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Zomer A, Ingham CJ, von Meijenfeldt FAB, Escobar Doncel Á, van de Kerkhof GT, Hamidjaja R, Schouten S, Schertel L, Müller KH, Catón L, Hahnke RL, Bolhuis H, Vignolini S, Dutilh BE. Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype. Proc Natl Acad Sci U S A 2024; 121:e2309757121. [PMID: 38990940 PMCID: PMC11260094 DOI: 10.1073/pnas.2309757121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 04/23/2024] [Indexed: 07/13/2024] Open
Abstract
Structural color is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural color (SC) is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here, we collected and sequenced a set of 87 structurally colored bacterial isolates and 30 related strains lacking SC. Optical analysis of colonies indicated that diverse bacteria from at least two different phyla (Bacteroidetes and Proteobacteria) can create two-dimensional packing of cells capable of producing SC. A pan-genome-wide association approach was used to identify genes associated with SC. The biosynthesis of uroporphyrin and pterins, as well as carbohydrate utilization and metabolism, was found to be involved. Using this information, we constructed a classifier to predict SC directly from bacterial genome sequences and validated it by cultivating and scoring 100 strains that were not part of the training set. We predicted that SCr is widely distributed within gram-negative bacteria. Analysis of over 13,000 assembled metagenomes suggested that SC is nearly absent from most habitats associated with multicellular organisms except macroalgae and is abundant in marine waters and surface/air interfaces. This work provides a large-scale ecogenomics view of SC in bacteria and identifies microbial pathways and evolutionary relationships that underlie this optical phenomenon.
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Affiliation(s)
- Aldert Zomer
- Division of Infectious Diseases and Immunology, Utrecht University, Utrecht3584 CL, the Netherlands
| | - Colin J. Ingham
- Hoekmine Besloten Vennootschap, Utrecht3515 GJ, the Netherlands
| | - F. A. Bastiaan von Meijenfeldt
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht3584 CH, the Netherlands
- Department of Marine Microbiology & Biogeochemistry, Royal Netherlands Institute for Sea Research, ‘t Horntje1797 SZ, The Netherlands
| | | | - Gea T. van de Kerkhof
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | | | - Sanne Schouten
- Hoekmine Besloten Vennootschap, Utrecht3515 GJ, the Netherlands
| | - Lukas Schertel
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Department of Physics, University of Fribourg, FribourgCH-1700, Switzerland
| | - Karin H. Müller
- Department of Physiology, Development and Neuroscience, Cambridge Advanced Imaging Centre, University of Cambridge, CambridgeCB2 3DY, United Kingdom
| | - Laura Catón
- Hoekmine Besloten Vennootschap, Utrecht3515 GJ, the Netherlands
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Richard L. Hahnke
- Leibniz Institute, German Collection of Microorganisms and Cell Cultures, Braunschweig38124, Germany
| | - Henk Bolhuis
- Department of Marine Microbiology & Biogeochemistry, Royal Netherlands Institute for Sea Research, ‘t Horntje1797 SZ, The Netherlands
| | - Silvia Vignolini
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Sustainable and Bio-inspired Materials, Max Planck Institute of Colloids and Interfaces, Potsdam14476, Germany
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht3584 CH, the Netherlands
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena07743, Germany
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2
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An MM, Shen L, Liang RN, Lu YJ, Zhao GZ. Alcanivorax quisquiliarum sp. nov., isolated from anaerobic fermentation liquid of food waste by high-throughput cultivation. Int J Syst Evol Microbiol 2023; 73. [PMID: 37093733 DOI: 10.1099/ijsem.0.005764] [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: 04/25/2023] Open
Abstract
Strain CY1518T was isolated from an anaerobic fermentation liquid of food waste treatment plant in Beijing, PR China, and characterized to assess its taxonomy. Cells of CY1518T were Gram-stain-negative, oxidase-negative, catalase-positive and ellipsoidal. Growth occurred at 20-42 °C (optimum, 37 °C), pH 6.0-10.0 (optimum, pH 8) and with 0-6.0 % (w/v) NaCl (optimum, 1.5%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CY1518T belongs to the genus Alcanivorax, with the highest sequence similarity to Alcanivorax pacificus W11-5T (95.97 %), followed by Alcanivorax indicus SW127T (95.08%). The similarity between strain CY1518T and other strains of Alcanivorax was less than 95 %. The genomic DNA G+C content of strain CY1518T was 60.88 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain CY1518T and the closely related taxa A. pacificus W11-5T and A. indicus SW127T were 77.61, 78.03 and 21.2 % and 74.15, 70.02 and 19.3%, respectively. The strain was able to use d-serine, Tween 40 and some organic acid compounds for growth. The polar lipids comprised aminophospholipid, diphosphatidylglycerol, glycolipid, an unknown polar lipid, phosphatidylethanolamine, phosphatidylglycerol and phospholipid. The principal fatty acids (>5 %) were C19 : 0 cyclo ω8c (36.3%), C16 : 0 (32.3%), C12 : 0 3-OH (8.3%) and C12 : 0 (7.6%). Based on its phenotypic, genotypic and genomic characteristics, strain CY1518T represents a novel species in the genus Alcanivorax, for which the name Alcanivorax quisquiliarum sp. nov. is proposed. The type strain is CY1518T (=GDMCC 1.2918T=JCM 35120T).
