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Chen H, Dai J, Yu P, Wang X, Wang J, Li Y, Wang S, Li S, Qiu D. Parathalassolituus penaei gen. nov., sp. nov., a novel member of the family Oceanospirillaceae isolated from a coastal shrimp pond in Guangxi, PR China. Int J Syst Evol Microbiol 2023; 73. [PMID: 37185048 DOI: 10.1099/ijsem.0.005867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
A Gram-stain-negative, strictly aerobic, rod-shaped and motile bacterium with bipolar flagella, designated G-43T, was isolated from a surface seawater sample collected from an aquaculture in Guangxi, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain G-43T was most closely related to the family Oceanospirillaceae and distantly to the most closely related genera Venatorbacter and Thalassolituus (95.52 % and 94.45-94.76 % 16S rRNA gene sequence similarity, respectively), while similarity values to other Oceanospirillaceae type strains were lower than 94.0 %. Strain G-43T was found to grow at 4-30 °C (optimum, 25-28 °C), pH 6-9.0 (optimum, pH 7.0) and with 0-4.0 % NaCl (w/v; optimum at 2 % NaCl). Chemotaxonomic analysis of strain G-43T indicated that the sole respiratory quinone was ubiquinone-8, the predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), and the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, aminolipid, diphosphatidylglycerol, phospholipids and an unidentified lipid. The G+C content of the genomic DNA was 55.4 mol%. The phylogenetic, genotypic, phenotypic and chemotaxonomic data demonstrate that strain G-43T represents a novel species in a novel genus within the family Oceanospirillaceae, for which the name Parathalassolituus penaei gen. nov., sp. nov. is proposed. Strain G-43T (=KCTC 72750T= CCTCC AB 2022321T) is the type and only strain of Parathalassolituus penaei.
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Affiliation(s)
- Han Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
- Jingchu University of Technology, Jingmen, 448000, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jingcheng Dai
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, PR China
| | - Ping Yu
- Sinochem Zhuhai Petrochemical Terminal Co. Ltd., Zhuhai, 519050, PR China
| | - Xin Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jing Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yan Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
- China University of Geosciences (CUG), Wuhan, 430074, PR China
| | - Shanhui Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shuyang Li
- Wuhan Ammunition Life-tech Co. Ltd., Wuhan, 430000, PR China
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
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2
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Unzueta-Martínez A, Scanes E, Parker LM, Ross PM, O'Connor W, Bowen JL. Microbiomes of the Sydney Rock Oyster are acquired through both vertical and horizontal transmission. Anim Microbiome 2022; 4:32. [PMID: 35590396 PMCID: PMC9118846 DOI: 10.1186/s42523-022-00186-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/07/2022] [Indexed: 11/10/2022] Open
Abstract
Background The term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a unit of selection in evolution. To demonstrate that natural selection acts on the hologenome, a significant portion of the associated microbial genomes should be transferred between generations. Using the Sydney Rock Oyster (Saccostrea glomerata) as a model, we tested if the microbes of this broadcast spawning species could be passed down to the next generation by conducting single parent crosses and tracking the microbiome from parent to offspring and throughout early larval stages using 16S rRNA gene amplicon sequencing. From each cross, we sampled adult tissues (mantle, gill, stomach, gonad, eggs or sperm), larvae (D-veliger, umbo, eyed pediveliger, and spat), and the surrounding environment (water and algae feed) for microbial community analysis. Results We found that each larval stage has a distinct microbiome that is partially influenced by their parental microbiome, particularly the maternal egg microbiome. We also demonstrate the presence of core microbes that are consistent across all families, persist throughout early life stages (from eggs to spat), and are not detected in the microbiomes of the surrounding environment. In addition to the core microbiomes that span all life cycle stages, there is also evidence of environmentally acquired microbial communities, with earlier larval stages (D-veliger and umbo), more influenced by seawater microbiomes, and later larval stages (eyed pediveliger and spat) dominated by microbial members that are specific to oysters and not detected in the surrounding environment. Conclusion Our study characterized the succession of oyster larvae microbiomes from gametes to spat and tracked selected members that persisted across multiple life stages. Overall our findings suggest that both horizontal and vertical transmission routes are possible for the complex microbial communities associated with a broadcast spawning marine invertebrate. We demonstrate that not all members of oyster-associated microbiomes are governed by the same ecological dynamics, which is critical for determining what constitutes a hologenome. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00186-9.
