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Li X, Li C, Liu Y, Han G, Lin C, Chen X, Mao J. Rheological and Structural Characterization of Carrageenans during Depolymerization Conducted by a Marine Bacterium Shewanella sp. LE8. Gels 2024; 10:502. [PMID: 39195031 DOI: 10.3390/gels10080502] [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: 07/05/2024] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 08/29/2024] Open
Abstract
Carrageenans were widely utilized as thickening and gelling agents in the food and cosmetic industries, and their oligosaccharides have been proven to possess enhanced physicochemical and biological properties. In this study, Shewanella sp. LE8 was utilized for the depolymerization of κ-, ι-, and λ-carrageenan under conditions of fermentation. During a 24-h fermentation at 28 °C, the apparent viscosity of κ-, ι-, and λ-carrageenan decreased by 53.12%, 84.10%, and 59.33%, respectively, accompanied by a decrease in storage modulus, and loss modulus. After a 72-h fermentation, the analysis of methylene blue and molecular weight distribution revealed that ι-carrageenan was extensively depolymerized into smaller polysaccharides by Shewanella sp. LE8, while exhibiting partial degradation on κ- and λ-carrageenan. However, the impact of Shewanella sp. LE8 on total sugars was found to be limited; nevertheless, a significant increase in reduced sugar content was observed. The ESIMS analysis results revealed that the purified components obtained through ι-carrageenan fermentation for 72 h were identified as tetrasaccharides, while the two purified components derived from λ-carrageenan fermentation consisted of a hexasaccharide and a tetrasaccharide, respectively. Overall, the present study first reported the depolymerization of ι-and λ-carrageenan by Shewanella and suggested that the Shewanella could be used to depolymerize multiple carrageenans, as well as complex polysaccharides derived from red algae, to further obtain their oligosaccharides.
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Affiliation(s)
- Xiong Li
- Guangdong Engineering Research Center of High-Value Utilization and Equipment Development of Marine Biological Resources, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Chuyi Li
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yizhou Liu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Gang Han
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Congyu Lin
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaoli Chen
- Guangdong Engineering Research Center of High-Value Utilization and Equipment Development of Marine Biological Resources, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jian Mao
- Guangdong Engineering Research Center of High-Value Utilization and Equipment Development of Marine Biological Resources, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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Ghotekar BK, Kulkarni SS. Total Synthesis of the Conjugation-Ready Tetrasaccharide Repeating Unit of Shewanella japonica Type Strain KMM 3299 T. Org Lett 2024; 26:4346-4350. [PMID: 38722236 DOI: 10.1021/acs.orglett.4c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Here we report the first total synthesis of the conjugation-ready tetrasaccharide repeating unit of Shewanella japonica type strain KMM 3299T. The presence of rare deoxyamino sugars and installation of three consecutive 1,2-cis glycosidic linkages makes the synthesis formidable. The challenging late-stage oxidation was overcome by using a galacturonate donor. The total synthesis was completed via a longest linear sequence of 22 steps in an overall yield of 3.5% starting from d-mannose.
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Affiliation(s)
- Balasaheb K Ghotekar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Suvarn S Kulkarni
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Lee YS, Jeong HR, Hwang EJ, Prakash Patil M, Seo YB, Kim GD. Shewanella goraebulensis sp. nov., isolated from sea water. Int J Syst Evol Microbiol 2024; 74. [PMID: 38180019 DOI: 10.1099/ijsem.0.006214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
A novel Gram-stain-negative, facultatively anaerobic and rod-shaped bacterial strain, designated as DAU312T, was isolated from the sea water of the eastern coast of the Republic of Korea. Optimal growth was observed at 25 °C, pH 7.0-8.0 and with NaCl concentrations of 2.0 % (w/v). Catalase and oxidase activities were detected. On the basis of 16S rRNA gene sequences, strain DAU312T showed the highest similarity (99.2 %) to the type strain Shewanella electrodiphila MAR441T. The complete genome sequence of strain DAU312T contains 4 893 483 bp and 40.5 mol% G+C. Phylogenetic analyses based on 16S rRNA gene sequences and the up-to-date bacterial core genes showed that strain DAU312T, S. electrodiphila MAR441T and S. olleyana were all part of the same monophyletic clade. Their average nucleotide identity, digital DNA-DNA hybridization and two-way average amino acid identity values with each other and type strains of close Shewanella species were 83.4-77.5 %, 27.3-22.0 % and 89.8-81.2 %, respectively. The major cellular fatty acids (>10 %) were iso-C15 : 0, summed feature 3 (C16 : 1 ω7с and/or C16 : 1 ω6с) and C16 : 0. Phosphatidylethanolamine and phosphatidylglycerol were the main polar lipids. The respiratory quinones were Q-7, Q-8, MK-7 and MMK-7. Based on these polyphasic taxonomic findings, the name Shewanella goraebulensis sp. nov. is suggested for strain DAU312T, which is considered to represent a novel species of the genus Shewanella. The type strain is DAU312T (=KCTC 72427 T=JCM 35744T=KCCM 43478T).
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Affiliation(s)
- Yong-Suk Lee
- Department of Microbiology, Pukyong National University, Busan 48513, Republic of Korea
- Department of Biotechnology, Dong-A University, Busan 49315, Republic of Korea
| | - Hae-Rin Jeong
- Department of Biotechnology, Dong-A University, Busan 49315, Republic of Korea
| | - Eun-Jung Hwang
- Department of Biotechnology, Dong-A University, Busan 49315, Republic of Korea
| | | | - Yong Bae Seo
- Department of Microbiology, Pukyong National University, Busan 48513, Republic of Korea
| | - Gun-Do Kim
- Department of Microbiology, Pukyong National University, Busan 48513, Republic of Korea
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4
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Yao S, Zhang X, Lin A, Xia X, Lin L, Yang G, Zhuang L. Characterization of two novel Fe(III)-reducing and electrogenic bacteria, Shewanella ferrihydritica sp. nov. and Shewanella electrica sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37823787 DOI: 10.1099/ijsem.0.006044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Three novel strains in the genus Shewanella, designated A3AT, C31T and C32, were isolated from mangrove sediment samples. They were facultative anaerobic, Gram-stain-negative, rod-shaped, flagellum-harbouring, oxidase- and catalase-positive, electrogenic and capable of using Fe(III) as an electron acceptor during anaerobic growth. Results of phylogenetic analysis based on 16S rRNA gene and genomic sequences revealed that the strains should be assigned to the genus Shewanella. The 16S rRNA gene similarity, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the isolates and their closely related species were below the respective cut-off values for species differentiation. The 16S rRNA gene similarity, ANI and dDDH values between strains C31T and C32 were 99.7, 99.9 and 99.9 %, respectively, indicating that they should belong to the same genospecies. Based on polyphasic taxonomic approach, two novel species are proposed, Shewanella ferrihydritica sp. nov. with type strain A3AT (GDMCC 1.2732T=JCM 34899T) and Shewanella electrica sp. nov. with type strain C31T (GDMCC 1.2736T=JCM 34902T).
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Affiliation(s)
- Sijie Yao
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| | - Xueying Zhang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| | - Annian Lin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| | - Xue Xia
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| | - Lijun Lin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| | - Guiqin Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| | - Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
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Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation. mSystems 2022; 7:e0151821. [PMID: 35311563 PMCID: PMC9040814 DOI: 10.1128/msystems.01518-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Shewanella spp. play important ecological and biogeochemical roles, due in part to their versatile metabolism and swift integration of stimuli. While Shewanella spp. are primarily considered environmental microbes, Shewanella algae is increasingly recognized as an occasional human pathogen. S. algae shares the broad metabolic and respiratory repertoire of Shewanella spp. and thrives in similar ecological niches. In S. algae, nitrate and dimethyl sulfoxide (DMSO) respiration promote biofilm formation strain specifically, with potential implication of taxis and cyclic diguanosine monophosphate (c-di-GMP) signaling. Signal transduction systems in S. algae have not been investigated. To fill these knowledge gaps, we provide here an inventory of the c-di-GMP turnover proteome and chemosensory networks of the type strain S. algae CECT 5071 and compare them with those of 41 whole-genome-sequenced clinical and environmental S. algae isolates. Besides comparative analysis of genetic content and identification of laterally transferred genes, the occurrence and topology of c-di-GMP turnover proteins and chemoreceptors were analyzed. We found S. algae strains to encode 61 to 67 c-di-GMP turnover proteins and 28 to 31 chemoreceptors, placing S. algae near the top in terms of these signaling capacities per Mbp of genome. Most c-di-GMP turnover proteins were predicted to be catalytically active; we describe in them six novel N-terminal sensory domains that appear to control their catalytic activity. Overall, our work defines the c-di-GMP and chemosensory signal transduction pathways in S. algae, contributing to a better understanding of its ecophysiology and establishing S. algae as an auspicious model for the analysis of metabolic and signaling pathways within the genus Shewanella. IMPORTANCEShewanella spp. are widespread aquatic bacteria that include the well-studied freshwater model strain Shewanella oneidensis MR-1. In contrast, the physiology of the marine and occasionally pathogenic species Shewanella algae is poorly understood. Chemosensory and c-di-GMP signal transduction systems integrate environmental stimuli to modulate gene expression, including the switch from a planktonic to sessile lifestyle and pathogenicity. Here, we systematically dissect the c-di-GMP proteome and chemosensory pathways of the type strain S. algae CECT 5071 and 41 additional S. algae isolates. We provide insights into the activity and function of these proteins, including a description of six novel sensory domains. Our work will enable future analyses of the complex, intertwined c-di-GMP metabolism and chemotaxis networks of S. algae and their ecophysiological role.