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Affiliation(s)
- Miao-Miao An
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Lei Shen
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
- College of Life Sciences, Langfang Normal University, Langfang 065000, PR China
| | - Rui-Na Liang
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Yan-Juan Lu
- Beijing Fairyland Environmental Technology Co., Ltd, Beijing 100085, PR China
| | - Guo-Zhu Zhao
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
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3
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Rai A, Suresh G, Ria B, L V, Pk S, Ipsita S, Sasikala C, Venkata Ramana C. Phylogenomic analysis of the genus Alcanivorax: proposal for division of this genus into the emended genus Alcanivorax and two novel genera Alloalcanivorax gen. nov. and Isoalcanivorax gen. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748586 DOI: 10.1099/ijsem.0.005672] [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: 01/12/2023] Open
Abstract
The members of the genus Alcanivorax are key players in the removal of petroleum hydrocarbons from polluted marine environments. More than half of the species were described in the last decade using 16S rRNA gene phylogeny and genomic-based metrics. However, the 16S rRNA gene identity (<94 %) between some members of the genus Alcanivorax suggested their imprecise taxonomic status. In this study, we examined the taxonomic positions of Alcanivorax species using 16S rRNA phylogeny and further validated them using phylogenomic-related indexes such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), percentage of conserved proteins (POCP) and comparative genomic studies. ANI and dDDH values confirmed that all the Alcanivorax species were well described at the species level. The phylotaxogenomic analysis showed that Alcanivorax species formed three clades. The inter-clade values of AAI and POCP were less than 70 %. The pan-genome evaluation depicted that the members shared 1223 core genes and its number increased drastically when analysed clade-wise. Therefore, these results necessitate the transfer of clade II and clade III members into Isoalcanivorax gen. nov. and Alloalcanivorax gen. nov., respectively, along with the emended description of the genus Alcanivorax sensu stricto.
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Affiliation(s)
- Anusha Rai
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Gandham Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Biswas Ria
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Vighnesh L
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Sreya Pk
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Sahu Ipsita
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad-500 085, India
| | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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4
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Alcanivorax limicola sp. nov., isolated from a soda alkali-saline soil. Arch Microbiol 2021; 204:106. [PMID: 34972960 DOI: 10.1007/s00203-021-02638-3] [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: 09/09/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 10/19/2022]
Abstract
An alkaliphilic and aerobic bacterium, designated as strain JB21T, was isolated from a soda alkali-saline soil sample in Heilongjiang, Northeast China. Strain JB21T is a Gram-stain-negative, rod-shaped, non-motile and amylase-positive bacterium. Growth occurred at 15-45 °C (optimum, 35-37 °C), in the presence of 0-15.0% (w/v) NaCl (optimum, 1.0%) and at pH 6.5-10.5 (optimum, pH 8.5-9.5). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JB21T was most closely related to type strains of the genus Alcanivorax, with the highest sequence similarity to Alcanivorax indicus SW127T (96.3%), and shared 95.4-93.1% sequence identity with other valid type strains of this genus. The major cellular fatty acids identified were C16:0 and summed feature 8 (C18:1ω6c and/or C18:1ω7c). The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. The genomic G + C content of strain JB21T was 61.3 mol%. The digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) between strain JB21T and type strains of the genus Alcanivorax were 18.3-23.2% and 69.2-79.0%, respectively. On the basis of its phenotypic and phylogenetic characteristics, we suggest the creation of a new species within the Alcanivorax genus, named Alcanivorax limicola sp. nov., type strain JB21T (= CGMCC 1.16632T = JCM 33717T).
