | | | - Kennda Lynch
- 10 Division of Biological Sciences, University of Montana , Missoula, Montana, USA
| | - Marie-Eve Naud
- 11 Institute for research on exoplanets (iREx) , Université de Montréal, Montréal, Canada
| | - Ivan G Paulino-Lima
- 12 Universities Space Research Association , Mountain View, California, USA
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | - Kelsi Singer
- 14 Southwest Research Institute , Boulder, Colorado, USA
| | | | - Ximena C Abrevaya
- 16 Instituto de Astronomía y Física del Espacio (IAFE) , UBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rika Anderson
- 17 Department of Biology, Carleton College , Northfield, Minnesota, USA
| | - Giada Arney
- 18 University of Washington Astronomy Department and Astrobiology Program , Seattle, Washington, USA
| | - Dimitra Atri
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | | | - Jeff S Bowman
- 19 Lamont-Doherty Earth Observatory, Columbia University , Palisades, New York, USA
| | | | | | - Regina Carns
- 22 Polar Science Center, Applied Physics Laboratory, University of Washington , Seattle, Washington, USA
| | - Aditya Chopra
- 23 Planetary Science Institute, Research School of Earth Sciences, Research School of Astronomy and Astrophysics, The Australian National University , Canberra, Australia
| | - Jesse Colangelo-Lillis
- 24 Earth and Planetary Science, McGill University , and the McGill Space Institute, Montréal, Canada
| | | | - Julia DeMarines
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | | | - Carie Frantz
- 27 Department of Geosciences, Weber State University , Ogden, Utah, USA
| | - Eduardo de la Fuente
- 28 IAM-Departamento de Fisica, CUCEI , Universidad de Guadalajara, Guadalajara, México
| | - Douglas Galante
- 29 Brazilian Synchrotron Light Laboratory , Campinas, Brazil
| | - Jennifer Glass
- 30 School of Earth and Atmospheric Sciences, Georgia Institute of Technology , Atlanta, Georgia , USA
| | | | | | - Colin Goldblatt
- 33 School of Earth and Ocean Sciences, University of Victoria , Victoria, Canada
| | - Rachel Horak
- 34 American Society for Microbiology , Washington, DC, USA
| | | | - Betül Kaçar
- 36 Harvard University , Organismic and Evolutionary Biology, Cambridge, Massachusetts, USA
| | - Akos Kereszturi
- 37 Research Centre for Astronomy and Earth Sciences , Hungarian Academy of Sciences, Budapest, Hungary
| | - Emily Knowles
- 38 Johnson & Wales University , Denver, Colorado, USA
| | - Paul Mayeur
- 39 Rensselaer Polytechnic Institute , Troy, New York, USA
| | - Shawn McGlynn
- 40 Earth Life Science Institute, Tokyo Institute of Technology , Tokyo, Japan
| | - Yamila Miguel
- 41 Laboratoire Lagrange, UMR 7293, Université Nice Sophia Antipolis , CNRS, Observatoire de la Côte d'Azur, Nice, France
| | | | - Catherine Neish
- 43 Department of Earth Sciences, The University of Western Ontario , London, Canada
| | - Lena Noack
- 44 Royal Observatory of Belgium , Brussels, Belgium
| | - Sarah Rugheimer
- 45 Department of Astronomy, Harvard University , Cambridge, Massachusetts, USA
- 46 University of St. Andrews , St. Andrews, UK
| | - Eva E Stüeken
- 47 University of Washington , Seattle, Washington, USA
- 48 University of California , Riverside, California, USA
| | | | - Sara Imari Walker
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
- 50 School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science, Arizona State University , Tempe, Arizona, USA
| | - Teresa Wong
- 51 Department of Earth and Planetary Sciences, Washington University in St. Louis , St. Louis, Missouri, USA
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Yoshida K, Hashimoto M, Hori R, Adachi T, Okuyama H, Orikasa Y, Nagamine T, Shimizu S, Ueno A, Morita N. Bacterial Long-Chain Polyunsaturated Fatty Acids: Their Biosynthetic Genes, Functions, and Practical Use. Mar Drugs 2016; 14:E94. [PMID: 27187420 PMCID: PMC4882568 DOI: 10.3390/md14050094] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/23/2016] [Accepted: 04/29/2016] [Indexed: 02/06/2023] Open
Abstract
The nutritional and pharmaceutical values of long-chain polyunsaturated fatty acids (LC-PUFAs) such as arachidonic, eicosapentaenoic and docosahexaenoic acids have been well recognized. These LC-PUFAs are physiologically important compounds in bacteria and eukaryotes. Although little is known about the biosynthetic mechanisms and functions of LC-PUFAs in bacteria compared to those in higher organisms, a combination of genetic, bioinformatic, and molecular biological approaches to LC-PUFA-producing bacteria and some eukaryotes have revealed the notably diverse organization of the pfa genes encoding a polyunsaturated fatty acid synthase complex (PUFA synthase), the LC-PUFA biosynthetic processes, and tertiary structures of the domains of this enzyme. In bacteria, LC-PUFAs appear to take part in specific functions facilitating individual membrane proteins rather than in the adjustment of the physical fluidity of the whole cell membrane. Very long chain polyunsaturated hydrocarbons (LC-HCs) such as hentriacontanonaene are considered to be closely related to LC-PUFAs in their biosynthesis and function. The possible role of LC-HCs in strictly anaerobic bacteria under aerobic and anaerobic environments and the evolutionary relationships of anaerobic and aerobic bacteria carrying pfa-like genes are also discussed.