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Affiliation(s)
- Andrea Unzueta-Martínez
- Department of Marine and Environmental Science, Northeastern University, Nahant, MA, 01908, USA. .,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Elliot Scanes
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Laura M Parker
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Kensington, NSW, 2052, Australia
| | - Pauline M Ross
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Wayne O'Connor
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, NSW, 2316, Australia
| | - Jennifer L Bowen
- Department of Marine and Environmental Science, Northeastern University, Nahant, MA, 01908, USA
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3
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Aoki M, Miyashita Y, Tran PT, Okuno Y, Watari T, Yamaguchi T. Enrichment of marine manganese-oxidizing microorganisms using polycaprolactone as a solid organic substrate. Biotechnol Lett 2021; 43:813-823. [PMID: 33496920 DOI: 10.1007/s10529-021-03088-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/13/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Heterotrophic manganese (Mn)-oxidizing microorganisms responsible for biogenic manganese oxide (Bio-MnOx) production are fastidious. Their enrichment is not easily accomplished by merely adding a soluble organic substrate to non-sterile mixed cultures. The objective of this study was to evaluate polycaprolactone (PCL), an aliphatic polyester, as an effective solid organic substrate for the enrichment of marine Mn-oxidizing microorganisms. RESULTS We successfully obtained marine microbial enrichment with the capacity for dissolved Mn removal and MnOx production using PCL as a solid organic substrate. The removal of dissolved Mn by the Mn-oxidizing enrichment culture followed first-order kinetics with a rate constant of 0.014 h-1. 16S rRNA gene amplicon sequencing analysis revealed that the Mn-oxidizing enrichment culture was highly dominated by operational taxonomic units related to the bacterial phyla Cyanobacteria, Planctomycetes, and Proteobacteria. CONCLUSIONS Our data demonstrate that PCL can serve as a potential substrate to enrich Mn-oxidizing microorganisms with the ability to produce MnOx under marine conditions.
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Affiliation(s)
- Masataka Aoki
- Department of Civil Engineering, National Institute of Technology, Wakayama College, 77 Noshima, Nada, Gobo, Wakayama, 644-0023, Japan.
| | - Yukina Miyashita
- Department of Civil Engineering, National Institute of Technology, Wakayama College, 77 Noshima, Nada, Gobo, Wakayama, 644-0023, Japan
| | - P Thao Tran
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Yoshiharu Okuno
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Gobo, Wakayama, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan.,Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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Thomson NM, Ferreira JL, Matthews-Palmer TR, Beeby M, Pallen MJ. Giant flagellins form thick flagellar filaments in two species of marine γ-proteobacteria. PLoS One 2018; 13:e0206544. [PMID: 30462661 PMCID: PMC6248924 DOI: 10.1371/journal.pone.0206544] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/15/2018] [Indexed: 01/04/2023] Open
Abstract
Flagella, the primary means of motility in bacteria, are helical filaments that function as microscopic propellers composed of thousands of copies of the protein flagellin. Here, we show that many bacteria encode “giant” flagellins, greater than a thousand amino acids in length, and that two species that encode giant flagellins, the marine γ-proteobacteria Bermanella marisrubri and Oleibacter marinus, produce monopolar flagellar filaments considerably thicker than filaments composed of shorter flagellin monomers. We confirm that the flagellum from B. marisrubri is built from its giant flagellin. Phylogenetic analysis reveals that the mechanism of evolution of giant flagellins has followed a stepwise process involving an internal domain duplication followed by insertion of an additional novel insert. This work illustrates how “the” bacterial flagellum should not be seen as a single, idealised structure, but as a continuum of evolved machines adapted to a range of niches.