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Ultrasonic pre-treatment of Bacillus velezensis for improved electrogenic response in a single chambered microbial fuel cell. 3 Biotech 2022; 12:18. [PMID: 34926122 PMCID: PMC8674389 DOI: 10.1007/s13205-021-03065-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023] Open
Abstract
Various microbial strains and techniques are being used to improve power production in microbial fuel cells. Cow dung is a peculiar source of anaerobic and micro-aerophilic organisms that were employed in this study to isolate exo-electrogenic microorganisms. To validate their exo-electrogenic nature, all eight visually distinct bacterial single-cell colonies were tested using the ferrocyanide reduction assay, which resulted in the selection of one bacterial strain AD1-ELB with the ability to reduce ferrocyanide for further biochemical, physiological and electrochemical characterization. The selected strain AD1-ELB was identified as Bacillus velezensis by 16 s rRNA gene sequencing. When used in a single-chambered MFC, the isolated AD1-ELB strain produced a maximum open-circuit voltage of 455 mV with a maximum current density of 51.78 µA/cm2 and maximum power density of 4.33 µW/cm2 on the 16th day. Bacillus velezensis AD1-ELB strain was treated with low-frequency ultrasound (40 kHz) for 1, 2, 3, 4, and 5 min to assess the effect of ultrasonic pre-treatment on an isolated pure culture-based microbial fuel cell. A 3-min exposure to low-frequency ultrasonic therapy resulted in an increase in maximum power of 4.33 µW/cm2 with a current density of 51.78 µA/cm2 in the MFC, which decreases significantly after 4 and 5 min. Thus, the overall power density achieved was 1.89 times greater than in MFCs with untreated strain. These findings support the use of low-frequency ultrasonic stimulation to improve the performance of microbial fuel cell devices and are restricted to the pure, single-cell strain AD1-ELB, with the potential for variation if some other isolated strain is utilized, hence requiring further study to determine its relative variations.
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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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Wang D, Wang J, Zeng R, Wu J, Michael SV, Qu W. The degradation activities for three seaweed polysaccharides of Shewanella sp. WPAGA9 isolated from deep-sea sediments. J Basic Microbiol 2021; 61:406-418. [PMID: 33729617 DOI: 10.1002/jobm.202000728] [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: 12/15/2020] [Revised: 02/03/2021] [Accepted: 03/01/2021] [Indexed: 11/06/2022]
Abstract
Seaweed oligosaccharides possess great bioactivities. However, different microbial strains are required to degrade multiple polysaccharides due to their limited biodegradability, thereby increasing the cost and complexity of production. Shewanella sp. WPAGA9 was isolated from deep-sea sediments in this study. According to the genomic and biochemical analyses, the extracellular fermentation broth of WPAGA9 had versatile degradation abilities for three typical seaweed polysaccharides including agar, carrageenan, and alginate. The maximum enzyme activities of the extracellular fermentation broth of WPAGA9 were 71.63, 76.4, and 735.13 U/ml for the degradation of agar, alginate, and carrageenan, respectively. Moreover, multiple seaweed oligosaccharides can be produced by the extracellular fermentation broth of WPAGA9 under similar optimum conditions. Therefore, WPAGA9 can simultaneously degrade three types of seaweed polysaccharides under similar conditions, thereby greatly reducing the production cost of seaweed oligosaccharides. This finding indicates that Shewanella sp. WPAGA9 is an ideal biochemical tool for producing multiple active seaweed oligosaccharides at low costs and is also an important participant in the carbon cycle process of the deep-sea environment.
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Affiliation(s)
- Dingquan Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Runying Zeng
- Technical Innovation Center for Utilization of Marine Biological Resources, Ministry of Natural Resources, Xiamen, China
| | - Jie Wu
- Technical Innovation Center for Utilization of Marine Biological Resources, Ministry of Natural Resources, Xiamen, China
| | - Shija V Michael
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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Neu AT, Hughes IV, Allen EE, Roy K. Decade-scale stability and change in a marine bivalve microbiome. Mol Ecol 2021; 30:1237-1250. [PMID: 33432685 DOI: 10.1111/mec.15796] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022]
Abstract
Predicting how populations and communities of organisms will respond to anthropogenic change is of paramount concern in ecology today. For communities of microorganisms, however, these predictions remain challenging, primarily due to data limitations. Information about long-term dynamics of host-associated microbial communities, in particular, is lacking. In this study, we use well-preserved and freshly collected samples of soft tissue from a marine bivalve host, Donax gouldii, at a single site to quantify the diversity and composition of its microbiome over a decadal timescale. Site-level measurements of temperature, salinity and chlorophyll a allowed us to test how the microbiome of this species responded to two natural experiments: a seasonal increase in temperature and a phytoplankton bloom. Our results show that ethanol-preserved tissue can provide high-resolution information about temporal trends in compositions of host-associated microbial communities. Specifically, we found that the richness of amplicon sequence variants (ASVs) associated with D.gouldii did not change significantly over time despite increases in water temperature (+1.6°C due to seasonal change) and chlorophyll a concentration (more than ninefold). The phylogenetic composition of the communities, on the other hand, varied significantly between all collection years, with only six ASVs persisting over our sampling period. Overall, these results suggest that the diversity of microbial taxa associated with D.gouldii has remained stable over time and in response to seasonal environmental change over the course of more than a decade, but such stability is underlain by substantial turnover in the composition of the microbiome.
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Affiliation(s)
- Alexander T Neu
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ian V Hughes
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Eric E Allen
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.,Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
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Liu X, Deng T, Liu X, Lai X, Feng Y, Lyu M, Wang S. Isomalto-Oligosaccharides Produced by Endodextranase Shewanellasp. GZ-7 From Sugarcane Plants. Nat Prod Commun 2020. [DOI: 10.1177/1934578x20953286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Oligosaccharides have important alimental and medical applications. Dextranase has been used to produce isomalto-oligosaccharides (IMOs). In this study, we isolated dextranase-producing bacteria from sugarcane-cultivated soil. Identification of the isolate based on its phenotypical, physiological, and biochemical characteristics, as well as 16S ribosomal deoxyribonucleic acid gene sequencing yielded Shewanella sp. strain GZ-7. The molecular weight of the dextranase produced by this strain was 100-135 kDa. The optimum temperature and pH for dextranase production were 40 °C and 7.5, respectively. The enzyme was found to be stable at the pH range of 6.0-8.0 and the temperature range of 20 °C-40 °C. Thin-layer chromatography and high-performance liquid chromatography of the enzymolysis products of the substrate confirmed the enzyme to be endodextranase. Under the optimal conditions, the ratio of IMOs could reach 91.8% of the hydrolyzate. The final products were found to efficiently scavenge the 2,2-diphenyl-1-picrylhydrazyl, hydroxyl, and superoxide anion radicals. In general, dextranase and hydrolyzates have high potential prospects for application in the future.