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Affiliation(s)
- Kiyohito Yoshida
- Laboratory of Ecological Genetics, Section of Environmental Biology, Faculty of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.
| | - Mikako Hashimoto
- Course in Ecological Genetics, Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.
| | - Ryuji Hori
- Technical Solution Center First Group, J-OIL MILLS, Inc., Chuo-ku, Tokyo 104-0044, Japan.
| | - Takumi Adachi
- Laboratory of Environmental Microbiology, Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-8589, Japan.
- Bioproduction Research Institute, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, Hokkaido 062-8517, Japan.
| | - Hidetoshi Okuyama
- Laboratory of Environmental Molecular Biology, Section of Environmental Biology, Faculty of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.
| | - Yoshitake Orikasa
- Department Food Science, Obihiro University Agriculture Veterinary Medicine, Inada-cho, Obihiro, Hokkaido 080-8555, Japan.
| | - Tadashi Nagamine
- ROM Co. Ltd., Togashi Bld., Chuo-ku, Sapporo, Hokkaido 060-0062, Japan.
| | - Satoru Shimizu
- Horonobe Research Institute for the Subsurface Environment, Northern Advancement Centre for Science and Technology, 5-3, Sakae-machi, Horonobe, Teshio-gun, Hokkaido 098-3221, Japan.
| | - Akio Ueno
- Horonobe Research Institute for the Subsurface Environment, Northern Advancement Centre for Science and Technology, 5-3, Sakae-machi, Horonobe, Teshio-gun, Hokkaido 098-3221, Japan.
| | - Naoki Morita
- Laboratory of Environmental Microbiology, Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-8589, Japan.
- Bioproduction Research Institute, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, Hokkaido 062-8517, Japan.
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29
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Zhang J, Burgess JG. Shewanella electrodiphila sp. nov., a psychrotolerant bacterium isolated from Mid-Atlantic Ridge deep-sea sediments. Int J Syst Evol Microbiol 2015; 65:2882-2889. [PMID: 25999594 DOI: 10.1099/ijs.0.000345] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Strains MAR441(T) and MAR445 were isolated from Mid-Atlantic Ridge sediments from a depth of 2734 m, and were found to belong to the genus Shewanella. The strains were rod-shaped, pigmented, non-motile and capable of anaerobic growth either by fermentation of carbohydrates or by anaerobic respiration. The strains utilized a variety of electron acceptors, including nitrate and ferric compounds, and could utilize peptone when grown anaerobically in a two-chambered microbial fuel cell, which used carbon cloth electrodes and delivered a stable power output of ,150-200 mW m(-2). The major fatty acids were typical of the genus Shewanella, with major components C13 : 0, iso-C13 : 0, iso-C15 : 0, C16 : 0, C16 : 1ω7c, C18 : 1ω7c and C20 : 5ω3 fatty acids. The DNA G+C content of strains MAR441(T) and MAR445 was 42.4 mol%. 16S rRNA gene sequence analysis indicated that strains MAR441(T) and MAR445 were most closely related to Shewanella olleyana (sequence similarities 97.9% to the type strain). DNA-DNA hybridization demonstrated only 15.6-37.2% relatedness between strain MAR441(T) and the type strains of related species of the genus Shewanella. Phenotypic characteristics confirmed that these isolates constituted a novel species of the genus Shewanella, for which the name Shewanella electrodiphila sp. nov. is proposed; the type strain is MAR441(T) (5ATCC BAA-2408(T) = DSM 24955(T)).