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Dong C, Lai Q, Liu X, Gu L, Zhang Y, Xie Z, Wang D, Shao Z. Alcanivorax profundimaris sp. nov., a Novel Marine Hydrocarbonoclastic Bacterium Isolated from Seawater and Deep-Sea Sediment. Curr Microbiol 2021; 78:1053-1060. [PMID: 33599831 DOI: 10.1007/s00284-020-02322-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022]
Abstract
Two novel Alcanivorax-related strains, designated ST75FaO-1T and 521-1, were isolated from the seawater of the South China Sea and the deep-sea sediment of the West Pacific Ocean, respectively. Both strains are Gram-stain-negative, rod-shaped, and non-motile, and grow at 10-40 °C, pH 5.0-10.0, in the presence of 1.0-15.0% (w/v) NaCl. Their 16S rRNA gene sequences showed 99.9% similarity. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that both strains belong to the genus Alcanivorax, and share 92.9-98.1% sequence similarity with all valid type strains of this genus, with the highest similarity being to type strain Alcanivorax venustensis DSM 13974T (98.0-98.1%). Digital DNA-DNA hybridization (dDDH) and average nucleotide identity values between strains ST75FaO-1T and 521-1 were 75.7% and 97.1%, respectively, while the corresponding values with A. venustensis DSM 13974T were only 25.4-25.6% and 82.4-82.7%, respectively. The two strains contained similar major cellular fatty acids including C16:0, C18:1 ω7c/ω6c, C19:0 cyclo ω8c, C16:1 ω7c/ω6c, C12:0 3-OH, and C12:0. The genomic G + C content of strains ST75FaO-1T and 521-1 were 66.3% and 66.1%, respectively. Phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, and one unidentified polar lipid were present in both strains. On the basis of phenotypic and genotypic characteristics, the two strains represent a novel species within the genus Alcanivorax, for which the name Alcanivorax profundimaris sp. nov. is proposed. The type strain is ST75FaO-1T (= MCCC 1A17714T = KCTC 82142T).
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Affiliation(s)
- Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- Fujian Key Laboratory of Marine Genetic Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- Fujian Key Laboratory of Marine Genetic Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
| | - Xiupian Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- Fujian Key Laboratory of Marine Genetic Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
| | - Li Gu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- Fujian Key Laboratory of Marine Genetic Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
| | - Yu Zhang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, Fujian, People's Republic of China
| | - Zhangxian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, Fujian, People's Republic of China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, Fujian, People's Republic of China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China.
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China.
- Fujian Key Laboratory of Marine Genetic Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China.
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Liao X, Lai Q, Yang J, Dong C, Li D, Shao Z. Alcanivorax sediminis sp. nov., isolated from deep-sea sediment of the Pacific Ocean. Int J Syst Evol Microbiol 2020; 70:4280-4284. [PMID: 32618558 DOI: 10.1099/ijsem.0.004285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain PA15-N-34T, which was isolated from deep-sea sediment of Pacific Ocean. The bacterium was Gram-stain-positive, oxidase- and catalase-positive and rod-shaped. Growth was observed at salinity of 0-15.0% NaCl and at temperatures of 10-45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PA15-N-34T belonged to the genus Alcanivorax, with the highest sequence similarity to Alcanivorax profundi MTEO17T (97.7 %), followed by Alcanivorax nanhaiticus 19 m-6T (97.3 %) and 12 other species of the genus Alcanivorax (93.4 %-97.0 %). The average nucleotide identity and DNA-DNA hybridization values between strain PA15-N-34T and type strains of the genus Alcanivorax were 71.46-81.78% and 18.7-25.2 %, respectively. The principal fatty acids (>10 %) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 31.2 %), C16 : 0 (25.0 %) and summed feature 3 (14.6 %). The DNA G+C content was 57.15 mol%. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, four unidentified aminolipids and three unidentified lipids. The novel strain can be differentiated from its closest type strain by a negative test for urease and the presence of diphosphatidylglycerol and aminolipid. The combined genotypic and phenotypic data show that strain PA15-N-34T represents a novel species within the genus Alcanivorax, for which the name Alcanivorax sediminis sp. nov. is proposed, with the type strain PA15-N-34T (=MCCC 1A14738T=KCTC 72163T).
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Affiliation(s)
- Xianzhi Liao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China.,School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Junpeng Yang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China.,School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Dengfeng Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China.,School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
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Liu J, Ren Q, Zhang Y, Li Y, Tian X, Wu Y, Tian J, Zhang XH. Alcanivorax profundi sp. nov., isolated from deep seawater of the Mariana Trench. Int J Syst Evol Microbiol 2018; 69:371-376. [PMID: 30543505 DOI: 10.1099/ijsem.0.003145] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, non-motile, strictly aerobic strain, designated as MTEO17T, was isolated from a 1000 m deep seawater sample of the Mariana Trench. Growth was observed at 10-45 °C (optimum, 37 °C), in the presence of 0.0-12.0 % NaCl (w/v; optimum, 3.0 %) and at pH 6.0-10.0 (optimum, pH 7.0-8.0). Phylogenetic analysis, based on the 16S rRNA gene sequence, revealed that strain MTEO17T belonged to the genus Alcanivorax and showed the highest sequence similarity of 97.9 % to Alcanivorax nanhaiticus MCCC 1A05629T. The estimated average nucleotide identity and DNA-DNA hybridization values between strain MTEO17T and A. nanhaiticus MCCC 1A05629T were 78.98 and 23.80 %, respectively. The significant dominant fatty acids were C16 : 0, summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The polar lipids comprised two phosphatidylethanolamines, one phosphatidylglycerol, one unidentified phospholipid and four unidentified polar lipids. The DNA G+C content of strain MTEO17T was 57.5 %. On the basis of the polyphasic evidence, strain MTEO17T is proposed to represent a novel species of the genus Alcanivorax, for which the name Alcanivorax profundi sp. nov. is proposed. The type strain is MTEO17T (=KCTC 52694T=MCCC 1K03252T).