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Affiliation(s)
- Xin Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/ Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, P. R. China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, P. R. China
| | - Tian Deng
- Jiangsu Key Laboratory of Marine Bioresources and Environment/ Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, P. R. China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, P. R. China
| | - Xueqin Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/ Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, P. R. China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, P. R. China
| | - Xiaohua Lai
- Jiangsu Key Laboratory of Marine Bioresources and Environment/ Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, P. R. China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, P. R. China
| | - Yanli Feng
- Jiangsu Key Laboratory of Marine Bioresources and Environment/ Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, P. R. China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, P. R. China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/ Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, P. R. China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, P. R. China
- Collaborative Innovation Center of Modern Biological Manufacturing, Anhui University, Hefei, P. R. China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/ Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, P. R. China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, P. R. China
- Collaborative Innovation Center of Modern Biological Manufacturing, Anhui University, Hefei, P. R. China
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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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12
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Hwang YJ, Jang GI, Cho BC, Lee JI, Hwang CY. Shewanella psychromarinicola sp. nov., a psychrophilic bacterium isolated from pelagic sediment of the Ross Sea (Antarctica), and reclassification of Shewanella arctica Kim et al. 2012 as a later heterotypic synonym of Shewanella frigidimarina Bowman et al. 1997. Int J Syst Evol Microbiol 2019; 69:2415-2423. [DOI: 10.1099/ijsem.0.003490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yeon Ju Hwang
- 1Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- 2Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Gwang Il Jang
- 1Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Byung Cheol Cho
- 2Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Jae Il Lee
- 3Division of Polar Paleoenvironment, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Chung Yeon Hwang
- 1Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
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Multilocus Sequence Analysis, a Rapid and Accurate Tool for Taxonomic Classification, Evolutionary Relationship Determination, and Population Biology Studies of the Genus Shewanella. Appl Environ Microbiol 2019; 85:AEM.03126-18. [PMID: 30902862 DOI: 10.1128/aem.03126-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/19/2019] [Indexed: 02/02/2023] Open
Abstract
The genus Shewanella comprises a group of marine-dwelling species with worldwide distribution. Several species are regarded as causative agents of food spoilage and opportunistic pathogens of human diseases. In this study, a standard multilocus sequence analysis (MLSA) based on six protein-coding genes (gyrA, gyrB, infB, recN, rpoA, and topA) was established as a rapid and accurate identification tool in 59 Shewanella type strains. This method yielded sufficient resolving power in regard to enough informative sites, adequate sequence divergences, and distinct interspecies branches. The stability of phylogenetic topology was supported by high bootstrap values and concordance with different methods. The reliability of the MLSA scheme was further validated by identical phylogenies and high correlations of genomes. The MLSA approach provided a robust system to exhibit evolutionary relationships in the Shewanella genus. The split network tree proposed twelve distinct monophyletic clades with identical G+C contents and high genetic similarities. A total of 86 tested strains were investigated to explore the population biology of the Shewanella genus in China. The most prevalent Shewanella species was Shewanella algae, followed by Shewanella xiamenensis, Shewanella chilikensis, Shewanella indica, Shewanella seohaensis, and Shewanella carassii The strains frequently isolated from clinical and food samples highlighted the importance of increasing the surveillance of Shewanella species. Based on the combined genetic, genomic, and phenotypic analyses, Shewanella upenei should be considered a synonym of S. algae, and Shewanella pacifica should be reclassified as a synonym of Shewanella japonica IMPORTANCE The MLSA scheme based on six housekeeping genes (HKGs) (gyrA, gyrB, infB, recN, rpoA, and topA) is well established as a reliable tool for taxonomic, evolutionary, and population diversity analyses of the genus Shewanella in this study. The standard MLSA method allows researchers to make rapid, economical, and precise identification of Shewanella strains. The robust phylogenetic network of MLSA provides profound insight into the evolutionary structure of the genus Shewanella The population genetics of Shewanella species determined by the MLSA approach plays a pivotal role in clinical diagnosis and routine monitoring. Further studies on remaining species and genomic analysis will enhance a more comprehensive understanding of the microbial systematics, phylogenetic relationships, and ecological status of the genus Shewanella.
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Yagi H, Fujise A, Itabashi N, Ohshiro T. Characterization of a novel endo-type alginate lyase derived from Shewanella sp. YH1. J Biochem 2018; 163:341-350. [PMID: 29319800 DOI: 10.1093/jb/mvy001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/24/2017] [Indexed: 12/18/2022] Open
Abstract
Alginate, which is an anionic polysaccharide, is widely distributed in the cell wall of brown algae. Alginate and the products of its degradation (oligosaccharides) are used in stabilizers, thickeners and gelling agents, especially in the food industry. The degradation of alginate generally involves a combination of several alginate lyases (exo-type, endo-type and oligoalginate lyase). Enhancing the efficiency of the production of alginate degradation products may require the identification of novel alginate lyases with unique characteristics. In this study, we isolated an alginate-utilizing bacterium, Shewanella sp. YH1, from seawater collected off the coast of Tottori prefecture, Japan. The detected novel alginate lyase was named AlgSI-PL7, and was classified in polysaccharide lyase family 7. The enzyme was purified from Shewanella sp. YH1 and a recombinant AlgSI-PL7 was produced in Escherichia coli. The optimal temperature and pH for enzyme activity were around 45°C and 8, respectively. Interestingly, we observed that AlgSI-PL7 was not thermotolerant, but could refold to its active form following an almost complete denaturation at approximately 60°C. Moreover, the degradation of alginate by AlgSI-PL7 produced two to five oligosaccharides, implying this enzyme was an endo-type lyase. Our findings suggest that AlgSI-PL7 may be useful as an industrial enzyme.
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Affiliation(s)
- Hisashi Yagi
- Center for Research on Green Sustainable Chemistry
| | - Asako Fujise
- Department of Chemistry and Biotechnology, Graduate School of Engineering
| | - Narumi Itabashi
- Department of Biotechnology, Faculty of Engineering, Tottori University, Tottori, Japan
| | - Takashi Ohshiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering
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15
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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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Jung-Schroers V, Jung A, Ryll M, Bauer J, Teitge F, Steinhagen D. Methods for identification and differentiation of different Shewanella spp. isolates for diagnostic use. JOURNAL OF FISH DISEASES 2018; 41:689-714. [PMID: 29280153 DOI: 10.1111/jfd.12772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/24/2017] [Accepted: 11/26/2017] [Indexed: 06/07/2023]
Abstract
Shewanella spp. are Gram-negative, rod-shaped, motile bacteria that are widely distributed in marine and freshwater environments. The bacteria are present in the physiological microflora of fish from temperate waters and are known as fish spoilage species. From clinically healthy fish and from fish with skin ulcerations, Shewanella spp. is regularly isolated, indicating a possible role as fish pathogen. In this study, 74 isolates of Shewanella spp. were analysed. For species identification, biochemical techniques, 16S rRNA sequencing, MALDI-TOF MS and the Sherlock Microbial Identification System (MIS) based on the composition of fatty acid ethyl esters were compared. The phylogenetic relationship, cytotoxicity in vitro and resistance against antibiotics were tested. The most reliable method for species identification was 16S rRNA sequencing. From diseased fish, clinically healthy fish and the aquatic environment, different Shewanella species were isolated. This indicates that Shewanella spp. is widespread in the aquatic milieu and acts as a secondary pathogen. The virulence of Shewanella spp. is probably not depending on the species but on the isolate itself. Many isolates of Shewanella spp. were showing multiresistances against antibiotic substances, especially in samples derived from retailers and in routine diagnostics, all Shewanella spp. should therefore be tested for resistances against antibiotic agents.
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Affiliation(s)
- V Jung-Schroers
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
| | - A Jung
- Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany
| | - M Ryll
- Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany
| | - J Bauer
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
| | - F Teitge
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
| | - D Steinhagen
- Fish Disease Research Unit, University of Veterinary Medicine, Hannover, Germany
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17
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Yagi H, Isobe N, Itabashi N, Fujise A, Ohshiro T. Characterization of a Long-Lived Alginate Lyase Derived from Shewanella Species YH1. Mar Drugs 2017; 16:md16010004. [PMID: 29280943 PMCID: PMC5793052 DOI: 10.3390/md16010004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 01/07/2023] Open
Abstract
Polysaccharides from seaweeds are widely used in various fields, including the food, biomedical material, cosmetic, and biofuel industries. Alginate, which is a major polysaccharide in brown algae, and the products of its degradation (oligosaccharides) have been used in stabilizers, thickeners, and gelling agents, especially in the food industry. Discovering novel alginate lyases with unique characteristics for the efficient production of oligosaccharides may be relevant for the food and pharmaceutical fields. In this study, we identified a unique alginate lyase derived from an alginate-utilizing bacterium, Shewanella species YH1. The recombinant enzyme (rAlgSV1-PL7) was produced in an Escherichia coli system and it was classified in the Polysaccharide Lyase family 7. The optimal temperature and pH for rAlgSV1-PL7 activity were around 45 °C and 8, respectively. Interestingly, we observed that rAlgSV1-PL7 retained over 80% of its enzyme activity after incubation at 30 °C for at least 20 days, indicating that rAlgSV1-PL7 is a long-lived enzyme. Moreover, the degradation of alginate by rAlgSV1-PL7 produced one to four sugars because of the broad substrate specificity of this enzyme. Our findings suggest that rAlgSV1-PL7 may represent a new commercially useful enzyme.