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Affiliation(s)
- Jinwei Zhang
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne NE30 4PZ, UK
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - J Grant Burgess
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne NE30 4PZ, UK
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Sato H, Nakasone K, Yoshida T, Kato C, Maruyama T. Increases of heat shock proteins and their mRNAs at high hydrostatic pressure in a deep-sea piezophilic bacterium, Shewanella violacea. Extremophiles 2015; 19:751-62. [PMID: 25982740 DOI: 10.1007/s00792-015-0751-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 04/26/2015] [Indexed: 11/30/2022]
Abstract
When non-extremophiles encounter extreme environmental conditions, which are natural for the extremophiles, stress reactions, e.g., expression of heat shock proteins (HSPs), are thought to be induced for survival. To understand how the extremophiles live in such extreme environments, we studied the effects of high hydrostatic pressure on cellular contents of HSPs and their mRNAs during growth in a piezophilic bacterium, Shewanella violacea. HSPs increased at high hydrostatic pressures even when optimal for growth. The mRNAs and proteins of these HSPs significantly increased at higher hydrostatic pressure in S. violacea. In the non-piezophilic Escherichia coli, however, their mRNAs decreased, while their proteins did not change. Several transcriptional start sites (TSSs) for HSP genes were determined by the primer extension method and some of them showed hydrostatic pressure-dependent increase of the mRNAs. A major refolding target of one of the HSPs, chaperonin, at high hydrostatic pressure was shown to be RplB, a subunit of the 50S ribosome. These results suggested that in S. violacea, HSPs play essential roles, e.g., maintaining protein complex machinery including ribosomes, in the growth and viability at high hydrostatic pressure, and that, in their expression, the transcription is under the control of σ(32).
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Affiliation(s)
- Hiroshi Sato
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midoriku, Yokohama, 226-8501, Japan
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31
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Tsubouchi T, Mori K, Miyamoto N, Fujiwara Y, Kawato M, Shimane Y, Usui K, Tokuda M, Uemura M, Tame A, Uematsu K, Maruyama T, Hatada Y. Aneurinibacillus tyrosinisolvens sp. nov., a tyrosine-dissolving bacterium isolated from organics- and methane-rich seafloor sediment. Int J Syst Evol Microbiol 2015; 65:1999-2005. [PMID: 25813364 DOI: 10.1099/ijs.0.000213] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-positive-staining, strictly aerobic and heterotrophic bacterium, designated strain LL-002T, was isolated from organics- and methane-rich seafloor sediment at a depth of 100 m in Kagoshima Bay, Kagoshima, Japan. Colonies were lustreless and translucent white in colour. The temperature, pH and salt concentration ranges for growth were 10-30 °C, pH 6.0-6.5 and 0-1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain LL-002T belongs to the genus Aneurinibacillus of the family Paenibacillaceae. 16S rRNA gene sequence similarities between strain LL-002T and the type strains of species of the genus Aneurinibacillus were 92.8-95.7 %; the highest sequence identity was with the type strain of Aneurinibacillus migulanus. The DNA G+C content of strain LL-002T was 46.2 mol%. MK-7 was the predominant menaquinone. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0, and the cell-wall peptidoglycan contained meso-diaminopimelic acid and glutamic acid, glycine and alanine in addition to muramic acid and glucosamine. The peptidoglycan type was A1γ. In DNA-DNA hybridization assays between strain LL-002T and the type strains of the other species of the genus Aneurinibacillus, the level of hybridization was 6.3-30.1 %. On the basis of its biological features and the 16S rRNA gene sequence comparison presented here, strain LL-002T is considered to represent a novel species of the genus Aneurinibacillus, for which the name Aneurinibacillus tyrosinisolvens sp. nov. is proposed; the type strain is LL-002T ( = NBRC 110097T = CECT 8536T).
