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Charalampous G, Fragkou E, Kalogerakis N, Antoniou E, Gontikaki E. Diversity links to functionality: Unraveling the impact of pressure disruption and culture medium on crude oil-enriched microbial communities from the deep Eastern Mediterranean Sea. MARINE POLLUTION BULLETIN 2024; 202:116275. [PMID: 38564821 DOI: 10.1016/j.marpolbul.2024.116275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/19/2024] [Accepted: 03/17/2024] [Indexed: 04/04/2024]
Abstract
Mesopelagic water from the deep Eastern Mediterranean Sea (EMS) was collected under disrupted (REPRESS) or undisturbed (HP) pressure conditions and was acclimated to oil (OIL) or dispersed-oil (DISPOIL) under in situ pressure and temperature (10 MPa, 14 °C). Decompression resulted in oil-acclimatised microbial communities of lower diversity despite the restoration of in situ pressure conditions during the 1-week incubation. Further biodiversity loss was observed when oil-acclimatised communities were transferred to ONR7 medium to facilitate the isolation of oil-degrading bacteria. Microbial diversity loss impacted the degradation of recalcitrant oil compounds, especially PAHs, as low-abundance taxa, linked with PAH degradation, were outcompeted in the enrichment process. Thalassomonas, Pseudoalteromonas, Halomonas and Alcanivorax were enriched in ONR7 under all experimental conditions. No effect of dispersant application on the microbial community structure was identified. A. venustensis was isolated under all tested conditions suggesting a potential key role of this species in hydrocarbons removal in the deep EMS.
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Affiliation(s)
- Georgia Charalampous
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece.
| | - Efsevia Fragkou
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece
| | - Nicolas Kalogerakis
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece
| | - Eleftheria Antoniou
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; School of Mineral Resources Engineering, Technical University of Crete, Chania, Greece
| | - Evangelia Gontikaki
- Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece.
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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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Dede B, Priest T, Bach W, Walter M, Amann R, Meyerdierks A. High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean. THE ISME JOURNAL 2023; 17:600-610. [PMID: 36721059 PMCID: PMC10030979 DOI: 10.1038/s41396-023-01366-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 02/02/2023]
Abstract
Species within the genus Alcanivorax are well known hydrocarbon-degraders that propagate quickly in oil spills and natural oil seepage. They are also inhabitants of the deep-sea and have been found in several hydrothermal plumes. However, an in-depth analysis of deep-sea Alcanivorax is currently lacking. In this study, we used multiple culture-independent techniques to analyze the microbial community composition of hydrothermal plumes in the Northern Tonga arc and Northeastern Lau Basin focusing on the autecology of Alcanivorax. The hydrothermal vents feeding the plumes are hosted in an arc volcano (Niua), a rear-arc caldera (Niuatahi) and the Northeast Lau Spreading Centre (Maka). Fluorescence in situ hybridization revealed that Alcanivorax dominated the community at two sites (1210-1565 mbsl), reaching up to 48% relative abundance (3.5 × 104 cells/ml). Through 16S rRNA gene and metagenome analyses, we identified that this pattern was driven by two Alcanivorax species in the plumes of Niuatahi and Maka. Despite no indication for hydrocarbon presence in the plumes of these areas, a high expression of genes involved in hydrocarbon-degradation was observed. We hypothesize that the high abundance and gene expression of Alcanivorax is likely due to yet undiscovered hydrocarbon seepage from the seafloor, potentially resulting from recent volcanic activity in the area. Chain-length and complexity of hydrocarbons, and water depth could be driving niche partitioning in Alcanivorax.