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Affiliation(s)
- Hisashi Yagi
- Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyamacho-minami, Tottori-city 680-8552, Tottori Prefecture, Japan.
| | - Natsuki Isobe
- Department of Biotechnology, Faculty of Engineering, Tottori University, 4-101 Koyamacho-minami, Tottori-city 680-8552, Tottori Prefecture, Japan.
| | - Narumi Itabashi
- Department of Biotechnology, Faculty of Engineering, Tottori University, 4-101 Koyamacho-minami, Tottori-city 680-8552, Tottori Prefecture, Japan.
| | - Asako Fujise
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyamacho-minami, Tottori-city 680-8552, Tottori Prefecture, Japan.
| | - Takashi Ohshiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyamacho-minami, Tottori-city 680-8552, Tottori Prefecture, Japan.
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Zhang J, Burgess JG. Enhanced eicosapentaenoic acid production by a new deep-sea marine bacterium Shewanella electrodiphila MAR441T. PLoS One 2017; 12:e0188081. [PMID: 29176835 PMCID: PMC5703452 DOI: 10.1371/journal.pone.0188081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 10/31/2017] [Indexed: 02/05/2023] Open
Abstract
Omega-3 fatty acids are products of secondary metabolism, essential for growth and important for human health. Although there are numerous reports of bacterial production of omega-3 fatty acids, less information is available on the biotechnological production of these compounds from bacteria. The production of eicosapentaenoic acid (EPA, 20:5ω3) by a new species of marine bacteria Shewanella electrodiphila MAR441T was investigated under different fermentation conditions. This strain produced a high percentage (up to 26%) of total fatty acids and high yields (mg / g of biomass) of EPA at or below the optimal growth temperature. At higher growth temperatures these values decreased greatly. The amount of EPA produced was affected by the carbon source, which also influenced fatty acid composition. This strain required Na+ for growth and EPA synthesis and cells harvested at late exponential or early stationary phase had a higher EPA content. Both the highest amounts (20 mg g-1) and highest percent EPA content (18%) occurred with growth on L-proline and (NH4)2SO4. The addition of cerulenin further enhanced EPA production to 30 mg g-1. Chemical mutagenesis using NTG allowed the isolation of mutants with improved levels of EPA content (from 9.7 to 15.8 mg g-1) when grown at 15°C. Thus, the yields of EPA could be substantially enhanced without the need for recombinant DNA technology, often a commercial requirement for food supplement manufacture.
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Affiliation(s)
- Jinwei Zhang
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Hatherly Laboratory, Exeter, United Kingdom
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - J. Grant Burgess
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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Leyva-Díaz JC, Poyatos JM, Barghini P, Gorrasi S, Fenice M. Kinetic modeling of Shewanella baltica KB30 growth on different substrates through respirometry. Microb Cell Fact 2017; 16:189. [PMID: 29100519 PMCID: PMC5670636 DOI: 10.1186/s12934-017-0805-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/31/2017] [Indexed: 11/11/2022] Open
Abstract
Background Shewanella baltica KB30 was isolated from seawater collected in Kandalaksha Bay, White Sea (Russia). This strain is known for its ability to grow on a pool of different substrates, including carbohydrates, carboxylic and amino acids, and lipids. However, no data are available on its metabolic efficiency in relation to the use of different carbon sources typologies. This work represents the first attempt to characterize S. baltica by its heterotrophic kinetic performance. Results Growth and substrate consumption, during the biodegradation of sodium acetate, glucose, tween 80 and peptone, were analyzed through a respirometric method. To find the model best fitting the experimental data and to obtain the kinetic parameters, the equations of Monod, Moser, Contois and Tessier were applied. The kinetic behavior of S. baltica was fitted to Monod model for sodium acetate and tween 80, while it was adjusted to Contois model for glucose and peptone. In this regard, peptone was consumed faster than the other substrates, as indicated by the highest values of substrate degradation rate, which exceeded 60 mg O2 L−1 h−1. Conclusions Proteolytic metabolism was favored than lipidic and glucidic metabolism, which could contribute much more to mineralization and recycling of proteins than lipids and carbohydrates.
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Affiliation(s)
- Juan Carlos Leyva-Díaz
- Department of Civil Engineering, University of Granada, 18071, Granada, Spain.,Institute for Water Research, University of Granada, 18071, Granada, Spain.,Department of Ecological and Biological Sciences, University of Tuscia, Largo Università snc, 01100, Viterbo, Italy
| | - José Manuel Poyatos
- Department of Civil Engineering, University of Granada, 18071, Granada, Spain.,Institute for Water Research, University of Granada, 18071, Granada, Spain
| | - Paolo Barghini
- Department of Ecological and Biological Sciences, University of Tuscia, Largo Università snc, 01100, Viterbo, Italy
| | - Susanna Gorrasi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo Università snc, 01100, Viterbo, Italy
| | - Massimiliano Fenice
- Department of Ecological and Biological Sciences, University of Tuscia, Largo Università snc, 01100, Viterbo, Italy. .,Laboratory of Applied Marine Microbiology, ConISMa, University of Tuscia, 01100, Viterbo, Italy.
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20
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Kim KM, Choe H, Kim BK, Nasir A. Complete genome of a metabolically-diverse marine bacterium Shewanella japonica KCTC 22435 T. Mar Genomics 2017; 35:39-42. [DOI: 10.1016/j.margen.2017.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 11/16/2022]
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Gai Y, Huang Z, Lai Q, Shao Z. Shewanella intestini sp. nov., isolated from the intestine of abalone, Haliotis diversicolor. Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001878] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yingbao Gai
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State of Oceanic Administration, Xiamen, PR China
| | - Zhaobin Huang
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State of Oceanic Administration, Xiamen, PR China
| | - Qiliang Lai
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State of Oceanic Administration, Xiamen, PR China
| | - Zongze Shao
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State of Oceanic Administration, Xiamen, PR China
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22
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23
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Draft Genome Sequence of Shewanella sp. Strain P1-14-1, a Bacterial Inducer of Settlement and Morphogenesis in Larvae of the Marine Hydroid Hydractinia echinata. GENOME ANNOUNCEMENTS 2016; 4:4/1/e00003-16. [PMID: 26893410 PMCID: PMC4759057 DOI: 10.1128/genomea.00003-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The assembly and annotation of the draft genome sequence of Shewanella sp. strain P1-14-1 are reported here to investigate the genes responsible for interkingdom interactions, secondary metabolite production, and microbial electrogenesis.
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24
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Martin M, Barbeyron T, Martin R, Portetelle D, Michel G, Vandenbol M. The Cultivable Surface Microbiota of the Brown Alga Ascophyllum nodosum is Enriched in Macroalgal-Polysaccharide-Degrading Bacteria. Front Microbiol 2015; 6:1487. [PMID: 26734000 PMCID: PMC4690005 DOI: 10.3389/fmicb.2015.01487] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/10/2015] [Indexed: 11/30/2022] Open
Abstract
Bacteria degrading algal polysaccharides are key players in the global carbon cycle and in algal biomass recycling. Yet the water column, which has been studied largely by metagenomic approaches, is poor in such bacteria and their algal-polysaccharide-degrading enzymes. Even more surprisingly, the few published studies on seaweed-associated microbiomes have revealed low abundances of such bacteria and their specific enzymes. However, as macroalgal cell-wall polysaccharides do not accumulate in nature, these bacteria and their unique polysaccharidases must not be that uncommon. We, therefore, looked at the polysaccharide-degrading activity of the cultivable bacterial subpopulation associated with Ascophyllum nodosum. From A. nodosum triplicates, 324 bacteria were isolated and taxonomically identified. Out of these isolates, 78 (~25%) were found to act on at least one tested algal polysaccharide (agar, ι- or κ-carrageenan, or alginate). The isolates “active” on algal-polysaccharides belong to 11 genera: Cellulophaga, Maribacter, Algibacter, and Zobellia in the class Flavobacteriia (41) and Pseudoalteromonas, Vibrio, Cobetia, Shewanella, Colwellia, Marinomonas, and Paraglaceciola in the class Gammaproteobacteria (37). A major part represents likely novel species. Different proportions of bacterial phyla and classes were observed between the isolated cultivable subpopulation and the total microbial community previously identified on other brown algae. Here, Bacteroidetes and Gammaproteobacteria were found to be the most abundant and some phyla (as Planctomycetes and Cyanobacteria) frequently encountered on brown algae weren't identified. At a lower taxonomic level, twelve genera, well-known to be associated with algae (with the exception for Colwellia), were consistently found on all three A. nosodum samples. Even more interesting, 9 of the 11 above mentioned genera containing polysaccharolytic isolates were predominant in this common core. The cultivable fraction of the bacterial community associated with A. nodosum is, thus, significantly enriched in macroalgal-polysaccharide-degrading bacteria and these bacteria seem important for the seaweed holobiont even though they are under-represented in alga-associated microbiome studies.