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Affiliation(s)
| | - Josie L. Ferreira
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
| | - Mark J. Pallen
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, United Kingdom
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5
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Bacterial Flagellins: Does Size Matter? Trends Microbiol 2017; 26:575-581. [PMID: 29258714 DOI: 10.1016/j.tim.2017.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/20/2017] [Accepted: 11/29/2017] [Indexed: 01/31/2023]
Abstract
The bacterial flagellum is the principal organelle of motility in bacteria. Here, we address the question of size when applied to the chief flagellar protein flagellin and the flagellar filament. Surprisingly, nature furnishes multiple examples of 'giant flagellins' greater than a thousand amino acids in length, with large surface-exposed hypervariable domains. We review the contexts in which these giant flagellins occur, speculate as to their functions, and highlight the potential for biotechnology to build on what nature provides.
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6
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Sidhu C, Thakur S, Sharma G, Tanuku NRS, Pinnaka AK. Oceanospirillum sanctuarii sp. nov., isolated from a sediment sample. Int J Syst Evol Microbiol 2017; 67:3428-3434. [PMID: 28829018 DOI: 10.1099/ijsem.0.002132] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-staining-negative, spiral-shaped, pale-yellow, non-sporulating, motile, aerobic bacterium, designated strain AK56T, was isolated from a sediment sample collected at the Coringa Wildlife Sanctuary, India. Colonies on marine agar were circular, pale yellow, shiny, translucent, 1-2 mm in diameter, convex and had an entire margin. The major fatty acids included C16 : 1, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c. Polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, one unidentified phospholipid and five unidentified lipids. DNA-DNA hybridization between strain AK56T and Oceanospirillum linum LMG 5214T and 'Oceanospirillum nioense ' NIO-S6 showed relatedness values of 39.91 and 23.62 %, respectively. The DNA G+C content of strain AK56T was found to be 50.3 mol%. A sequence similarity search for the 16S rRNA gene sequence revealed that O. linum and O. nioense were the nearest phylogenetic neighbours, with a pair-wise sequence similarity of 98.9 and 98.2 %, respectively. Phylogenetic analysis also showed the formation of a cluster including strain AK56T with close relative O. linum and O. nioense. Based on the observed phenotypic, chemotaxonomic characteristics and phylogenetic analysis, strain AK56T is described in this study as a novel species in the genus Oceanospirillum, for which the name Oceanospirillum sanctuarii sp. nov. is proposed. The type strain of Oceanospirillumsanctuarii is AK56T (=MTCC 12005T=JCM 19193T=KCTC 52973T).
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Affiliation(s)
- Chandni Sidhu
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Suresh Thakur
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Gunjan Sharma
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Naga Radha Srinivas Tanuku
- CSIR-National Institute of Oceanography, Regional Centre, 176, Lawsons Bay Colony, Visakhapatnam-530017, India
| | - Anil Kumar Pinnaka
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
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7
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Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. Proc Natl Acad Sci U S A 2017; 114:7432-7437. [PMID: 28652349 DOI: 10.1073/pnas.1703424114] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Deepwater Horizon (DWH) accident released an estimated 4.1 million barrels of oil and 1010 mol of natural gas into the Gulf of Mexico, forming deep-sea plumes of dispersed oil droplets and dissolved gases that were largely degraded by bacteria. During the course of this 3-mo disaster a series of different bacterial taxa were enriched in succession within deep plumes, but the metabolic capabilities of the different populations that controlled degradation rates of crude oil components are poorly understood. We experimentally reproduced dispersed plumes of fine oil droplets in Gulf of Mexico seawater and successfully replicated the enrichment and succession of the principal oil-degrading bacteria observed during the DWH event. We recovered near-complete genomes, whose phylogeny matched those of the principal biodegrading taxa observed in the field, including the DWH Oceanospirillales (now identified as a Bermanella species), multiple species of Colwellia, Cycloclasticus, and other members of Gammaproteobacteria, Flavobacteria, and Rhodobacteria. Metabolic pathway analysis, combined with hydrocarbon compositional analysis and species abundance data, revealed substrate specialization that explained the successional pattern of oil-degrading bacteria. The fastest-growing bacteria used short-chain alkanes. The analyses also uncovered potential cooperative and competitive relationships, even among close relatives. We conclude that patterns of microbial succession following deep ocean hydrocarbon blowouts are predictable and primarily driven by the availability of liquid petroleum hydrocarbons rather than natural gases.