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Affiliation(s)
- Taishi Tsubouchi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Kozue Mori
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Norio Miyamoto
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yoshihiro Fujiwara
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Masaru Kawato
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yasuhiro Shimane
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Keiko Usui
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Maki Tokuda
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Moeka Uemura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Akihiro Tame
- Section1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Katsuyuki Uematsu
- Section1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yuji Hatada
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
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32
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Abe F. Effects of High Hydrostatic Pressure on Microbial Cell Membranes: Structural and Functional Perspectives. Subcell Biochem 2015; 72:371-381. [PMID: 26174391 DOI: 10.1007/978-94-017-9918-8_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biological processes associated with dynamic structural features of membranes are highly sensitive to changes in hydrostatic pressure and temperature. Marine organisms potentially experience a broad range of pressure and temperature fluctuations. Hence, they have specialized cell membranes to perform membrane protein functions under various environmental conditions. Although the effects of high pressure on artificial lipid bilayers have been investigated in detail, little is known about how high pressure affects the structure of natural cell membranes and how organisms cope with pressure alterations. This review focused on the recent advances in research on the effects of high pressure on microbial membranes, particularly on the use of time-resolved fluorescence anisotropy measurement to determine membrane dynamics in deep-sea piezophiles.
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Affiliation(s)
- Fumiyoshi Abe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, 252-5258, Japan,
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Abstract
In order to elucidate the molecular adaptation mechanisms of enzymes to the high hydrostatic pressure of the deep sea, we cloned, purified, and characterized more than ten dihydrofolate reductases (DHFRs) from bacteria living in deep-sea and ambient atmospheric pressure environments. The nucleotide and amino acid sequences of these DHFRs indicate the deep-sea bacteria are adapted to their environments after the differentiation of their genus from ancestors inhabiting atmospheric pressure environments. In particular, the backbone structure of the deep-sea DHFR from Moritella profunda (mpDHFR) almost overlapped with the normal homolog from Escherichia coli (ecDHFR). Thus, those of other DHFRs would also overlap on the basis of their sequence similarities. However, the structural stability of both DHFRs was quite different: compared to ecDHFR, mpDHFR was more thermally stable but less stable against urea and pressure unfolding. The smaller volume changes due to unfolding suggest that the native structure of mpDHFR has a smaller cavity and/or enhanced hydration compared to ecDHFR. High hydrostatic pressure reduced the enzymatic activity of many DHFRs, but three deep-sea DHFRs and the D27E mutant of ecDHFR exhibited pressure-dependent activation. The inverted activation volumes from positive to negative values indicate the modification of their structural dynamics, conversion of the rate-determining step of the enzymatic reaction, and different contributions of the cavity and hydration to the transition-state structure. Since the cavity and hydration depend on amino acid side chains, DHFRs would adapt to the deep-sea environment by regulating the cavity and hydration by substituting their amino acid side chains without altering their backbone structure. The results of this study clearly indicate that the cavity and hydration play important roles in the adaptation of enzymes to the deep-sea environment.
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Abstract
The deep biosphere is composed of very different biotopes located in the depth of the oceans, the ocean crust or the lithosphere. Although very different, deep biosphere biotopes share one common feature, high hydrostatic pressure. The deep biosphere is colonized by specific organisms, called piezophiles, that are able to grow under high hydrostatic pressure. Bacterial piezophiles are mainly psychrophiles belonging to five genera of γ-proteobacteria, Photobacterium, Shewanella, Colwellia, Psychromonas and Moritella, while piezophilic Archaea are mostly (hyper)thermophiles from the Thermococcales. None of these genera are specific for the deep biosphere. High pressure deeply impacts the activity of cells and cellular components, and reduces the activity of numerous key processes, eventually leading to cell death of piezosensitive organisms. Biochemical and genomic studies yield a fragmented view on the adaptive mechanisms in piezophiles. It is yet unclear whether piezophilic adaptation requires the modification of a few genes, or metabolic pathways, or a more profound reorganization of the genome, the fine tuning of gene expression to compensate the pressure-induced loss of activity of the proteins most affected by high pressure, or a stress-like physiological cell response. In contrast to what has been seen for thermophily or halophily, the adaptation to high pressure is diffuse in the genome and may concern only a small fraction of the genes.
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Bacteria in Nanoparticle Synthesis: Current Status and Future Prospects. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:359316. [PMID: 27355054 PMCID: PMC4897565 DOI: 10.1155/2014/359316] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 07/09/2014] [Accepted: 08/04/2014] [Indexed: 11/17/2022]
Abstract
Microbial metal reduction can be a strategy for remediation of metal contaminations and wastes. Bacteria are capable of mobilization and immobilization of metals and in some cases, the bacteria which can reduce metal ions show the ability to precipitate metals at nanometer scale. Biosynthesis of nanoparticles (NPs) using bacteria has emerged as rapidly developing research area in green nanotechnology across the globe with various biological entities being employed in synthesis of NPs constantly forming an impute alternative for conventional chemical and physical methods. Optimization of the processes can result in synthesis of NPs with desired morphologies and controlled sizes, fast and clean. The aim of this review is, therefore, to make a reflection on the current state and future prospects and especially the possibilities and limitations of the above mentioned bio-based technique for industries.