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Affiliation(s)
- Bledina Dede
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Taylor Priest
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wolfgang Bach
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Geoscience Department, University of Bremen, Bremen, Germany
| | - Maren Walter
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Institute of Environmental Physics, University of Bremen, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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4
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Abufalgha AA, Curson ARJ, Lea-Smith DJ, Pott RWM. The effect of Alcanivorax borkumensis SK2, a hydrocarbon-metabolising organism, on gas holdup in a 4-phase bubble column bioprocess. Bioprocess Biosyst Eng 2023; 46:635-644. [PMID: 36757455 DOI: 10.1007/s00449-023-02849-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/21/2023] [Indexed: 02/10/2023]
Abstract
To design bioprocesses utilising hydrocarbon-metabolising organisms (HMO) as biocatalysts, the effect of the organism on the hydrodynamics of bubble column reactor (BCR), such as gas holdup, needs to be investigated. Therefore, this study investigates the first use of an HMO, Alcanivorax borkumensis SK2, as a solid phase in the operation and hydrodynamics of a BCR. The study investigated the gas holdup in 3-phase and 4-phase systems in a BCR under ranges of superficial gas velocities (UG) from 1 to 3 cm/s, hydrocarbon (chain length C13-21) concentrations (HC) of 0, 5, and 10% v/v and microbial concentrations (MC) of 0, 0.35, 0.6 g/l. The results indicated that UG was the most significant parameter, as gas holdup increases linearly with increasing UG from 1 to 3 cm/s. Furthermore, the addition of hydrocarbons into the air-deionized water -SK2 system showed the highest increase in the gas holdup, particularly at high UG (above 2 cm/s). The solids (yeast, cornflour, and SK2) phases had differing effects on gas holdup, potentially due to the difference in surface activity. In this work, SK2 addition caused a reduction in the fluid surface tension in the bioprocess which therefore resulted in an increase in the gas holdup in BCR. This work builds upon previous investigations in optimising the hydrodynamics for bubble column hydrocarbon bioprocesses for the application of alkane bioactivation.
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Affiliation(s)
- Ayman A Abufalgha
- Department of Process Engineering, Stellenbosch University, Banghoek Road, Stellenbosch, 7600, South Africa.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,DST-NRF Centre of Excellence in Catalysis (C* Change), Rondebosch, South Africa
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,DST-NRF Centre of Excellence in Catalysis (C* Change), Rondebosch, South Africa
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,DST-NRF Centre of Excellence in Catalysis (C* Change), Rondebosch, South Africa
| | - Robert W M Pott
- Department of Process Engineering, Stellenbosch University, Banghoek Road, Stellenbosch, 7600, South Africa. .,DST-NRF Centre of Excellence in Catalysis (C* Change), Rondebosch, South Africa.
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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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Cao Y, Zhang B, Cai Q, Zhu Z, Liu B, Dong G, Greer CW, Lee K, Chen B. Responses of Alcanivorax species to marine alkanes and polyhydroxybutyrate plastic pollution: Importance of the ocean hydrocarbon cycles. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120177. [PMID: 36116568 DOI: 10.1016/j.envpol.2022.120177] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
Understanding microbial responses to hydrocarbon and plastic pollution are crucial for limiting the detrimental impacts of environmental contaminants on marine ecosystems. Herein, we reported a new Alcanivorax species isolated from the North Atlantic Ocean capable of degrading alkanes and polyhydroxybutyrate (PHB) plastic (one of the emerging bioplastics that may capture the future plastic market). The whole-genome sequencing showed that the species harbors three types of alkane 1-monooxygenases (AlkB) and one PHB depolymerase (PhaZ) to initiate the degradation of alkanes and plastics. Growth profiling demonstrated that n-pentadecane (C15, the main alkane in the marine environment due to cyanobacterial production other than oil spills) and PHB could serve as preferential carbon sources. However, the cell membrane composition, PhaZ activity, and expression of three alkB genes were utterly different when grown on C15 and PHB. Further, Alcanivorax was a well-recognized alkane-degrader that participated in the ocean hydrocarbon cycles linking with hydrocarbon production and removal. Our discovery supported that the existing biogeochemical processes may add to the marine ecosystem's resilience to the impacts of plastics.