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Affiliation(s)
- Marjolaine Martin
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Tristan Barbeyron
- Sorbonne Université, UPMC, Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models Roscoff, France
| | - Renee Martin
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Daniel Portetelle
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Gurvan Michel
- Sorbonne Université, UPMC, Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models Roscoff, France
| | - Micheline Vandenbol
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
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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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Busch J, Nascimento JR, Magalhães ACR, Dutilh BE, Dinsdale E. Copper tolerance and distribution of epibiotic bacteria associated with giant kelp Macrocystis pyrifera in southern California. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:1131-40. [PMID: 25893330 PMCID: PMC4460293 DOI: 10.1007/s10646-015-1460-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 04/06/2015] [Indexed: 06/04/2023]
Abstract
Kelp forests in southern California are important ecosystems that provide habitat and nutrition to a multitude of species. Macrocystis pyrifera and other brown algae that dominate kelp forests, produce negatively charged polysaccharides on the cell surface, which have the ability to accumulate transition metals such as copper. Kelp forests near areas with high levels of boating and other industrial activities are exposed to increased amounts of these metals, leading to increased concentrations on the algal surface. The increased concentration of transition metals creates a harsh environment for colonizing microbes altering community structure. The impact of altered bacterial populations in the kelp forest have unknown consequences that could be harmful to the health of the ecosystem. In this study we describe the community of microorganisms associated with M. pyrifera, using a culture based approach, and their increasing tolerance to the transition metal, copper, across a gradient of human activity in southern California. The results support the hypothesis that M. pyrifera forms a distinct marine microhabitat and selects for species of bacteria that are rarer in the water column, and that copper-resistant isolates are selected for in locations with elevated exposure to transition metals associated with human activity.
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Affiliation(s)
- Julia Busch
- />Biology Department, San Diego State University, San Diego, California USA
- />Scripps Institution of Oceanography, University of California, San Diego, USA
| | | | | | - Bas E. Dutilh
- />Computer Science Department, San Diego State University, California, USA
- />Centre for Molecular and Biomolecular Informatics, CMBI, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Crooteplein 28, 6526 GA Nijmegen, The Netherlands
| | - Elizabeth Dinsdale
- />Biology Department, San Diego State University, San Diego, California USA
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27
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Szöllősi A, Rezessy-Szabó JM, Hoschke Á, Nguyen QD. Novel method for screening microbes for application in microbial fuel cell. BIORESOURCE TECHNOLOGY 2015; 179:123-127. [PMID: 25536509 DOI: 10.1016/j.biortech.2014.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 06/04/2023]
Abstract
The ability to produce and to transport exo-electrons by microbes either to external acceptors or to electrodes are reported in our study. All investigated microorganisms (exception of Lactobacillus plantarum) exhibited strong iron-reducing capabilities in the absence of mediator meaning production and secretion of exo-electrons to the growth medium. L.plantarum, Saccharomyces cerevisiae and Escherichia coli need an electron shuttle molecule to reduce Fe(3+) ion. Significant correlation was observed between growth and iron-reducing capacity, as well as between initial cell counts and iron-reducing capacity. Changes of bio-current generated in MFC and iron-reduction were experimentally monitored, and a mathematical model was established by regression analysis. Based on these results, a novel and rapid screening method was developed for the selection of microorganisms for potential application in MFC. The method is based on the measurement of absorbance of bacterial and yeast cultures at 460 nm, providing a robust and high sample throughput approach.
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Affiliation(s)
- Attila Szöllősi
- Department of Brewing and Distilling, Corvinus University of Budapest, Ménesi út 45., 1118 Budapest, Hungary
| | - Judit M Rezessy-Szabó
- Department of Brewing and Distilling, Corvinus University of Budapest, Ménesi út 45., 1118 Budapest, Hungary
| | - Ágoston Hoschke
- Department of Brewing and Distilling, Corvinus University of Budapest, Ménesi út 45., 1118 Budapest, Hungary
| | - Quang D Nguyen
- Department of Brewing and Distilling, Corvinus University of Budapest, Ménesi út 45., 1118 Budapest, Hungary.
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Manzari C, Fosso B, Marzano M, Annese A, Caprioli R, D’Erchia AM, Gissi C, Intranuovo M, Picardi E, Santamaria M, Scorrano S, Sgaramella G, Stabili L, Piraino S, Pesole G. The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0810-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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Bianchi AC, Olazábal L, Torre A, Loperena L. Antarctic microorganisms as source of the omega-3 polyunsaturated fatty acids. World J Microbiol Biotechnol 2014; 30:1869-78. [PMID: 24474389 DOI: 10.1007/s11274-014-1607-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 01/17/2014] [Indexed: 12/22/2022]
Abstract
Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) are long-chain polyunsaturated fatty acids (PUFAs) that belong to the omega-3 group. They are essential fatty acids found in phospholipid of cell membranes. There is strong evidence that these nutrients may also favorably modulate many diseases. Primary sources of omega-3 PUFAs in the human diet are fish and fish-derived products. The fishing industry worldwide, however, is becoming unable to satisfy the growing demand for these PUFAs. A promising cost-effective alternative source of PUFAs is bacterial production. We identified 40 Antarctic marine bacterial isolates by 16S rRNA gene sequence analysis. Fifteen genera in three phyla were represented in the collection. Isolates were tested for ability to produce EPA using a method in which their ability to reduce 2,3,5-triphenyltetrazolium chloride (TTC) is determined and by gas chromatography coupled to mass spectrometry (GC-MS). All isolates could reduce TTC, and GC-MS analysis showed that four produced EPA and that six produced DHA. We show for the first time that isolates identified as Cellulophaga, Pibocella and Polaribacter can produce EPA and DHA, only DHA or only EPA, respectively. One isolate, Shewanella sp. (strain 8-5), is indicated to be a good candidate for further study to optimize growth and EPA production. In conclusion, a rapid method was tested for identification of new EPA producing strains from marine environments. New EPA and DHA producing strains were found as well as a potentially useful PUFA production strain.
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Affiliation(s)
- Ana Clara Bianchi
- Departamento de Bioingeniería, Facultad de Ingeniería, Instituto de Ingeniería Química, Julio Herrera y Reissig 565, 11300, Montevideo, Uruguay
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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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Biffinger JC, Fitzgerald LA, Ray R, Little BJ, Lizewski SE, Petersen ER, Ringeisen BR, Sanders WC, Sheehan PE, Pietron JJ, Baldwin JW, Nadeau LJ, Johnson GR, Ribbens M, Finkel SE, Nealson KH. The utility of Shewanella japonica for microbial fuel cells. BIORESOURCE TECHNOLOGY 2011; 102:290-297. [PMID: 20663660 DOI: 10.1016/j.biortech.2010.06.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 06/09/2010] [Accepted: 06/17/2010] [Indexed: 05/29/2023]
Abstract
Shewanella-containing microbial fuel cells (MFCs) typically use the fresh water wild-type strain Shewanella oneidensis MR-1 due to its metabolic diversity and facultative oxidant tolerance. However, S. oneidensis MR-1 is not capable of metabolizing polysaccharides for extracellular electron transfer. The applicability of Shewanella japonica (an agar-lytic Shewanella strain) for power applications was analyzed using a diverse array of carbon sources for current generation from MFCs, cellular physiological responses at an electrode surface, biofilm formation, and the presence of soluble extracellular mediators for electron transfer to carbon electrodes. Critically, air-exposed S. japonica utilizes biosynthesized extracellular mediators for electron transfer to carbon electrodes with sucrose as the sole carbon source.
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Affiliation(s)
- Justin C Biffinger
- Chemistry Division, US Naval Research Laboratory, 4555 Overlook Avenue, SW, Washington, DC 20375, USA.
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Possible biosynthetic pathways for all cis-3,6,9,12,15,19,22, 25,28-hentriacontanonaene in bacteria. Lipids 2010; 45:167-77. [PMID: 20037794 DOI: 10.1007/s11745-009-3380-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 11/25/2009] [Indexed: 10/20/2022]
Abstract
A very long chain polyunsaturated hydrocarbon, hentriacontanonaene (C31:9), was detected in an eicosapentaenoic acid (EPA)-producing marine bacterium, which was isolated from the mid-latitude seashore of Hokkaido, Japan, and was tentatively identified as mesophilic Shewanella sp. strain osh08 from 16S rRNA gene sequencing. The geometry and position of the double bonds in this compound were determined physicochemically to be all cis at positions 3, 6, 9, 12, 15, 19, 22, 25, and 28. Although C31:9 was detected in all of the seven EPA- or/and docosahexaenoic acid-producing bacteria tested, an EPA-deficient mutant (strain IK-1Delta8) of one of these bacteria had no C31:9. Strain IK-1Delta8 had defects in the pfaD gene, one of the five pfa genes responsible for the biosynthesis of EPA. Although Escherichia coli DH5alpha does not produce EPA or DHA inherently, cells transformed with the pfa genes responsible for the biosynthesis of EPA and DHA produced EPA and DHA, respectively, but not C31:9. These results suggest that the Pfa protein complex is involved in the biosynthesis of C31:9 and that pfa genes must not be the only genes responsible for the formation of C31:9. In this report, we determined for the first time the molecular structure of the C31:9 and discuss the possible biosynthetic pathways of this compound.