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Affiliation(s)
- Jiwen Liu
- 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China.,2Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Qiaomeng Ren
- 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yunhui Zhang
- 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yuying Li
- 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaorong Tian
- 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yanhong Wu
- 1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Jiwei Tian
- 3Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao 266100, PR China.,4Marine Dynamic Process and Climate Function Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China
| | - Xiao-Hua Zhang
- 2Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China.,1College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
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8
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Yang S, Li M, Lai Q, Li G, Shao Z. Alcanivorax mobilis sp. nov., a new hydrocarbon-degrading bacterium isolated from deep-sea sediment. Int J Syst Evol Microbiol 2018; 68:1639-1643. [PMID: 29620491 DOI: 10.1099/ijsem.0.002612] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain MT13131T, which was isolated from deep-sea sediment of the Indian Ocean during the screening of oil-degrading bacteria. The chain length range of n-alkanes (C8 to C32) oxidized by strain MT13131T was determined in this study. The bacterium was Gram-negative, oxidase- and catalase-positive, single rod shaped, and motile by peritrichous flagella. Growth was observed at salinities of 1-12 % and at temperatures of 10-42 °C. The isolate was capable of Tween 20, 40 and 80 hydrolysis, but incapable of gelatin, cellulose or starch hydrolysis. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MT13131T belonged to the genus Alcanivorax, with highest sequence similarity to Alcanivorax marinus R8-12T (96.92 %), other species of genus Alcanivorax shared 92.96-96.69 % sequence similarity. The principal fatty acids were summed feature 3 (C16 : 1ω6c/ω7c), summed feature 8 (C18 : 1ω7c/ω6c), C16 : 0 and C12 : 0 3OH. The G+C content of the chromosomal DNA was 64.2 mol%. Phosphatidylglycerol, phosphatidylethanolamine, three aminolipids and three phospholipids were present. The combined genotypic and phenotypic data showed that strain MT13131T represents a novel species within the genus Alcanivorax, for which the name Alcanivorax mobilis sp. nov. is proposed, with the type strain MT13131T (=MCCC 1A11581T=KCTC 52985T).
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Affiliation(s)
- Shuo Yang
- Key Laboratory of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen 361005, PR China
| | - Meiqing Li
- Key Laboratory of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen 361005, PR China
| | - Guizhen Li
- Key Laboratory of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen 361005, PR China.,School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| | - Zongze Shao
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China.,Key Laboratory of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen 361005, PR China.,School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
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9
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León-Barrios M, Ramírez-Bahena MH, Igual JM, Peix Á, Velázquez E. Phyllobacterium salinisoli sp. nov., isolated from a Lotus lancerottensis root nodule in saline soil from Lanzarote. Int J Syst Evol Microbiol 2018; 68:1085-1089. [DOI: 10.1099/ijsem.0.002628] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética. Universidad de La Laguna, Tenerife, Spain
| | - Martha Helena Ramírez-Bahena
- Instituto de Recursos Naturales y Agrobiología de Salamanca. Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
| | - José M. Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca. Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC “Interacciones Planta-Microorganismo”, Salamanca, Spain
| | - Álvaro Peix
- Instituto de Recursos Naturales y Agrobiología de Salamanca. Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
- Unidad Asociada Universidad de Salamanca-CSIC “Interacciones Planta-Microorganismo”, Salamanca, Spain
| | - Encarna Velázquez
- Unidad Asociada Universidad de Salamanca-CSIC “Interacciones Planta-Microorganismo”, Salamanca, Spain
- Departamento de Microbiología y Genética and Centro Hispanoluso de Investigaciones Agrarias (CIALE). Universidad de Salamanca, Salamanca, Spain
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10
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Fu X, Lai Q, Dong C, Wang W, Shao Z. Complete genome sequence of Alcanivorax xenomutans P40, an alkane-degrading bacterium isolated from deep seawater. Mar Genomics 2018. [DOI: 10.1016/j.margen.2017.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Comparative metabolomic studies of Alkanivorax xenomutans showing differential power output in a three chambered microbial fuel cell. World J Microbiol Biotechnol 2017; 33:102. [PMID: 28466301 DOI: 10.1007/s11274-017-2268-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
Abstract
Metabolomic study of electrogenic bacteria is a necessity to understand the extent of complex organic matter degradation and to invent new co-culture techniques to achieve complete degradation. In this study, we have subjected Alkanivorax xenomutans (KCTC 23751T; NBRC 108843T), a bacterium capable for biodegradation of complex hydrocarbons, to oxic and anoxic conditions in a three chambered microbial fuel cell. In an attempt to understand the molecular mechanisms during the electrogenic processes of A. xenomutans, intra cellular (endo metabolome or the fingerprint) and exo metabolome (extracellular metabolome or the foot print) were analyzed under oxic and anoxic conditions, using FTIR and GC-MS. Interpretation of the data revealed higher number of metabolites in the anoxic fraction as compared to oxic fraction. In addition, expression of putative metabolites that influence electron transfer like flavins, fumarate and quinones were found to be predominant in the organisms when grown in anoxic conditions. Hence, the presence of anoxic conditions governed the electrogenic bacteria to produce enhanced power output by modulating differential metabolomic profiling, compared to the culture grown in oxic conditions.