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Affiliation(s)
- Yiqi Cao
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada
| | - Baiyu Zhang
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
| | - Qinhong Cai
- Gaia Refinery, Saint John, NB E2J 2E7, Canada
| | - Zhiwen Zhu
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada
| | - Bo Liu
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada
| | - Guihua Dong
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, QC H4P 2R2, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Ecosystem Science, Ottawa, ON K1A 0E6, Canada
| | - Bing Chen
- Northern Region Persistent Organic Pollutant Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada
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7
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Ataeian M, Liu Y, Kouris A, Hawley AK, Strous M. Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration. Front Microbiol 2022; 13:780346. [PMID: 35222325 PMCID: PMC8880816 DOI: 10.3389/fmicb.2022.780346] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Lack of robustness is a major barrier to foster a sustainable cyanobacterial biotechnology. Use of cyanobacterial consortium increases biodiversity, which provides functional redundancy and prevents invading species from disrupting the production ecosystem. Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. This consortium has been grown in open laboratory culture for 4 years without crashes. Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea. In combination with metaproteomics, the overall stability of the consortium was determined under different cultivation conditions. Genome information from each heterotrophic population was investigated for six ecological niches created by cyanobacterial metabolism and one niche for phototrophy. Genome-resolved metaproteomics with stable isotope probing using 13C-bicarbonate (protein/SIP) showed tight coupling of carbon transfer from cyanobacteria to the heterotrophic populations, specially Wenzhouxiangella. The community structure was compared to a previously described consortium of a closely related cyanobacteria, which indicated that the results may be generalized. Productivity losses associated with heterotrophic metabolism were relatively small compared to other losses during photosynthesis.
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Affiliation(s)
- Maryam Ataeian
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Yihua Liu
- Department Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K. Hawley
- School of Engineering, University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
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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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10
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Sinha RK, Krishnan KP, Kurian PJ. Complete genome sequence and comparative genome analysis of Alcanivorax sp. IO_7, a marine alkane-degrading bacterium isolated from hydrothermally-influenced deep seawater of southwest Indian ridge. Genomics 2020; 113:884-891. [PMID: 33096255 DOI: 10.1016/j.ygeno.2020.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/16/2020] [Accepted: 10/16/2020] [Indexed: 11/29/2022]
Abstract
Genome of Alcanivorax sp. IO_7, an alkane degrading deep-sea bacteria isolated from hydrothermally-influenced Southwest Indian Ridge was sequenced and analysed. Genomic data mining revealed gene clusters for degrading n-alkane and cycloalkanes, including biosurfactant production. The strain was shown to grow on hexadecane as its sole carbon source, supporting the findings of genomic analysis. Presence of cyclohexanone monooxygenase among genomic islands suggest that this strain may have used gene transfer to enhance its hydrocarbon degradation ability. Genes encoding for heavy metal resistance, multidrug resistance and multiple natural product biosynthesis crucial for survival in the hydrothermally influenced deep sea environment were detected. In our comparative genome analysis, it was evident that marine Alcanivorax strains contain a suite of enzymes for n-alkane and haloalkanoate degradation. Comparative genome and genomic synteny analysis provided insights into the physiological features and adaptation strategies of Alcanivorax sp. IO_7 in the deep-sea hydrothermal environment.
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Affiliation(s)
- Rupesh Kumar Sinha
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco da Gama 403804, Goa, India.
| | - K P Krishnan
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco da Gama 403804, Goa, India.
| | - P John Kurian
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco da Gama 403804, Goa, India.
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11
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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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12
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Zadjelovic V, Chhun A, Quareshy M, Silvano E, Hernandez-Fernaud JR, Aguilo-Ferretjans MM, Bosch R, Dorador C, Gibson MI, Christie-Oleza JA. Beyond oil degradation: enzymatic potential of Alcanivorax to degrade natural and synthetic polyesters. Environ Microbiol 2020; 22:1356-1369. [PMID: 32079039 PMCID: PMC7187450 DOI: 10.1111/1462-2920.14947] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022]
Abstract
Pristine marine environments are highly oligotrophic ecosystems populated by well‐established specialized microbial communities. Nevertheless, during oil spills, low‐abundant hydrocarbonoclastic bacteria bloom and rapidly prevail over the marine microbiota. The genus Alcanivorax is one of the most abundant and well‐studied organisms for oil degradation. While highly successful under polluted conditions due to its specialized oil‐degrading metabolism, it is unknown how they persist in these environments during pristine conditions. Here, we show that part of the Alcanivorax genus, as well as oils, has an enormous potential for biodegrading aliphatic polyesters thanks to a unique and abundantly secreted alpha/beta hydrolase. The heterologous overexpression of this esterase proved a remarkable ability to hydrolyse both natural and synthetic polyesters. Our findings contribute to (i) better understand the ecology of Alcanivorax in its natural environment, where natural polyesters such as polyhydroxyalkanoates (PHA) are produced by a large fraction of the community and, hence, an accessible source of carbon and energy used by the organism in order to persist, (ii) highlight the potential of Alcanivorax to clear marine environments from polyester materials of anthropogenic origin as well as oils, and (iii) the discovery of a new versatile esterase with a high biotechnological potential.