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35
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Korbekandi H, Iravani S, Abbasi S. Production of nanoparticles using organisms. Crit Rev Biotechnol 2009; 29:279-306. [DOI: 10.3109/07388550903062462] [Citation(s) in RCA: 200] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Park SC, Baik KS, Kim MS, Kim D, Seong CN. Shewanella marina sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2009; 59:1888-94. [PMID: 19567571 DOI: 10.1099/ijs.0.005470-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A motile, rod-shaped, pale-brown-pigmented bacterium, designated strain C4T, was isolated from seawater collected from the South Sea (Republic of Korea). Cells were Gram-negative, facultatively anaerobic, and catalase- and oxidase-positive. The major fatty acids were summed feature 3 (C16:1omega7c and/or iso-C15:0 2-OH; 19.4%), C16:0 (16.3%), C17:1omega8c (9.5%) and iso-C15:0 (7.7%). The DNA G+C content was 40.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain C4T formed a lineage within the genus Shewanella (92.7-96.1% sequence similarity to representative strains of the genus Shewanella) and was part of a distinct branch with the clade comprising Shewanella haliotis DW01T and Shewanella algae ATCC 51192T. Phenotypic characteristics enabled strain C4T to be distinguished from S. haliotis and S. algae. On the basis of the data presented in this study, strain C4T represents a novel species, for which the name Shewanella marina sp. nov. is proposed. The type strain is C4T (=KCTC 22185T=JCM 15074T).
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Affiliation(s)
- Seong Chan Park
- Department of Biology, Sunchon National University, Suncheon 540-742, Republic of Korea
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37
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Freese E, Rütters H, Köster J, Rullkötter J, Sass H. Gammaproteobacteria as a possible source of eicosapentaenoic acid in anoxic intertidal sediments. MICROBIAL ECOLOGY 2009; 57:444-454. [PMID: 18777187 DOI: 10.1007/s00248-008-9443-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Accepted: 08/18/2008] [Indexed: 05/26/2023]
Abstract
Eicosapentaenoic acid (EPA; n-20:5omega3) was found to be a constituent of phospholipids in three mesophilic strains of Gammaproteobacteria, which were isolated from anoxic most probable number series prepared with sediments from an intertidal flat of the German North Sea coast. Their partial 16S rRNA gene sequences identified the isolates as close relatives of Shewanella colwelliana, Vibrio splendidus, and Photobacterium lipolyticum. So far, eicosapentaenoic acid has mainly been reported to occur in eukaryotes and some piezophilic or psychrophilic bacteria. With decreasing temperature, relative contents of EPA (up to 14% of total fatty acids) increased in all strains. Additionally, Shewanella and Vibrio spp. showed a significant increase in monounsaturated fatty acids with lower growth temperature. Analysis of the phospholipid compositions revealed that EPA was present in all three major phospholipid types, namely, phosphatidyl glycerol (PG), cardiolipin and phosphatidyl ethanolamine (PE). However, EPA was enriched in PG and cardiolipin relative to PE. In the tidal flat sediments from which the isolates were obtained, substantial amounts of EPA-containing PG were detected, whereas other typical microeukaryotic phospholipids-being also a possible source of EPA-were abundant at the sediment surface but were present in clearly lower amounts in the anoxic layers beneath 5 cm depth. Therefore, the EPA-containing PG species in the deeper layers in these sediments may indicate the presence of Gammaproteobacteria closely related to the isolates. These bacteria appear to be an important source of EPA in buried, anoxic sediments beneath the layers harboring significant populations of benthic eukaryotes.
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Affiliation(s)
- Elke Freese
- Institute of Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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38
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Hosoya S, Suzuki S, Adachi K, Matsuda S, Kasai H. Paramoritella alkaliphila gen. nov., sp. nov., a member of the family Moritellaceae isolated in the Republic of Palau. Int J Syst Evol Microbiol 2009; 59:411-6. [DOI: 10.1099/ijs.0.65809-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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39
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Khalid A, Arshad M, Crowley DE. Decolorization of azo dyes by Shewanella sp. under saline conditions. Appl Microbiol Biotechnol 2008; 79:1053-9. [DOI: 10.1007/s00253-008-1498-y] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 04/07/2008] [Accepted: 04/08/2008] [Indexed: 11/30/2022]
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40
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Cristóbal HA, Breccia JD, Abate CM. Isolation and molecular characterization of Shewanella sp. G5, a producer of cold-active beta-D-glucosidases. J Basic Microbiol 2008; 48:16-24. [PMID: 18247390 DOI: 10.1002/jobm.200700146] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
beta -Glucosidase is a highly desired glycosidase, especially for hydrolysis of glycoconjugated precursors in musts and wines for the release of active aromatic compounds. A Shewanella sp. G5 strain was isolated from the intestinal content of benthonic organism (Munida subrrugosa) from different coastal areas of the Beagle Channel, Tierra del Fuego (Argentina). This marine bacterium was able to grow at a temperature range between 4 to 20 degrees C using different beta-glycoside substrates, such as cellobiose, as carbon source. In this work, the Shewanella sp. G5 strain exhibited high beta-glucosidase activity on plate at low temperature (4 and 20 degrees C). Two genes encoding different cold-active beta-glucosidases were amplified and sequenced and the nucleotide sequences were submitted to the GenBank. 16S rDNA and gyrB gene sequences were used for the molecular characterization of Shewanella sp. G5.
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Affiliation(s)
- Héctor Antonio Cristóbal
- Planta Piloto de Procesos Industriales y Microbiológicos, CONICET, Av. Belgrano y Pje, Caseros, Tucumán, Argentina
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41
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Bodor A, Elxnat B, Thiel V, Schulz S, Wagner-Döbler I. Potential for luxS related signalling in marine bacteria and production of autoinducer-2 in the genus Shewanella. BMC Microbiol 2008; 8:13. [PMID: 18215278 PMCID: PMC2233627 DOI: 10.1186/1471-2180-8-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Accepted: 01/23/2008] [Indexed: 12/27/2022] Open
Abstract
Background The autoinducer-2 (AI-2) group of signalling molecules are produced by both Gram positive and Gram negative bacteria as the by-product of a metabolic transformation carried out by the LuxS enzyme. They are the only non species-specific quorum sensing compounds presently known in bacteria. The luxS gene coding for the AI-2 synthase enzyme was found in many important pathogens. Here, we surveyed its occurrence in a collection of 165 marine isolates belonging to abundant marine phyla using conserved degenerated PCR primers and sequencing of selected positive bands to determine if the presence of the luxS gene is phylogenetically conserved or dependent on the habitat. Results The luxS gene was not present in any of the Alphaproteobacteria (n = 71) and Bacteroidetes strains (n = 29) tested; by contrast, these bacteria harboured the sahH gene, coding for an alternative enzyme for the detoxification of S-adenosylhomocysteine (SAH) in the activated methyl cycle. Within the Gammaproteobacteria (n = 76), luxS was found in all Shewanella, Vibrio and Alteromonas isolates and some Pseudoalteromonas and Halomonas species, while sahH was detected in Psychrobacter strains. A number of Gammaproteobacteria (n = 27) appeared to have neither the luxS nor the sahH gene. We then studied the production of AI-2 in the genus Shewanella using the Vibrio harveyi bioassay. All ten species of Shewanella tested produced a pronounced peak of AI-2 towards the end of the exponential growth phase in several media investigated. The maximum of AI-2 activity was different in each Shewanella species, ranging from 4% to 46% of the positive control. Conclusion The data are consistent with those of fully sequenced bacterial genomes and show that the potential for luxS related signalling is dependent on phylogenetic affiliation rather than ecological niche and is largest in certain groups of Gammaproteobacteria in the marine environment. This is the first report on AI-2 production in Shewanella species; its signalling role in these organisms remains to be elucidated.
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Affiliation(s)
- Agnes Bodor
- Helmholtz-Center for Infection Research, Group Microbial Communication, Division of Cell Biology, Inhoffenstr, 7, 38124 Braunschweig, Germany.