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Nogi Y, Abe M, Kawagucci S, Hirayama H. Psychrobium conchae gen. nov., sp. nov., a psychrophilic marine bacterium isolated from the Iheya North hydrothermal field. Int J Syst Evol Microbiol 2014; 64:3668-3675. [PMID: 25096326 DOI: 10.1099/ijs.0.066738-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel psychrophilic, marine, bacterial strain designated BJ-1(T) was isolated from the Iheya North hydrothermal field in the Okinawa Trough off Japan. Cells were Gram-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 16 °C, with the optimum between 9 and 12 °C. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the closest relatives of strain BJ-1(T) were Shewanella denitrificans OS-217(T) (93.5% similarity), Shewanella profunda DSM 15900(T) (92.9%), Shewanella gaetbuli TF-27(T) (92.9%), Paraferrimonas sedimenticola Mok-106(T) (92.1%) and Ferrimonas kyonanensis Asr22-7(T) (91.7%). The major respiratory quinone was Q-8. The predominant fatty acids were C(16:1)ω7c and C(16:0). The G+C content of the novel strain was 40.5 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, it is proposed that strain BJ-1(T) represents a novel species in a new genus, for which the name Psychrobium conchae gen. nov., sp. nov. is proposed. The type strain of Psychrobium conchae is BJ-1(T) ( =JCM 30103(T) =DSM 28701(T)).
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Affiliation(s)
- Yuichi Nogi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Mariko Abe
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shinsuke Kawagucci
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hisako Hirayama
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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Kawano H, Nakasone K, Abe F, Kato C, Yoshida Y, Usami R, Horikoshi K. Protein–DNA Interactions under High-Pressure Conditions, Studied by Capillary Narrow-Tube Electrophoresis. Biosci Biotechnol Biochem 2014; 69:1415-7. [PMID: 16041150 DOI: 10.1271/bbb.69.1415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The method of electrophoretic mobility shift assay under high-pressure conditions was improved using a high-pressure electrophoresis apparatus with capillary narrow-tube gel. It was found that the protein-DNA complex in the gel was stained as a high-resolution spot with ethidium bromide. Using this method, it was found that the behavior under high-pressure conditions of the protein-DNA complex composed of NtrC protein and its target promoter DNA is important for the pressure-regulated transcription process, and it was confirmed that the complex was dissociated above a pressure of 70 MPa.
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Affiliation(s)
- Hiroaki Kawano
- Extremobiosphere Research Center (XBR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
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Masanari M, Wakai S, Ishida M, Kato C, Sambongi Y. Correlation between the optimal growth pressures of four Shewanella species and the stabilities of their cytochromes c 5. Extremophiles 2014; 18:617-27. [DOI: 10.1007/s00792-014-0644-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/23/2014] [Indexed: 11/29/2022]
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Thermodynamic and functional characteristics of deep-sea enzymes revealed by pressure effects. Extremophiles 2014; 17:701-9. [PMID: 23798033 DOI: 10.1007/s00792-013-0556-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 06/13/2013] [Indexed: 01/14/2023]
Abstract
Hydrostatic pressure analysis is an ideal approach for studying protein dynamics and hydration. The development of full ocean depth submersibles and high pressure biological techniques allows us to investigate enzymes from deep-sea organisms at the molecular level. The aim of this review was to overview the thermodynamic and functional characteristics of deep-sea enzymes as revealed by pressure axis analysis after giving a brief introduction to the thermodynamic principles underlying the effects of pressure on the structural stability and function of enzymes.