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Affiliation(s)
| | - Audam Chhun
- School of Life Sciences, University of Warwick, Warwick, UK
| | - Mussa Quareshy
- School of Life Sciences, University of Warwick, Warwick, UK
| | | | - Juan R Hernandez-Fernaud
- School of Life Sciences, University of Warwick, Warwick, UK.,Unidad de investigación-HUC, La Laguna-Tenerife, Spain
| | - María M Aguilo-Ferretjans
- School of Life Sciences, University of Warwick, Warwick, UK.,Department of Biology, University of the Balearic Islands, Spain
| | - Rafael Bosch
- Department of Biology, University of the Balearic Islands, Spain.,IMEDEA (CSIC-UIB), Esporles, Spain
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Warwick, UK.,Warwick Medical School, University of Warwick, Warwick, UK
| | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Warwick, UK.,Department of Biology, University of the Balearic Islands, Spain.,IMEDEA (CSIC-UIB), Esporles, Spain
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13
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Steiner PA, De Corte D, Geijo J, Mena C, Yokokawa T, Rattei T, Herndl GJ, Sintes E. Highly variable mRNA half-life time within marine bacterial taxa and functional genes. Environ Microbiol 2019; 21:3873-3884. [PMID: 31298776 PMCID: PMC7379614 DOI: 10.1111/1462-2920.14737] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 02/04/2023]
Abstract
Messenger RNA can provide valuable insights into the variability of metabolic processes of microorganisms. However, due to uncertainties that include the stability of RNA, its application for activity profiling of environmental samples is questionable. We explored different factors affecting the decay rate of transcripts of three marine bacterial isolates using qPCR and determined mRNA half‐life time of specific bacterial taxa and of functional genes by metatranscriptomics of a coastal environmental prokaryotic community. The half‐life time of transcripts from 11 genes from bacterial isolates ranged from 1 to 46 min. About 80% of the analysed transcripts exhibited half‐live times shorter than 10 min. Significant differences were found in the half‐life time between mRNA and rRNA. The half‐life time of mRNA obtained from a coastal metatranscriptome ranged from 9 to 400 min. The shortest half‐life times of the metatranscriptome corresponded to transcripts from the same clusters of orthologous groups (COGs) in all bacterial classes. The prevalence of short mRNA half‐life time in genes related to defence mechanisms and motility indicate a tight connection of RNA decay rate to environmental stressors. The short half‐life time of RNA and its high variability needs to be considered when assessing metatranscriptomes especially in environmental samples.
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Affiliation(s)
- Paul A Steiner
- Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Daniele De Corte
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natushima 2-15, Yokosuka, Kanagawa, Japan
| | - Javier Geijo
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Catalina Mena
- Instituto Español de Oceanografia, Centre Oceanogràfic de les Balears, Moll de Ponent s/n, 07015, Palma, Spain
| | - Taichi Yokokawa
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natushima 2-15, Yokosuka, Kanagawa, Japan
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Gerhard J Herndl
- Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, PO Box 59, Alberta Den Burg, 1790, The Netherlands
| | - Eva Sintes
- Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.,Instituto Español de Oceanografia, Centre Oceanogràfic de les Balears, Moll de Ponent s/n, 07015, Palma, Spain
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14
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Imachi H, Tasumi E, Takaki Y, Hoshino T, Schubotz F, Gan S, Tu TH, Saito Y, Yamanaka Y, Ijiri A, Matsui Y, Miyazaki M, Morono Y, Takai K, Hinrichs KU, Inagaki F. Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation. Sci Rep 2019; 9:2305. [PMID: 30783143 PMCID: PMC6381156 DOI: 10.1038/s41598-019-38754-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/09/2019] [Indexed: 11/08/2022] Open
Abstract
Recent explorations of scientific ocean drilling have revealed the presence of microbial communities persisting in sediments down to ~2.5 km below the ocean floor. However, our knowledge of these microbial populations in the deep subseafloor sedimentary biosphere remains limited. Here, we present a cultivation experiment of 2-km-deep subseafloor microbial communities in 20-million-year-old lignite coalbeds using a continuous-flow bioreactor operating at 40 °C for 1029 days with lignite particles as the major energy source. Chemical monitoring of effluent samples via fluorescence emission-excitation matrices spectroscopy and stable isotope analyses traced the transformation of coalbed-derived organic matter in the dissolved phase. Hereby, the production of acetate and 13C-depleted methane together with the increase and transformation of high molecular weight humics point to an active lignite-degrading methanogenic community present within the bioreactor. Electron microscopy revealed abundant microbial cells growing on the surface of lignite particles. Small subunit rRNA gene sequence analysis revealed that diverse microorganisms grew in the bioreactor (e.g., phyla Proteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Bacteroidetes, Spirochaetes, Tenericutes, Ignavibacteriae, and SBR1093). These results indicate that activation and adaptive growth of 2-km-deep microbes was successfully accomplished using a continuous-flow bioreactor, which lays the groundwork to explore networks of microbial communities of the deep biosphere and their physiologies.