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12
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Lai Q, Zhou Z, Li G, Li G, Shao Z. Alcanivorax nanhaiticus sp. nov., isolated from deep sea sediment. Int J Syst Evol Microbiol 2016; 66:3651-3655. [PMID: 27307296 DOI: 10.1099/ijsem.0.001247] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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 19-m-6T, which was isolated from deep sea sediment of the South China Sea during the screening of alkane-degrading bacteria. The isolate was Gram-reaction-negative, and oxidase- and catalase- positive. On the basis of 16S rRNA gene sequence similarity, strain 19-m-6T was shown to belong to the genus Alcanivorax, related to Alcanivorax jadensis T9T (97.5 %), Alcanivorax hongdengensis A-11-3T (97.3 %), A. lcanivorax borkumensis SK2T (96.6 %) and seven other species of the genus Alcanivorax(93.9-95.4 %). Average nucleotide identity values between strain 19-m-6T and A. jadensis T9T, A. hongdengensis A-11-3T and A. borkumensis SK2T were 85.12, 85.87 and 84.35 %, respectively. The estimated DNA-DNA hybridization values between strain 19-m-6T and these three type strains were 22.0, 22.6 and 21.2 %, respectively. Four alkane hydroxylase (alkB) genes were obtained from the draft genome sequence. The G+C content of the chromosomal DNA was 56.44 mol%. The major fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, one aminolipid, three phospholipids, two glycolipids and two aminophospholipids. According to its phenotypic features, fatty acid composition and 16S rRNA gene sequence, the novel strain fitted well into the genus Alcanivorax, but could be clearly distinguished from all other known Alcanivorax species described to date. The nameAlcanivorax nanhaiticus sp. nov. is thus proposed, with 19-m-6T (=MCCC 1A05629T=KCTC 52137T) as the type strain.
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Affiliation(s)
- Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Zhongwen Zhou
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Guizhen Li
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Guangyu Li
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
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13
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Campos FF, Garcia JE, Luna-Finkler CL, Davolos CC, Lemos MVF, Pérez CD. Alcanivorax dieselolei, an alkane-degrading bacterium associated with the mucus of the zoanthid Palythoa caribaeorum (Cnidaria, Anthozoa). BRAZ J BIOL 2016; 75:431-4. [PMID: 26132028 DOI: 10.1590/1519-6984.16113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/20/2014] [Indexed: 11/21/2022] Open
Abstract
Analyses of 16S rDNA genes were used to identify the microbiota isolated from the mucus of the zoanthid Palythoa caribaeorum at Porto de Galinhas on the coast of Pernambuco State, Brazil. This study is important as the first report of this association, because of the potential biotechnological applications of the bacterium Alcanivorax dieselolei, and as evidence for the presence of a hydrocarbon degrading bacterium in a reef ecosystem such as Porto de Galinhas.
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Affiliation(s)
- F F Campos
- Programa de Pós-Graduação em Saúde Humana e Meio Ambiente, Centro Acadêmico de Vitória, Universidade Federal de Pernambuco, Vitória de Santo Antão, PE, Brazil
| | - J E Garcia
- Programa de Pós-Graduação em Saúde Humana e Meio Ambiente, Centro Acadêmico de Vitória, Universidade Federal de Pernambuco, Vitória de Santo Antão, PE, Brazil
| | - C L Luna-Finkler
- Programa de Pós-Graduação em Saúde Humana e Meio Ambiente, Centro Acadêmico de Vitória, Universidade Federal de Pernambuco, Vitória de Santo Antão, PE, Brazil
| | - C C Davolos
- Laboratório de Genética de Bactérias, Departamento de Biologia Aplicada, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - M V F Lemos
- Laboratório de Genética de Bactérias, Departamento de Biologia Aplicada, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - C D Pérez
- Programa de Pós-Graduação em Saúde Humana e Meio Ambiente, Centro Acadêmico de Vitória, Universidade Federal de Pernambuco, Vitória de Santo Antão, PE, Brazil
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14
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Wang G, Tang M, Wu H, Dai S, Li T, Chen C, He H, Fan J, Xiang W, Li X. Aliikangiella marina gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122, and proposal of Kangiellaceae fam. nov. in the order Oceanospirillales. Int J Syst Evol Microbiol 2015; 65:4488-4494. [DOI: 10.1099/ijsem.0.000601] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, non-spore-forming, long rod-shaped bacterium, designated strain GYP-15T, was isolated from the culture broth of a marine microalga, Picochloruma sp. 122. Phylogenetic analyses revealed that strain GYP-15T shared 90.6 % 16S rRNA gene sequence similarity with its closest relative, Kangiella aquimarina KCTC 12183T, and represents a distinct phylogenetic lineage in a robust clade consisting of GYP-15T and members of the genera Kangiella and Pleionea in the order Oceanospirillales. Chemotaxonomic and physiological characteristics, including major cellular fatty acids, NaCl tolerance and pattern of carbon source utilization, could also readily distinguish strain GYP-15T from all established genera and species. Thus, it is concluded that strain GYP-15T represents a novel species of a new genus, for which the name Aliikangiella marina gen. nov., sp. nov. is proposed. The type strain of Aliikangiella marina is GYP-15T ( = MCCC 1K01163T = KCTC 42667T). Based on phylogenetic results, 16S rRNA gene signature nucleotide pattern and some physiological characteristics, the three genera Kangiella, Pleionea and Aliikangiella are proposed to make up a novel family, Kangiellaceae fam. nov., in the order Oceanospirillales.