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Abstract
The shewanellae are aquatic microorganisms with worldwide distribution. Their hallmark features include unparalleled respiratory diversity and the capacity to thrive at low temperatures. As a genus the shewanellae are physiologically diverse, and this review provides an overview of the varied roles they serve in the environment and describes what is known about how they might survive in such extreme and harsh environments. In light of their fascinating physiology, these organisms have several biotechnological uses, from bioremediation of chlorinated compounds, radionuclides, and other environmental pollutants to energy-generating biocatalysis. The ecology and biotechnology of these organisms are intertwined, with genomics playing a key role in our understanding of their physiology.
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Affiliation(s)
- Heidi H Hau
- Department of Microbiology and The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, USA
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43
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Significance of antioxidative functions of eicosapentaenoic and docosahexaenoic acids in marine microorganisms. Appl Environ Microbiol 2007; 74:570-4. [PMID: 18065628 DOI: 10.1128/aem.02256-07] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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44
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Kim D, Baik KS, Kim MS, Jung BM, Shin TS, Chung GH, Rhee MS, Seong CN. Shewanella haliotis sp. nov., isolated from the gut microflora of abalone, Haliotis discus hannai. Int J Syst Evol Microbiol 2007; 57:2926-2931. [DOI: 10.1099/ijs.0.65257-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A motile, rod-shaped, pink–orange pigmented bacterium, designated strain DW01T, was isolated from the gut microflora of abalone collected from the South Sea (Republic of Korea). Cells were Gram-negative, facultatively anaerobic, catalase- and oxidase-positive. The major fatty acids were iso-C15 : 0 (17.7 %), C16 : 0 (13.4 %), iso-C15 : 0 2-OH and/or C16 : 1
ω7c (12.5 %) and C17 : 1
ω8c (10.7 %). The DNA G+C content was 53.7 mol%. A phylogenetic tree based on the 16S rRNA gene sequences showed that strain DW01T forms a lineage of the genus Shewanella and is closely related to Shewanella algae ATCC 51192T (98.3 % sequence similarity) and to other members of the genus Shewanella (91.0–94.9 %). The phenotypic characteristics and DNA–DNA hybridization relatedness data indicate that strain DW01T should be distinguished from S. algae ATCC 51192T. On the basis of the data presented in this study, strain DW01T represents a novel species, for which the name Shewanella haliotis sp. nov. is proposed. The type strain is DW01T (=KCTC 12896T=JCM 14758T).
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Affiliation(s)
- Duwoon Kim
- Division of Food Science and Aqualife Medicine, Chonnam National University, Yeosu 550-749, Republic of Korea
| | - Keun Sik Baik
- Department of Biology, College of Natural Sciences, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Mi Sun Kim
- Department of Biology, College of Natural Sciences, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Bok-Mi Jung
- Division of Food Science and Aqualife Medicine, Chonnam National University, Yeosu 550-749, Republic of Korea
| | - Tai-Sun Shin
- Division of Food Science and Aqualife Medicine, Chonnam National University, Yeosu 550-749, Republic of Korea
| | - Gyu-Hwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu 550-749, Republic of Korea
| | - Moon Soo Rhee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-600, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Natural Sciences, Sunchon National University, Suncheon 540-742, Republic of Korea
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45
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Maran BAV, Iwamoto E, Okuda J, Matsuda S, Taniyama S, Shida Y, Asakawa M, Ohtsuka S, Nakai T, Boxshall GA. Isolation and characterization of bacteria from the copepod Pseudocaligus fugu ectoparasitic on the panther puffer Takifugu pardalis with the emphasis on TTX. Toxicon 2007; 50:779-90. [PMID: 17698158 DOI: 10.1016/j.toxicon.2007.06.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 06/13/2007] [Accepted: 06/13/2007] [Indexed: 11/25/2022]
Abstract
A total of 50 bacterial isolates was obtained from the copepod Pseudocaligus fugu, which is a common parasite, collected from the body surface of the panther puffer Takifugu pardalis. On the basis of colony characteristics, these bacterial isolates were grouped into six types, of which only two (Types-I and -II) showed a high affinity for adhesion to the carapace of the banana shrimp Penaeus merguiensis. These two types of adhesive bacteria were identified through 16S rRNA sequence analysis as Shewanella woodyi (Type-I) and Roseobacter sp. (Type-II). Representative isolates of these two adhesive bacteria were examined for tetrodotoxin (TTX) production by high-performance liquid chromatography (HPLC)-fluorometric system, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). It was rather unexpectedly revealed that TTX and anhydroTTX were present in the supernatant of culture of the Type-II isolate Roseobacter sp.
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Affiliation(s)
- B A Venmathi Maran
- Takehara Marine Science Station, Setouchi Field Science Center, Graduate School of Biosphere Science, Hiroshima University, 5-8-1 Minato-machi, Takehara 725 0024, Japan.
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46
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Yang SH, Lee JH, Ryu JS, Kato C, Kim SJ. Shewanella donghaensis sp. nov., a psychrophilic, piezosensitive bacterium producing high levels of polyunsaturated fatty acid, isolated from deep-sea sediments. Int J Syst Evol Microbiol 2007; 57:208-212. [PMID: 17267951 DOI: 10.1099/ijs.0.64469-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, motile, rod-shaped, psychrophilic bacterium, LT17T, was isolated from deep-sea sediments (3300 m depth) of the East Sea (Sea of Japan). Optimal growth of LT17T requires the presence of 2.5 % (w/v) NaCl, a pH of 7.0–7.5 and a temperature of 17 °C. The isolate grows optimally under a hydrostatic pressure of 10 MPa and growth is possible between 0.1 and <30 MPa. The novel strain is positive in tests for catalase, oxidase, lipase, β-glucosidase and gelatinase activities and reduces nitrate to nitrate. The predominant cellular fatty acids are iso-C13 : 0, iso-C15 : 0, C16 : 0, C16 : 1ω7 and C20 : 5ω3. The DNA G+C content of strain LT17T is 38.8 mol%. Phylogenetic analysis of 16S rRNA gene sequences places this bacterium in the class Gammaproteobacteria, within the genus Shewanella. The closest relatives of strain LT17T are Shewanella japonica (97.8 % gene sequence similarity), Shewanella pacifica (97.5 %), Shewanella olleyana (96.8 %), Shewanella frigidimarina (96.5 %) and Shewanella gelidimarina (95.4 %). The DNA–DNA hybridization levels between the novel isolate and its closest known phylogenetic relatives, S. japonica and S. pacifica, are lower than 14 %. On the basis of this polyphasic evidence, strain LT17T represents a novel species of the genus Shewanella, for which the name Shewanella donghaensis sp. nov. is proposed. The type strain is LT17T (=KCTC 10635BPT=JCM 12524T).
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MESH Headings
- Bacterial Proteins/analysis
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Enzymes/analysis
- Fatty Acids/analysis
- Fatty Acids, Unsaturated/biosynthesis
- Genes, rRNA/genetics
- Geologic Sediments/microbiology
- Hydrogen-Ion Concentration
- Hydrostatic Pressure
- Japan
- Molecular Sequence Data
- Movement
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Saline Solution, Hypertonic
- Seawater/microbiology
- Sequence Analysis, DNA
- Shewanella/classification
- Shewanella/cytology
- Shewanella/isolation & purification
- Shewanella/metabolism
- Temperature
- Water Microbiology
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Affiliation(s)
- Sung-Hyun Yang
- Marine Biotechnology Research Centre, Korea Ocean Research & Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Centre, Korea Ocean Research & Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
| | - Ji-Sun Ryu
- Marine Biotechnology Research Centre, Korea Ocean Research & Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
| | - Chiaki Kato
- Research Program for Marine Biology and Ecology, Extremobiosphere Research Center, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Sang-Jin Kim
- Marine Biotechnology Research Centre, Korea Ocean Research & Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
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47
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Yang SH, Kwon KK, Lee HS, Kim SJ. Shewanella spongiae sp. nov., isolated from a marine sponge. Int J Syst Evol Microbiol 2006; 56:2879-2882. [PMID: 17158991 DOI: 10.1099/ijs.0.64540-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A psychrophilic bacterium, designated strain HJ039T, was isolated from a marine sponge collected in the East Sea of Korea (also known as the Sea of Japan). Cells were Gram-negative, motile and rod-shaped (1.8–3.54 μm×0.27–0.73 μm). Growth was observed between 5 and 26 °C (optimum 15 °C), at pH 5.0–8.5 (optimum pH 6.0–6.5) and in the presence of 0–6.0 % NaCl (optimum 2.0 %). The 16S rRNA gene sequence of strain HJ039T showed high levels of similarity (93.7–95.4 %) with members of the genus Shewanella, especially with Shewanella gaetbuli TF-27T (95.2 %), Shewanella decolorationis S12T (94.9 %), Shewanella putrefaciens LMG 26268T (94.6 %), Shewanella hafniensis P010T (94.6 %), Shewanella algae ATCC 51192T (94.5 %) and Shewanella kaireitica c931T (94.5 %). However, phylogenetic analysis revealed that strain HJ039T shared a phyletic line with S. algae and Shewanella amazonensis. The major respiratory quinone was Q-8. The DNA G+C content was 52.8 mol%. The major fatty acids were i-13 : 0 (8.5 %), 15 : 0 (4.2 %), i-15 : 0 (23.2 %), i-15 : 1 (7.9 %), 16 : 0 (8.7 %), 16 : 1ω7 (21.0 %) and 17 : 1ω8 (6.4 %). From this polyphasic taxonomic evidence, strain HJ039T is considered to represent a novel species of the genus Shewanella, for which the name Shewanella spongiae sp. nov. is proposed. The type strain is HJ039T (=KCCM 42304T=JCM 13830T).