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Affiliation(s)
- Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan.
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Eiji Tasumi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Tatsuhiko Hoshino
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi, 783-8502, Japan
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359, Bremen, Germany
| | - Shuchai Gan
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359, Bremen, Germany
| | - Tzu-Hsuan Tu
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Institute of Oceanography, National Taiwan University, Taipei, 106, Taiwan
| | - Yumi Saito
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Yuko Yamanaka
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Akira Ijiri
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Yohei Matsui
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Masayuki Miyazaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Yuki Morono
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi, 783-8502, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359, Bremen, Germany
| | - Fumio Inagaki
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi, 783-8502, Japan
- Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama, Kanagawa, 236-0001, Japan
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15
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Radwan SS, Khanafer MM, Al-Awadhi HA. Ability of the So-Called Obligate Hydrocarbonoclastic Bacteria to Utilize Nonhydrocarbon Substrates Thus Enhancing Their Activities Despite their Misleading Name. BMC Microbiol 2019; 19:41. [PMID: 30777002 PMCID: PMC6379940 DOI: 10.1186/s12866-019-1406-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The group of the so-called obligate hydrocarbonoclastic bacteria (OHCB) are marine microorganisms affiliated with the genera Alcanivorax, Cycloclasticus, Oleiphilus and Thalassolituus. This small group plays a major role in oil-bioremediation in marine ecosystems. Marinobacter and Planomicrobium are considered related to this group. The OHCB are claimed to be obligate to hydrocarbon nutrition. This study argues against this claim. RESULTS Four Alcanivorax species, three Marinobacter species and Planomicrobium okeanokoites from the Arabian/Persian Gulf proved to be not obligate to hydrocarbon nutrition. Although the eight strains grew on crude oil, n-octadecane and phenanthrene as sole carbon substrates, their growth was weaker than on certain nonhydrocarbon, organic compounds viz. peptone, glutamic acid, pyruvic acid, sucrose, mannose and others. Glucose and lactose failed to support the growth of seven of the eight tested strains. Mannose was utilized by five and sucrose by six strains. The well-known intermediate metabolite; pyruvic acid was utilized by all the eight strains, and lactic acid by five strains. In batch cultures, all the tested species consumed higher proportions of peptone than of n-alkanes and phenanthrene. When peptone and crude oil were provided together into the medium, the OHCB started to consume peptone first, and the enriched bacterial populations consumed oil effectively. Added nonhydrocarbon substrates biostimulated oil-consumption by all OHCB species. CONCLUSION The tested OHCB species are not obligate hydrocarbon-utilizers. This provides them with the merit of survival, should their marine ecosystems become oil- or hydrocarbon-free. The fact that conventional, organic substrates biostimulated hydrocarbon-consumption by the tested bacterial species confirms the facultative nature of those organisms and is interesting from the practical point of view.
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Affiliation(s)
- Samir S Radwan
- Present address, Von Einem Str. 25, 48159, Münster, Germany.
| | - Majida M Khanafer
- Microbiology program, Department of Biological Sciences, Faculty of Science, Kuwait University, P.O. Box 5969, 13060, Safat, Kuwait
| | - Husain A Al-Awadhi
- Microbiology program, Department of Biological Sciences, Faculty of Science, Kuwait University, P.O. Box 5969, 13060, Safat, Kuwait.