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Affiliation(s)
- Guanghua Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Mingxing Tang
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Huanlian Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Shikun Dai
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Tao Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Chenghao Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hui He
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Jiewei Fan
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Wenzhou Xiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Xiang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
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15
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Kyoung Kwon K, Hye Oh J, Yang SH, Seo HS, Lee JH. Alcanivorax gelatiniphagus sp. nov., a marine bacterium isolated from tidal flat sediments enriched with crude oil. Int J Syst Evol Microbiol 2015; 65:2204-2208. [PMID: 25858250 DOI: 10.1099/ijs.0.000244] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, rod-shaped marine bacterium, designated MEBiC08158(T), was isolated from sediments collected from Taean County, Korea, near the Hebei Spirit tanker oil spill accident. 16S rRNA gene sequence analysis revealed that strain MEBiC08158(T) was closely related to Alcanivorax marinus R8-12(T) (99.5% similarity) but was distinguishable from other members of the genus Alcanivorax (93.7-97.1%). The DNA-DNA hybridization value between strain MEBiC08158(T) and A. marinus R8-12(T) was 58.4%. Growth of strain MEBiC08158(T) was observed at 15-43 °C (optimum 37-40 °C), at pH 6.0-9.5 (optimum pH 7.0-8.0) and with 0.5-16% NaCl (optimum 1.5-3.0%). The dominant fatty acids were C16 : 0, C19 : 0 cyclo ω8c, C12 : 0, C18 : 1ω7c, C12 : 0 3-OH and summed feature 3 (comprising C15 : 0 2-OH and/or C16 : 1ω7c). Several phenotypic characteristics differentiate strain MEBiC08158(T) from phylogenetically close members of the genus Alcanivorax. Therefore, strain MEBiC08158(T) should be classified as representing a novel species of the genus Alcanivorax, for which the name Alcanivorax gelatiniphagus sp. nov. is proposed. The type strain is MEBiC08158(T) ( = KCCM 42990(T) = JCM 18425(T)).
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Affiliation(s)
- Kae Kyoung Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, PO Box 29, Ansan 425-600, Republic of Korea
| | - Ji Hye Oh
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, PO Box 29, Ansan 425-600, Republic of Korea
| | - Sung-Hyun Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, PO Box 29, Ansan 425-600, Republic of Korea
| | - Hyun-Seok Seo
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, PO Box 29, Ansan 425-600, Republic of Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, PO Box 29, Ansan 425-600, Republic of Korea
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16
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Rahul K, Sasikala C, Tushar L, Debadrita R, Ramana CV. Alcanivorax xenomutans sp. nov., a hydrocarbonoclastic bacterium isolated from a shrimp cultivation pond. Int J Syst Evol Microbiol 2014; 64:3553-3558. [DOI: 10.1099/ijs.0.061168-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains (JC109T and JC261) were isolated from a sediment sample collected from a shrimp cultivation pond in Tamil Nadu (India). Cells were Gram-stain-negative, motile rods. Both strains were positive for catalase and oxidase, hydrolysed Tween 80, and grew chemo-organoheterotrophically with an optimal pH of 6 (range pH 4–9) and at 30 °C (range 25–40 °C). Based on 16S rRNA gene sequence analysis, strains JC109T and JC261 were identified as belonging to the genus
Alcanivorax
with
Alcanivorax dieselolei
B-5T (sequence similarity values of 99.3 and 99.7 %, respectively) and
Alcanivorax balearicus
MACL04T (sequence similarity values of 98.8 and 99.2 %, respectively) as their closest phylogenetic neighbours. The 16S rRNA gene sequence similarity between strains JC109T and JC261 was 99.6 %. The level of DNA–DNA relatedness between the two strains was 88 %. Strain JC109T showed 31±1 and 26±2 % DNA–DNA relatedness with
A. dieselolei
DSM 16502T and
A. balearicus
DSM 23776T, respectively. The DNA G+C content of strains JC109T and JC261 was 54.5 and 53.4 mol%, respectively. Polar lipids of strain JC109T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and two unidentified lipids. The major fatty acids were C10 : 0, C12 : 0, C16 : 0, C12 : 0 3-OH, C16 : 1ω7c, C18 : 1ω7c and C19 : 0 cyclo ω8c. Both strains could utilize diesel oil and a variety of xenobiotics as carbon and energy sources. The results of physiological, biochemical, chemotaxonomic and molecular analyses allowed the clear differentiation of strains JC109T and JC261 from all other members of the genus
Alcanivorax
. Strains JC109T and JC261 are thus considered to represent a novel species, for which the name Alcanivorax xenomutans sp. nov. is proposed. The type strain is JC109T ( = KCTC 23751T = NBRC 108843T).