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8
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Arahal DR, Lucena T, Macián MC, Ruvira MA, González JM, Lekumberri I, Pinhassi J, Pujalte MJ. Marinomonas blandensis sp. nov., a novel marine gammaproteobacterium. Int J Syst Evol Microbiol 2016; 66:5544-5549. [PMID: 27902199 DOI: 10.1099/ijsem.0.001554] [Citation(s) in RCA: 8] [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 novel Gram-staining-negative, chemoorganotrophic, moderately halophilic, strictly aerobic bacterium, strain MED121T, was isolated from a seawater sample collected at the Blanes Bay Microbial Observatory in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to Marinomonas dokdonensis and other Marinomonas species (96.3 and 93.3-95.7 % sequence similarities, respectively), within the family Oceanospirillaceae. Strain MED121T was included into a whole-genome sequencing study and, subsequently, it was characterized using a polyphasic taxonomic approach. It was found to be oxidase and catalase positive, its cells are cocci to short rods, it does not ferment carbohydrates and does not reduce nitrate to nitrite or gas and it requires at least 2.5 % (w/v) marine salts and tolerates up to 7 % (w/v) salts. Its major cellular fatty acids in order of abundance are C16 : 1ω7c/C16 : 1ω6c, C18 : 1ω7c, C16 : 0 and C10 : 0 3-OH. Its genome had an approximate length of 5.1 million bases and a DNA G+C content equal to 40.9 mol%. Analysis of the annotated genes reveals the capacity for the synthesis of ubiquinone 8 (Q8) and the polar lipids phosphatidylglycerol and phosphatidylethanolamine, in agreement with other members of the genus. All the data collected supported the creation of a novel species to accommodate this bacterium, for which the name Marinomonas blandensis sp. nov. is proposed. The type strain is MED121T (=CECT 7076T=LMG 29722T).
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Affiliation(s)
- David R Arahal
- Departamento de Microbiología y Ecología, Universitat de València, 46100 Burjassot (València), Spain.,Colección Española de Cultivos Tipo (CECT), Universitat de València, 46980 Paterna (València), Spain
| | - Teresa Lucena
- Colección Española de Cultivos Tipo (CECT), Universitat de València, 46980 Paterna (València), Spain
| | - M Carmen Macián
- Colección Española de Cultivos Tipo (CECT), Universitat de València, 46980 Paterna (València), Spain
| | - María A Ruvira
- Colección Española de Cultivos Tipo (CECT), Universitat de València, 46980 Paterna (València), Spain
| | - José M González
- Departament of Microbiology, University of La Laguna, La Laguna ES-38200, Spain
| | - Itziar Lekumberri
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Kalmar SE-39182, Sweden
| | - María J Pujalte
- Departamento de Microbiología y Ecología, Universitat de València, 46100 Burjassot (València), Spain.,Colección Española de Cultivos Tipo (CECT), Universitat de València, 46980 Paterna (València), Spain
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9
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Brakstad OG, Throne-Holst M, Netzer R, Stoeckel DM, Atlas RM. Microbial communities related to biodegradation of dispersed Macondo oil at low seawater temperature with Norwegian coastal seawater. Microb Biotechnol 2015; 8:989-98. [PMID: 26485443 PMCID: PMC4621451 DOI: 10.1111/1751-7915.12303] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/19/2015] [Accepted: 05/28/2015] [Indexed: 11/29/2022] Open
Abstract