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16
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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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17
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Song L, Liu H, Cai S, Huang Y, Dai X, Zhou Y. Alcanivorax indicus sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2018; 68:3785-3789. [PMID: 30307386 DOI: 10.1099/ijsem.0.003058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, motile, rod-shaped bacterium, designated SW127T, was isolated from a seawater sample collected from the Indian Ocean. Strain SW127T was aerobic, catalase- and oxidase-positive, and grew at 8-42 °C (optimum, 30 °C), at pH 5.5-9.0 (optimum, pH 7.5) and in the presence of 0.5-11.0 % (w/v) NaCl (optimum, 3.0-4.0 %). Comparative analysis of 16S rRNA gene sequences indicated that strain SW127T belonged to the genus Alcanivorax, and closely related to Alcanivorax pacificus MCCC 1A00474T (96.7 % sequence similarity). The predominant cellular fatty acids of strain SW127T were C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). Strain SW127T contained phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G+C content of strain SW127T was 62.8 mol%. On the basis of its phenotypic characteristics and phylogenetic data, strain SW127T represents a novel species of the genus Alcanivorax, for which the name Alcanivorax indicus sp. nov. is proposed. The type strain is SW127T (=CGMCC 1.16233T=KCTC 62652T).
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Affiliation(s)
- Lei Song
- 1China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hongcan Liu
- 1China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shichun Cai
- 1China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Huang
- 2State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xin Dai
- 2State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yuguang Zhou
- 2State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,1China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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18
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Rizzo C, Rappazzo AC, Michaud L, De Domenico E, Rochera C, Camacho A, Lo Giudice A. Efficiency in hydrocarbon degradation and biosurfactant production by Joostella sp. A8 when grown in pure culture and consortia. J Environ Sci (China) 2018; 67:115-126. [PMID: 29778143 DOI: 10.1016/j.jes.2017.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 08/11/2017] [Accepted: 08/14/2017] [Indexed: 06/08/2023]
Abstract
Joostella strains are emerging candidates for biosurfactant production. Here such ability was analyzed for Joostella strain A8 in comparison with Alcanivorax strain A53 and Pseudomonas strain A6, all previously isolated from hydrocarbon enrichment cultures made of polychaete homogenates. In pure cultures Joostella sp. A8 showed the highest stable emulsion percentage (78.33%), hydrophobicity rate (62.67%), and an optimal surface tension reduction during growth in mineral medium supplemented with diesel oil (reduction of about 12mN/m), thus proving to be highly competitive with Alcanivorax and Pseudomonas strains. During growth in pure culture different level of biodegradation were detected for Alcanivorax strain A53 (52.7%), Pseudomonas strain A6 (38.2%) and Joostella strain A8 (26.8%). When growing in consortia, isolates achieved similar abundance values, with the best efficiency that was observed for the Joostella-Pseudomonas co-culture. Gas-chromatographic analysis revealed an increase in the biodegradation efficiency in co-cultures (about 90%), suggesting that the contemporary action of different bacterial species could improve the process. Results were useful to compare the efficiencies of well-known biosurfactant producers (i.e. Pseudomonas and Alcanivorax representatives) with a still unknown biosurfactant producer, i.e. Joostella, and to confirm them as optimal biosurfactant-producing candidates.
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Affiliation(s)
- Carmen Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Viale Ferdinando Stagno d'Alcontrès 31, 98166 Messina, Italy.