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Affiliation(s)
- K. Rahul
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J.N.T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J.N.T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - L. Tushar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - R. Debadrita
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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17
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Zhang L, Gao G, Tang X, Shao K. Can the freshwater bacterial communities shift to the “marine-like” taxa? J Basic Microbiol 2014; 54:1264-72. [DOI: 10.1002/jobm.201300818] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 03/02/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Lei Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology; Chinese Academy of Sciences; Nanjing China
- University of Chinese Academy of Sciences; Beijing; China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology; Chinese Academy of Sciences; Nanjing China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology; Chinese Academy of Sciences; Nanjing China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology; Chinese Academy of Sciences; Nanjing China
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18
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Lai Q, Wang J, Gu L, Zheng T, Shao Z. Alcanivorax marinus sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2013; 63:4428-4432. [PMID: 23847282 DOI: 10.1099/ijs.0.049957-0] [Citation(s) in RCA: 31] [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 taxonomic study was carried out on strain R8-12(T), which was isolated from deep-sea water of the Indian Ocean during the screening of oil-degrading bacteria. The isolate was Gram-stain-negative, oxidase and catalase-positive. Growth was observed at salinities from 0.5 to 15 % (optimum 3 %), at pH from 6-10 (optimum 7-8) and at temperatures from 10 to 42 °C (optimum 28 °C). On the basis of 16S rRNA gene sequence similarity, strain R8-12(T) was shown to belong to the genus Alcanivorax and to be related to Alcanivorax venustensis DSM 13974(T) (97.2 %), A. dieselolei B-5(T) (95.0 %), A. balearicus MACL04(T) (94.6 %), A. hongdengensis A-11-3(T) (94.3 %), A. jadensis T9(T) (93.8 %), A. borkumensis SK2(T) (93.7 %) and A. pacificus W11-5(T) (93.7 %). The gyrB sequence similarities between R8-12(T) and other species of the genus Alcanivorax ranged from 77.9 % to 86.9 %. The major fatty acids were C16 : 0 (31.8 %), C18 : 1ω7c (20.3 %), C19 : 0ω8c cyclo (15.8 %) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) (8.9 %). The polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two aminolipids (AL1-AL2) and two phospholipids (PL1-PL2). Three alkane hydroxylase (alkB) genes were identified in the genome. The G+C content of the chromosomal DNA was 66.1 mol%. DNA-DNA hybridization showed that strain R8-12(T) and A. venustensis DSM 13974(T) had a DNA-DNA relatedness of 63±3 %. According to its phenotypic features and fatty acid composition as well as the 16S rRNA and gyrB gene sequences, the novel strain represents a member of the genus Alcanivorax, but could be easily distinguished from all other known species of the genus Alcanivorax described to date. The name Alcanivorax marinus sp. nov. is proposed, with the type strain R8-12(T) ( = MCCC 1A00382(T) = LMG 24621(T) = CCTCC AB 208234(T)).
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Affiliation(s)
- Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China.,MOE of Key Lab for Coast and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen 361005, People's Republic of China
| | - Jianning Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China.,MOE of Key Lab for Coast and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen 361005, People's Republic of China
| | - Li Gu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Tianling Zheng
- MOE of Key Lab for Coast and Wetland Ecosystem, School of Life Sciences, Xiamen University, Xiamen 361005, People's Republic of China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
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19
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Duan J, Jiang W, Cheng Z, Heikkila JJ, Glick BR. The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4. PLoS One 2013; 8:e58640. [PMID: 23516524 PMCID: PMC3596284 DOI: 10.1371/journal.pone.0058640] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/05/2013] [Indexed: 11/18/2022] Open
Abstract
The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.