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Abe F. Dynamic structural changes in microbial membranes in response to high hydrostatic pressure analyzed using time-resolved fluorescence anisotropy measurement. Biophys Chem 2013; 183:3-8. [DOI: 10.1016/j.bpc.2013.05.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 05/10/2013] [Accepted: 05/14/2013] [Indexed: 02/03/2023]
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Regulation of cytochrome c- and quinol oxidases, and piezotolerance of their activities in the deep-sea piezophile Shewanella violacea DSS12 in response to growth conditions. Biosci Biotechnol Biochem 2013; 77:1522-8. [PMID: 23832349 DOI: 10.1271/bbb.130197] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The facultative piezophile Shewanella violacea DSS12 is known to have respiratory components that alter under the influence of hydrostatic pressure during growth, suggesting that its respiratory system is adapted to high pressure. We analyzed the expression of the genes encoding terminal oxidases and some respiratory components of DSS12 under various growth conditions. The expression of some of the genes during growth was regulated by both the O2 concentration and hydrostatic pressure. Additionally, the activities of cytochrome c oxidase and quinol oxidase of the membrane fraction of DSS12 grown under various conditions were measured under high pressure. The piezotolerance of cytochrome c oxidase activity was dependent on the O2 concentration during growth, while that of quinol oxidase was influenced by pressure during growth. The activity of quinol oxidase was more piezotolerant than that of cytochrome c oxidase under all growth conditions. Even in the membranes of the non-piezophile Shewanella amazonensis, quinol oxidase was more piezotolerant than cytochrome c oxidase, although both were highly piezosensitive as compared to the activities in DSS12. By phylogenetic analysis, piezophile-specific cytochrome c oxidase, which is also found in the genome of DSS12, was identified in piezophilic Shewanella and related genera. Our observations suggest that DSS12 constitutively expresses piezotolerant respiratory terminal oxidases, and that lower O2 concentrations and higher hydrostatic pressures induce higher piezotolerance in both types of terminal oxidases. Quinol oxidase might be the dominant terminal oxidase in high-pressure environments, while cytochrome c oxidase might also contribute. These features should contribute to adaptation of DSS12 in deep-sea environments.
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42
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Draft Genome Sequence of the Deep-Sea Bacterium Shewanella benthica Strain KT99. GENOME ANNOUNCEMENTS 2013; 1:1/3/e00210-13. [PMID: 23723392 PMCID: PMC3668000 DOI: 10.1128/genomea.00210-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
We report the draft genome sequence of the obligately piezophilic Shewanella benthica strain KT99 isolated from the abyssal South Pacific Ocean. Strain KT99 is the first piezophilic isolate from the Tonga-Kermadec trench, and its genome provides many clues on high-pressure adaptation and the evolution of deep-sea piezophilic bacteria.
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43
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Cao Y, Cao Y, Zhao M. Biotechnological production of eicosapentaenoic acid: From a metabolic engineering point of view. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.05.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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44
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The respiratory system of the piezophile Photobacterium profundum SS9 grown under various pressures. Biosci Biotechnol Biochem 2012; 76:1506-10. [PMID: 22878211 DOI: 10.1271/bbb.120237] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
It is known that the facultative piezophile Shewanella violacea DSS12 alters its respiratory components under the influence of hydrostatic pressure during growth. This can be considered one of the mechanisms of bacterial adaptation to high pressure. In this study, we investigated the respiratory system of another well-studied piezophile, Photobacterium profundum SS9. We analyzed cytochrome contents, the expression of genes encoding respiratory components in P. profundum SS9 grown under various conditions, and the pressure dependency of the terminal oxidase activities. Activity was more tolerant of relatively high pressures, such as 125 MPa when the cells were grown under high pressure as compared with cells grown under atmospheric pressure. Such properties observed are similar to the case of S. violacea. However, the contents of the cytochromes and expression of the respiratory genes were not influenced by growth pressure in P. profundum SS9, inconsistent with the case of S. violacea. We suggest that the mechanism of the piezoadaptation of the respiratory system of P. profundum SS9 differs from that of S. violacea, as described above, and that each strain chooses its own strategy.
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45
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Sung HR, Yoon JH, Ghim SY. Shewanella dokdonensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2012; 62:1636-1643. [DOI: 10.1099/ijs.0.032995-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, designated UDC329T, was isolated from a sample of seawater collected at Dong-do, on the coast of Dokdo Island, in the East Sea of the Republic of Korea. The Gram-staining-negative, motile, facultatively anaerobic, non-spore-forming rods of the strain developed into dark orange–yellow colonies. The strain grew optimally between 25 and 30 °C, with 1 % (w/v) NaCl and at pH 7. It grew in the absence of NaCl, but not with NaCl at >7 % (w/v). The predominant menaquinone was MK-7, the predominant ubiquinones were Q-7 and Q-8, and the major fatty acids were iso-C15 : 0 (33.52 %) and C17 : 1ω8c (11.73 %). The genomic DNA G+C content of strain UDC329T was 50.2 mol%. In phylogenetic analyses based on 16S rRNA and gyrB gene sequences, strain UDC329T was grouped with members of the genus
Shewanella
and appeared most closely related to
Shewanella fodinae
JC15T (97.9 % 16S rRNA gene sequence similarity),
Shewanella indica
KJW27T (95.0 %),
Shewanella algae
ATCC 51192T (94.8 %),
Shewanella haliotis
DW01T (94.5 %) and
Shewanella chilikensis
JC5T (93.9 %). The level of DNA–DNA relatedness between strain UDC329T and
S. fodinae
JC15T was, however, only 27.4 %. On the basis of phenotypic, genotypic and DNA–DNA relatedness data, strain UDC329T represents a novel species in the genus
Shewanella
, for which the name Shewanella dokdonensis sp. nov. is proposed. The type strain is UDC329T ( = KCTC 22898T = DSM 23626T).