The Deepwater Horizon (DWH) accident in 2010 created a deepwater plume of small oil droplets from a deepwater well in the Mississippi Canyon lease block 252 ('Macondo oil'). A novel laboratory system was used in the current study to investigate biodegradation of Macondo oil dispersions (10 μm or 30 μm median droplet sizes) at low oil concentrations (2 mg l(-1)) in coastal Norwegian seawater at a temperature of 4-5°C. Whole metagenome analyses showed that oil biodegradation was associated with the successive increased abundances of Gammaproteobacteria, while Alphaproteobacteria (Pelagibacter) became dominant at the end of the experiment. Colwellia and Oceanospirillales were related to n-alkane biodegradation, while particularly Cycloclasticus and Marinobacter were associated with degradation of aromatic hydrocarbons (HCs). The larger oil droplet dispersions resulted in delayed sequential changes of Oceanospirillales and Cycloclasticus, related with slower degradation of alkanes and aromatic HCs. The bacterial successions associated with oil biodegradation showed both similarities and differences when compared with the results from DWH field samples and laboratory studies performed with deepwater from the Gulf of Mexico.
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Affiliation(s)
- Odd G Brakstad
- Department Applied Environmental Biology and Chemistry, SINTEF Materials and Chemistry, Environmental Technology, Trondheim, N-7465, Norway
| | - Mimmi Throne-Holst
- Department Applied Environmental Biology and Chemistry, SINTEF Materials and Chemistry, Environmental Technology, Trondheim, N-7465, Norway
| | - Roman Netzer
- Department Applied Environmental Biology and Chemistry, SINTEF Materials and Chemistry, Environmental Technology, Trondheim, N-7465, Norway
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10
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Li Y, Zhu H, Lai Q, Lei X, Zhang H, Chen Z, Zheng W, Tian Y, Xu H, Zheng T. Litoribrevibacter albus gen. nov. sp. nov., isolated from coastal seawater, Fujian Province, China. Antonie van Leeuwenhoek 2014; 106:911-8. [PMID: 25193025 DOI: 10.1007/s10482-014-0260-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/11/2014] [Indexed: 11/27/2022]
Abstract
A Gram-stain negative, short rod-shaped aerobic bacterium with flagella, designated strain Y32(T), was isolated from coastal seawater in Xiamen, Fujian Province of China. 16S rRNA gene sequence comparisons showed that strain Y32(T) is a member of the family Oceanospirillaceae, forming a distinct lineage with species of the genus Litoribacillus. The 16S rRNA gene sequence similarities between strain Y32(T) and other strains were all less than 94.0 %. Strain Y32(T) was found to grow optimally at 28 °C, at pH 7.0-8.0 and in the presence of 4-5 % (w/v) NaCl. The major fatty acids were identified as Summed Feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c, 49.4 %), C16:0 (17.7 %), C14:0 (6.9 %) and C18:1 ω9c (5.4 %). The major respiratory quinone was identified as ubiquinone-8 (Q-8). The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain Y32(T) was determined to be 55.6 mol%. According to its morphology, physiology, fatty acid composition, polar lipids composition and 16S rRNA gene sequence data, strain Y32(T) represents a novel species of a new genus in the family Oceanospirillaceae, for which the name Litoribrevibacter albus gen. nov. sp. nov. is proposed. The type strain of Litoribrevibacter albus is Y32(T) (=MCCC 1F01211(T)=NBRC 110071(T)).