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Affiliation(s)
- Jin Duan
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
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20
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Kientz B, Vukusic P, Luke S, Rosenfeld E. Iridescence of a marine bacterium and classification of prokaryotic structural colors. Appl Environ Microbiol 2012; 78:2092-9. [PMID: 22267664 PMCID: PMC3302594 DOI: 10.1128/aem.07339-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/10/2012] [Indexed: 11/20/2022] Open
Abstract
Iridescence is a property of structural color that is occasionally encountered in higher eukaryotes but that has been poorly documented in the prokaryotic kingdom. In the present work, we describe a marine bacterium, identified as Cellulophaga lytica, isolated from the surface of an anemone, that exhibits bright green iridescent colonies under direct epi-illumination. This phenomenon has not previously been investigated in detail. In this study, color changes of C. lytica colonies were observed at various angles of direct illumination or observation. Its iridescent green appearance was dominant on various growth media. Red and violet colors were also discerned on colony edges. Remarkable C. lytica bacterial iridescence was revealed and characterized using high-resolution optical spectrometry. In addition to this, by culturing other bacterial strains to which various forms of faintly iridescent traits have previously been attributed, we identify four principal appearance characteristics of structural color in prokaryotes. A new general classification of bacterial iridescence is therefore proposed in this study. Furthermore, a specific separate class is described for iridescent C. lytica strains because they exhibit what is so far a unique intense glitter-like iridescence in reflection. C. lytica is the first prokaryote discovered to produce the same sort of intense iridescence under direct illumination as that associated with higher eukaryotes, like some insects and birds. Due to the nature of bacterial biology, cultivation, and ubiquity, this discovery may be of significant interest for both ecological and nanoscience endeavors.
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Affiliation(s)
- Betty Kientz
- UMR 7266 CNRS-ULR LIENSs, UFR Sciences, Université de La Rochelle, La Rochelle, France
| | - Peter Vukusic
- School of Physics, University of Exeter, Exeter, United Kingdom
| | - Stephen Luke
- School of Physics, University of Exeter, Exeter, United Kingdom
| | - Eric Rosenfeld
- UMR 7266 CNRS-ULR LIENSs, UFR Sciences, Université de La Rochelle, La Rochelle, France
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21
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Lai Q, Wang L, Liu Y, Fu Y, Zhong H, Wang B, Chen L, Wang J, Sun F, Shao Z. Alcanivorax pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium. Int J Syst Evol Microbiol 2011; 61:1370-1374. [DOI: 10.1099/ijs.0.022368-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [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 a novel bacterial strain, designated W11-5T, which was isolated from a pyrene-degrading consortium enriched from deep-sea sediment of the Pacific Ocean. The isolate was Gram-reaction-negative and oxidase- and catalase-positive. Growth was observed in 0.5–12 % (w/v) NaCl and at 10–42 °C. On the basis of 16S rRNA gene sequence analysis, strain W11-5T was shown to belong to the genus Alcanivorax with a close relation to A. dieselolei B-5T (93.9 % 16S rRNA sequence similarity), A. balearicus MACL04T (93.1 %), A. hongdengensis A-11-3T (93.1 %), A. borkumensis SK2T (93.0 %), A. venustensis ISO4T (93.0 %) and A. jadensis T9T (92.9 %). Similarities between the gyrB gene sequences of W11-5T and other species of the genus Alcanivorax were between 76.8 and 80.8 %. The principal fatty acids were C12 : 0 3-OH (8.0 %), C16 : 0 (29.1 %) and C18 : 1ω7c (27.4 %). The G+C content of the chromosomal DNA was 60.8 mol%. Based on its morphology, physiology and fatty acid composition as well as the results of 16S rRNA and gyrB gene sequence analyses, strain W11-5T ( = MCCC 1A00474T = CCTCC AB 208236T = LMG 25514T) represents a novel species of the genus Alcanivorax, for which the name Alcanivorax pacificus sp. nov. is proposed.
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Affiliation(s)
- Qiliang Lai
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | - Liping Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | - Yuhui Liu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | - Yuanyuan Fu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | - Huanzi Zhong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | - Baojiang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | - Liang Chen
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | - Jianning Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | - Fengqin Sun
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
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22
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Occurrence, production, and export of lipophilic compounds by hydrocarbonoclastic marine bacteria and their potential use to produce bulk chemicals from hydrocarbons. Appl Microbiol Biotechnol 2010; 86:1693-706. [DOI: 10.1007/s00253-010-2515-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 02/15/2010] [Accepted: 02/18/2010] [Indexed: 10/19/2022]
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23
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Peix A, Ramírez-Bahena MH, Velázquez E. Historical evolution and current status of the taxonomy of genus Pseudomonas. INFECTION GENETICS AND EVOLUTION 2009; 9:1132-47. [DOI: 10.1016/j.meegid.2009.08.001] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2009] [Revised: 08/02/2009] [Accepted: 08/18/2009] [Indexed: 10/20/2022]
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24
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Wu Y, Lai Q, Zhou Z, Qiao N, Liu C, Shao Z. Alcanivorax hongdengensis sp. nov., an alkane-degrading bacterium isolated from surface seawater of the straits of Malacca and Singapore, producing a lipopeptide as its biosurfactant. Int J Syst Evol Microbiol 2009; 59:1474-9. [DOI: 10.1099/ijs.0.001552-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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