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Affiliation(s)
- Hye-Ri Sung
- School of Life Sciences, Research Institute for Ulleungdo and Dokdo Islands, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Daejeon 306-809, Republic of Korea
| | - Sa-Youl Ghim
- School of Life Sciences, Research Institute for Ulleungdo and Dokdo Islands, Kyungpook National University, Daegu 702-701, Republic of Korea
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Howard EC, Hamdan LJ, Lizewski SE, Ringeisen BR. High frequency of glucose-utilizing mutants in Shewanella oneidensis MR-1. FEMS Microbiol Lett 2011; 327:9-14. [DOI: 10.1111/j.1574-6968.2011.02450.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 08/22/2011] [Accepted: 10/26/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - Leila J. Hamdan
- Marine Biogeochemistry Section, Code 6114; U.S. Naval Research Laboratory; Washington; DC; USA
| | - Stephen E. Lizewski
- Laboratory for Biosensors & Biomaterials, Code 6910; U.S. Naval Research Laboratory; Washington; DC; USA
| | - Bradley R. Ringeisen
- Bioenergy and Biofabrication Section, Code 6115; U.S. Naval Research Laboratory; Washington; DC; USA
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Hiraki T, Sekiguchi T, Kato C, Hatada Y, Maruyama T, Abe F, Konishi M. New type of pressurized cultivation method providing oxygen for piezotolerant yeast. J Biosci Bioeng 2011; 113:220-3. [PMID: 22019406 DOI: 10.1016/j.jbiosc.2011.09.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/21/2011] [Accepted: 09/23/2011] [Indexed: 10/16/2022]
Abstract
For efficient oxygen supply to pressurized culture, we developed a method using a highly pressurized membrane reactor with an air-saturated medium circulation system. The new method increased the cell growth of aerobic yeast approximately 20 folds larger than that in the case of using a conventional method.
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Affiliation(s)
- Toshiki Hiraki
- Institute of Biogeoscience (Biogeos), Japan Agency of Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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48
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Eicosapentaenoic acid plays a role in stabilizing dynamic membrane structure in the deep-sea piezophile Shewanella violacea: a study employing high-pressure time-resolved fluorescence anisotropy measurement. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:574-83. [PMID: 22037146 DOI: 10.1016/j.bbamem.2011.10.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 09/29/2011] [Accepted: 10/10/2011] [Indexed: 11/24/2022]
Abstract
Shewanella violacea DSS12 is a psychrophilic piezophile that optimally grows at 30MPa. It contains a substantial amount of eicosapentaenoic acid (EPA) in the membrane. Despite evidence linking increased fatty acid unsaturation and bacterial growth under high pressure, little is known of how the physicochemical properties of the membrane are modulated by unsaturated fatty acids in vivo. By means of the newly developed system performing time-resolved fluorescence anisotropy measurement under high pressure (HP-TRFAM), we demonstrate that the membrane of S. violacea is highly ordered at 0.1MPa and 10°C with the order parameter S of 0.9, and the rotational diffusion coefficient D(w) of 5.4μs(-1) for 1-[4-(trimethylamino)pheny]-6-phenyl-1,3,5-hexatriene in the membrane. Deletion of pfaA encoding the omega-3 polyunsaturated fatty acid synthase caused disorder of the membrane and enhanced the rotational motion of acyl chains, in concert with a 2-fold increase in the palmitoleic acid level. While the wild-type membrane was unperturbed over a wide range of pressures with respect to relatively small effects of pressure on S and D(w), the ΔpfaA membrane was disturbed judging from the degree of increased S and decreased D(w). These results suggest that EPA prevents the membrane from becoming hyperfluid and maintains membrane stability against significant changes in pressure. Our results counter the generally accepted concept that greater fluidity is a membrane characteristic of microorganisms that inhabit cold, high-pressure environments. We suggest that retaining a certain level of membrane physical properties under high pressure is more important than conferring membrane fluidity alone.