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Affiliation(s)
- Yi Li
- Key Lab of the Ministry of Education for Coastal and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen, 361005, People's Republic of China
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11
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Raedts J, Lundgren M, Kengen SWM, Li JP, van der Oost J. A novel bacterial enzyme with D-glucuronyl C5-epimerase activity. J Biol Chem 2013; 288:24332-9. [PMID: 23824188 DOI: 10.1074/jbc.m113.476440] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycosaminoglycans are biologically active polysaccharides that are found ubiquitously in the animal kingdom. The biosynthesis of these complex polysaccharides involves complicated reactions that turn the simple glycosaminoglycan backbone into highly heterogeneous structures. One of the modification reactions is the epimerization of D-glucuronic acid to its C5-epimer L-iduronic acid, which is essential for the function of heparan sulfate. Although L-iduronic acid residues have been shown to exist in polysaccharides of some prokaryotes, there has been no experimental evidence for the existence of a prokaryotic D-glucuronyl C5-epimerase. This work for the first time reports on the identification of a bacterial enzyme with D-glucuronyl C5-epimerase activity. A gene of the marine bacterium Bermanella marisrubri sp. RED65 encodes a protein (RED65_08024) of 448 amino acids that has an overall 37% homology to the human D-glucuronic acid C5-epimerase. Alignment of this peptide with the human and mouse sequences revealed a 60% similarity at the carboxyl terminus. The recombinant protein expressed in Escherichia coli showed epimerization activity toward substrates generated from heparin and the E. coli K5 capsular polysaccharide, thereby providing the first evidence for bacterial D-glucuronyl C5-epimerase activity. These findings may eventually be used for modification of mammalian glycosaminoglycans.
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Affiliation(s)
- John Raedts
- Laboratory of Microbiology, Wageningen University, 6703 HB Wageningen, The Netherlands
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12
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Su J, Zhou Y, Lai Q, Li X, Dong P, Yang X, Zhang B, Zhang J, Zheng X, Tian Y, Zheng T. Sinobacterium caligoides gen. nov., sp. nov., a new member of the family
Oceanospirillaceae
isolated from the South China Sea, and emended description of
Amphritea japonica. Int J Syst Evol Microbiol 2013; 63:2095-2100. [DOI: 10.1099/ijs.0.030965-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain SCSWE24T, isolated from a seawater sample collected from the South China Sea. Cells of strain SCSWE24T were Gram-negative, rod-shaped, non-motile, moderately halophilic and capable of reducing nitrate to nitrite. Growth was observed at salinities from 1.5 to 4.5 % and at 4–37 °C; it was unable to degrade gelatin. The dominant fatty acids (>15 %) were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 50.4 %) and C16 : 0 (21.1 %). The G+C content of the chromosomal DNA was 58.8 mol%. 16S rRNA gene sequence comparisons showed that strain SCSWE24T was most closely related to an uncultured bacterium clone Tun3b.F5 (98 %; GenBank accession no. FJ169216), and showed 92 % similarity to an endosymbiont bacterium from the bone-eating worm Osedax mucofloris (clone Omu 9 c4791; FN773233). Levels of similarity between strain SCSWE24T and type strains of recognized species in the family
Oceanospirillaceae
were less than 93 %; the highest similarity was 92 %, to both
Amphritea japonica
JAMM 1866T and ‘Oceanicoccus sagamiensis’ PZ-5. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SCSWE24T formed a distinct evolutionary lineage within the family
Oceanospirillaceae
. Strain SCSWE24T was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data, strain SCSWE24T represents a novel species of a new genus, for which the name Sinobacterium caligoides gen. nov., sp. nov. is proposed. The type strain of Sinobacterium caligoides is SCSWE24T ( = CCTCC AB 209289T = LMG 25705T = MCCC 1F01088T). An emended description of
Amphritea japonica
is also provided.