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Affiliation(s)
- Sung-Hyun Yang
- Marine and Extreme Genome Research Center, Korea Ocean Research and Development Institute, PO Box 29, Ansan, 425-600, Republic of Korea
| | - Kae Kyoung Kwon
- Marine and Extreme Genome Research Center, Korea Ocean Research and Development Institute, PO Box 29, Ansan, 425-600, Republic of Korea
| | - Hee-Soon Lee
- Marine and Extreme Genome Research Center, Korea Ocean Research and Development Institute, PO Box 29, Ansan, 425-600, Republic of Korea
| | - Sang-Jin Kim
- Marine and Extreme Genome Research Center, Korea Ocean Research and Development Institute, PO Box 29, Ansan, 425-600, Republic of Korea
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48
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Lee OO, Lau SCK, Tsoi MMY, Li X, Plakhotnikova I, Dobretsov S, Wu MCS, Wong PK, Weinbauer M, Qian PY. Shewanella irciniae sp. nov., a novel member of the family Shewanellaceae, isolated from the marine sponge Ircinia dendroides in the Bay of Villefranche, Mediterranean Sea. Int J Syst Evol Microbiol 2006; 56:2871-2877. [PMID: 17158990 DOI: 10.1099/ijs.0.64562-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain UST040317-058T, comprising non-pigmented, rod-shaped, facultatively anaerobic, Gram-negative cells that are motile by means of single polar flagella, was isolated from the surface of a marine sponge (Ircinia dendroides) collected from the Mediterranean Sea. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a separate cluster with the recognized bacterium Shewanella algae IAM 14159T, with which it showed a sequence similarity of 95.0 %. The sequence similarity between strain UST040317-058T and its other (six) closest relatives ranged from 91.6 to 93.8 %. Strain UST040317-058T showed oxidase, catalase and gelatinase activities. The typical respiratory quinones for shewanellas, menaquinone MK-7 and ubiquinones Q-7 and Q-8, were also detected. The predominant fatty acids in strain UST040317-058T were i15 : 0, 16 : 0, 17 : 1ω8c and summed feature 3 (comprising i15 : 0 2-OH and/or 16 : 1ω7c), altogether representing 56.9 % of the total. The DNA G+C content was 39.9 mol%. The strain could be differentiated from other Shewanella species by its inability to reduce nitrate or produce H2S and by 10–22 additional phenotypic characteristics. On the basis of the phylogenetic and phenotypic data presented in this study, strain UST040317-058T represents a novel species in the genus Shewanella, for which the name Shewanella irciniae sp. nov. is proposed. The type strain is UST040317-058T (=JCM 13528T=NRRL B-41466T).
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Affiliation(s)
- On On Lee
- Coastal Marine Laboratory/Department of Biology, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, People's Republic of China
| | - Stanley C K Lau
- Division of Environmental Science and Engineering, The National University of Singapore, Singapore
| | - Mandy M Y Tsoi
- Coastal Marine Laboratory/Department of Biology, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, People's Republic of China
| | - Xiancui Li
- Coastal Marine Laboratory/Department of Biology, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, People's Republic of China
| | - Ioulia Plakhotnikova
- Coastal Marine Laboratory/Department of Biology, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, People's Republic of China
| | - Sergey Dobretsov
- Coastal Marine Laboratory/Department of Biology, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, People's Republic of China
| | - Madeline C S Wu
- Coastal Marine Laboratory/Department of Biology, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, People's Republic of China
| | - Po-Keung Wong
- Department of Biology, The Chinese University of Hong Kong, Shatin, N. T., Hong Kong SAR, People's Republic of China
| | - Markus Weinbauer
- Microbial Ecology and Biogeochemistry Group, Laboratoire d'Océanographie de Villefranche-sur-Mer, Villefranche-sur-Mer, France
| | - Pei-Yuan Qian
- Coastal Marine Laboratory/Department of Biology, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, People's Republic of China
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Miyazaki M, Nogi Y, Usami R, Horikoshi K. Shewanella surugensis sp. nov., Shewanella kaireitica sp. nov. and Shewanella abyssi sp. nov., isolated from deep-sea sediments of Suruga Bay, Japan. Int J Syst Evol Microbiol 2006; 56:1607-1613. [PMID: 16825637 DOI: 10.1099/ijs.0.64173-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six strains representing three novel species were isolated from deep-sea sediment in Suruga Bay, Japan, at a depth of 2406-2409 m. On the basis of 16S rRNA gene sequence analysis, the isolated strains, c931(T), c941(T), d943, c952, d954 and c959(T), are closely affiliated with members of the genus Shewanella. The hybridization values for DNA-DNA relatedness between these strains and Shewanella reference strains were significantly lower than that which is accepted as the phylogenetic definition of a species. On the basis of their distinct taxonomic characteristics, the isolated strains represent three novel Shewanella species, for which the names Shewanella kaireitica sp. nov. (three strains, type strain c931(T)=JCM 11836(T)=DSM 17170(T)), Shewanella abyssi sp. nov. (two strains, type strain c941(T)=JCM 13041(T)=DSM 17171(T)) and Shewanella surugensis sp. nov. (type strain c959(T)=JCM 11835(T)=DSM 17177(T)) are proposed.
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MESH Headings
- Bacterial Typing Techniques
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Genes, rRNA
- Geologic Sediments/microbiology
- Japan
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Shewanella/classification
- Shewanella/cytology
- Shewanella/genetics
- Shewanella/isolation & purification
- Water Microbiology
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Affiliation(s)
- Masayuki Miyazaki
- Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yuichi Nogi
- Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ron Usami
- Faculty of Engineering, Toyo University, 2100 Kuzirai, Kawagoe 350-8585, Japan
| | - Koki Horikoshi
- Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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50
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Gao H, Obraztova A, Stewart N, Popa R, Fredrickson JK, Tiedje JM, Nealson KH, Zhou J. Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean. Int J Syst Evol Microbiol 2006; 56:1911-1916. [PMID: 16902030 DOI: 10.1099/ijs.0.64354-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel marine bacterial strain, PV-4(T), isolated from a microbial mat located at a hydrothermal vent of Loihi Seamount in the Pacific Ocean, has been characterized. This micro-organism is orangey in colour, Gram-negative, polarly flagellated, facultatively anaerobic and psychrotolerant (temperature range, 0-42 degrees C). No growth was observed with nitrate, nitrite, DMSO or thiosulfate as the electron acceptor and lactate as the electron donor. The major fatty acid detected in strain PV-4(T) was iso-C(15 : 0). Strain PV-4(T) had ubiquinones consisting mainly of Q-7 and Q-8, and possessed menaquinone MK-7. The DNA G+C content of the strain was 53.8 mol% and the genome size was about 4.5 Mbp. Phylogenetic analyses based on 16S rRNA gene sequences placed PV-4(T) within the genus Shewanella. PV-4(T) exhibited 16S rRNA gene sequence similarity levels of 99.6 and 97.5 %, respectively, with respect to the type strains of Shewanella aquimarina and Shewanella marisflavi. DNA from strain PV-4(T) showed low mean levels of relatedness to the DNAs of S. aquimarina (50.5 %) and S. marisflavi (8.5 %). On the basis of phylogenetic and phenotypic characteristics, the bacterium was classified in the genus Shewanella within a distinct novel species, for which the name Shewanella loihica sp. nov. is proposed. The type strain is PV-4(T) (=ATCC BAA-1088(T)=DSM 17748(T)).
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Affiliation(s)
- Haichun Gao
- Stephenson Research and Technology Center, Institute for Environmental Genomics, University of Oklahoma, 101 David L. Boren Boulevard, Norman, OK 73019, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Anna Obraztova
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Nathan Stewart
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Radu Popa
- Department of Biology, Portland State University, Portland, OR, USA
| | | | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Kenneth H Nealson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jizhong Zhou
- Stephenson Research and Technology Center, Institute for Environmental Genomics, University of Oklahoma, 101 David L. Boren Boulevard, Norman, OK 73019, USA
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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