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Miyazaki M, Koide O, Kobayashi T, Mori K, Shimamura S, Nunoura T, Imachi H, Inagaki F, Nagahama T, Nogi Y, Deguchi S, Takai K. Geofilum rubicundum gen. nov., sp. nov., isolated from deep subseafloor sediment. Int J Syst Evol Microbiol 2011; 62:1075-1080. [PMID: 21705444 DOI: 10.1099/ijs.0.032326-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, facultatively anaerobic bacterium (strain JAM-BA0501(T)) was isolated from a deep subseafloor sediment sample at a depth of 247 m below seafloor off the Shimokita Peninsula of Japan in the north-western Pacific Ocean (Site C9001, 1180 m water depth). Cells of strain JAM-BA0501(T) were gram-negative, filamentous, non-spore-forming and motile on solid medium by gliding. Phylogenetic analysis based on the 16S rRNA gene sequence of strain JAM-BA0501(T) indicated a distant relationship to strains representing genera within the order Bacteroidales, such as Alkaliflexus imshenetskii Z-7010(T) (91.1 % similarity), Marinilabilia salmonicolor ATCC 19041(T) (86.2 %) and Anaerophaga thermohalophila Fru22(T) (89.3 %). The new isolate produced isoprenoid quinones with menaquinone MK-7 as the major component, and the predominant fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0). The DNA G+C content of the isolate was 42.9 mol%. Based on its taxonomic distinctiveness, strain JAM-BA0501(T) is considered to represent a novel species of a new genus within the family Marinilabiliaceae, for which the name Geofilum rubicundum gen. nov., sp. nov. is proposed. The type strain of Geofilum rubicundum is JAM-BA0501(T) ( = JCM 15548(T) = NCIMB 14482(T)).
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Affiliation(s)
- Masayuki Miyazaki
- Subsurface Geobiology Advanced Research (SUGAR) project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Osamu Koide
- Soft Matter and Extremophiles Research Team, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Tohru Kobayashi
- Soft Matter and Extremophiles Research Team, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kozue Mori
- Marine Bioresource Exploration Research Team and Institute of Biogeosciences (BioGeos), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shigeru Shimamura
- Subsurface Geobiology Advanced Research (SUGAR) project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Takuro Nunoura
- Subsurface Geobiology Advanced Research (SUGAR) project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hiroyuki Imachi
- Subsurface Geobiology Advanced Research (SUGAR) project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Takahiko Nagahama
- Soft Matter and Extremophiles Research Team, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yuichi Nogi
- Soft Matter and Extremophiles Research Team, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shigeru Deguchi
- Soft Matter and Extremophiles Research Team, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Subsurface Geobiology Advanced Research (SUGAR) project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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Piezotolerance of the respiratory terminal oxidase activity of the piezophilic Shewanella violacea DSS12 as compared with non-piezophilic Shewanella species. Biosci Biotechnol Biochem 2011; 75:919-24. [PMID: 21597190 DOI: 10.1271/bbb.100882] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The facultative piezophile Shewanella violacea DSS12 is known to alter its respiratory components under the influence of hydrostatic pressure during growth, suggesting that it has a respiratory system that functions in adaptation to high pressure. We investigated the pressure- and temperature-dependencies of the respiratory terminal oxidase activity of the membrane of S. violacea relative to non-piezophilic Shewanella species. We observed that the activity in the membrane of S. violacea was more resistant to high pressure than those of non-piezophilic Shewanella even though DSS12 was cultured under atmospheric pressure. On the other hand, the temperature dependency of this activity was almost the same for all of the tested strain regardless of optimal growth temperature. Both high pressure and low temperature are expected to lower protein flexibility, causing a decrease in enzyme activity, but the results of this study suggest that the mechanism maintaining enzyme activity under high hydrostatic pressure is different from that at low temperature. Additionally, the responses of the activity to the pressure- and temperature-changes were independent of membrane lipid composition. Therefore, the piezotolerance of the respiratory terminal oxidases of S. violacea is perhaps dependent on the properties of the protein itself and not on the lipid composition of the membrane. Our observations suggest that S. violacea constitutively express piezotolerant respiratory terminal oxidases that serve adaptation to the deep-sea environment.
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