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Affiliation(s)
- Jianqiang Su
- The Institute of Urban Environment (IUE), Chinese Academy of Sciences, Xiamen 361005, PR China
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the MOE for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Yanyan Zhou
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the MOE for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Xinyi Li
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the MOE for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Peiyan Dong
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the MOE for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Xiaoru Yang
- The Institute of Urban Environment (IUE), Chinese Academy of Sciences, Xiamen 361005, PR China
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the MOE for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Bangzhou Zhang
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the MOE for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Jinlong Zhang
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the MOE for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Xiaowei Zheng
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the MOE for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Yun Tian
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the MOE for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Tianling Zheng
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the MOE for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
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13
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Litoribacillus peritrichatus gen. nov. sp. nov., isolated from coastal sediment of an amphioxus breeding zone in Qingdao, China. Antonie van Leeuwenhoek 2012; 103:357-66. [DOI: 10.1007/s10482-012-9815-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 09/10/2012] [Indexed: 10/27/2022]
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14
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Oleispira lenta sp. nov., a novel marine bacterium isolated from Yellow sea coastal seawater in Qingdao, China. Antonie van Leeuwenhoek 2012; 101:787-94. [PMID: 22228140 DOI: 10.1007/s10482-011-9693-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 12/21/2011] [Indexed: 10/14/2022]
Abstract
The taxonomic position of strain DFH11(T), which was isolated from coastal seawater off Qingdao, People's Republic of China in 2007, was determined. Strain DFH11(T) comprised Gram-negative, motile, strictly aerobic spirilli that did not produce catalase. Comparative 16S rRNA gene sequence analysis revealed that strain DFH11(T) shared ~97.2, 93.3, 91.8, 91.7 and 91.5% sequence similarities with Oleispira antarctica, Spongiispira norvegica, Bermanella marisrubri, Oceaniserpentilla haliotis and Reinekea aestuarii, respectively. DNA-DNA hybridization experiments indicated that the strain was distinct from its closest phylogenetic neighbour, O. antarctica. The strain grew optimally in 2-3% (w/v) NaCl, at pH 5.0-10.0 (optimally at pH 7.0) and between 0 and 30°C (optimum growth temperature 28°C). The strain exhibited a restricted substrate profile, with a preference for aliphatic hydrocarbons, that is consistent with its closest phylogenetic neighbour O. antarctica. Growth of the isolate at different temperatures affected the cellular fatty acid profile. 28°C cultured cells contained C(16:1)ω7c and/or iso-C(15:0) 2-OH (50.4%) and C(16:0) (19.2%) as the major fatty acids. However, the major fatty acids of the cells cultured at 4°C were C(16:1)ω7c and/or C(16:1)ω6c (40.2%), C(16:0) (17.2%) and C(17:1)ω8c (10.1%). The G+C content of the genomic DNA was 42.7 mol%. Phylogeny based on 16S rRNA gene sequences together with data from DNA-DNA hybridization, phenotypic and chemotaxonomic characterization revealed that DFH11(T) should be classified as a novel species of the genus Oleispira, for which the name Oleispira lenta sp. nov. is proposed, with the type strain DFH11(T) (=NCIMB 14529(T) = LMG 24829(T)).
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15
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Wang L, Chen S, Vergin KL, Giovannoni SJ, Chan SW, DeMott MS, Taghizadeh K, Cordero OX, Cutler M, Timberlake S, Alm EJ, Polz MF, Pinhassi J, Deng Z, Dedon PC. DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc Natl Acad Sci U S A 2011; 108:2963-8. [PMID: 21285367 PMCID: PMC3041111 DOI: 10.1073/pnas.1017261108] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.
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Affiliation(s)
- Lianrong Wang
- Department of Biological Engineering
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
- College of Pharmacy, Wuhan University, Wuhan 430071, China
| | - Shi Chen
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
- College of Pharmacy, Wuhan University, Wuhan 430071, China
| | - Kevin L. Vergin
- Department of Microbiology, Oregon State University, Corvallis, OR 97331; and
| | | | | | | | | | - Otto X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michael Cutler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Eric J. Alm
- Department of Biological Engineering
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Martin F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jarone Pinhassi
- Marine Microbiology, School of Natural Sciences, Linnaeus University, SE-39182 Kalmar, Sweden
| | - Zixin Deng
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
- College of Pharmacy, Wuhan University, Wuhan 430071, China
| | - Peter C. Dedon
- Department of Biological Engineering
- Center for Environmental Health Sciences, and
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