| | - Alessandro Ciro Rappazzo
- Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Spianata San Raineri 86, 98122 Messina, Italy
| | - Luigi Michaud
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Viale Ferdinando Stagno d'Alcontrès 31, 98166 Messina, Italy
| | - Emilio De Domenico
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Viale Ferdinando Stagno d'Alcontrès 31, 98166 Messina, Italy
| | - Carlos Rochera
- Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Carrer del Catedrátic José Beltrán Martinez 2, 46980 Paterna, Valencia, Spain; Regional Centre for Water Studies (CREA), University of Castilla-La Mancha, C/ Altagracia 50, 13071 Ciudad Real, Spain
| | - Antonio Camacho
- Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Carrer del Catedrátic José Beltrán Martinez 2, 46980 Paterna, Valencia, Spain
| | - Angelina Lo Giudice
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Viale Ferdinando Stagno d'Alcontrès 31, 98166 Messina, Italy; Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Spianata San Raineri 86, 98122 Messina, Italy
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19
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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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20
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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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21
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Sevilla E, Yuste L, Moreno R, Rojo F. Differential expression of the three Alcanivorax borkumensis SK2 genes coding for the P450 cytochromes involved in the assimilation of hydrocarbons. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:797-808. [PMID: 29052944 DOI: 10.1111/1758-2229.12598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 10/04/2017] [Indexed: 06/07/2023]
Abstract
Alcanivorax borkumensis, a marine bacterium highly specialized in degrading linear and branched alkanes, plays a key ecological role in the removal of marine oil spills. It contains several alternative enzyme systems for terminal hydroxylation of alkanes, including three P450 cytochromes (P450-1, P450-2 and P450-3). The present work shows cytochrome P450-1 to be expressed from the promoter of the upstream gene fdx. Promoter Pfdx was more active when C8 -C18 n-alkanes or pristane were assimilated than when pyruvate was available. The product of ABO_0199 (named CypR) was identified as a transcriptional activator of Pfdx . The inactivation of cypR impaired growth on tetradecane, showing the importance of the fdx-P450-1 and/or cypR genes. P450-2 expression was low-level and constitutive under all conditions tested, while that of P450-3 from promoter P450-3 was much higher when cells assimilated pristane than when n-alkanes or pyruvate were available. However, the inactivation of P450-3 had no visible impact on pristane assimilation. Cyo terminal oxidase, a component of the electron transport chain, was found to stimulate promoter PP450-3 activity, but it did not affect promoters Pfdx or PP450-2 . A. borkumensis, therefore, appears to carefully coordinate the expression of its multiple hydrocarbon degradation genes using both specific and global regulatory systems.
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Affiliation(s)
- Emma Sevilla
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Luis Yuste
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Renata Moreno
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
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22
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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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23
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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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24
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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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25
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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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26
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Reduction of the temperature sensitivity of Halomonas hydrothermalis by iron starvation combined with microaerobic conditions. Appl Environ Microbiol 2015; 81:2156-62. [PMID: 25595757 DOI: 10.1128/aem.03639-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The limits to biological processes on Earth are determined by physicochemical parameters, such as extremes of temperature and low water availability. Research into microbial extremophiles has enhanced our understanding of the biophysical boundaries which define the biosphere. However, there remains a paucity of information on the degree to which rates of microbial multiplication within extreme environments are determined by the availability of specific chemical elements. Here, we show that iron availability and the composition of the gaseous phase (aerobic versus microaerobic) determine the susceptibility of a marine bacterium, Halomonas hydrothermalis, to suboptimal and elevated temperature and salinity by impacting rates of cell division (but not viability). In particular, iron starvation combined with microaerobic conditions (5% [vol/vol] O2, 10% [vol/vol] CO2, reduced pH) reduced sensitivity to temperature across the 13°C range tested. These data demonstrate that nutrient limitation interacts with physicochemical parameters to determine biological permissiveness for extreme environments. The interplay between resource availability and stress tolerance, therefore, may shape the distribution and ecology of microorganisms within Earth's biosphere.
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27
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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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28
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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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29
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Mishamandani S, Gutierrez T, Aitken MD. DNA-based stable isotope probing coupled with cultivation methods implicates Methylophaga in hydrocarbon degradation. Front Microbiol 2014; 5:76. [PMID: 24578702 PMCID: PMC3936186 DOI: 10.3389/fmicb.2014.00076] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 02/11/2014] [Indexed: 11/13/2022] Open
Abstract
Marine hydrocarbon-degrading bacteria perform a fundamental role in the oxidation and ultimate removal of crude oil and its petrochemical derivatives in coastal and open ocean environments. Those with an almost exclusive ability to utilize hydrocarbons as a sole carbon and energy source have been found confined to just a few genera. Here we used stable isotope probing (SIP), a valuable tool to link the phylogeny and function of targeted microbial groups, to investigate hydrocarbon-degrading bacteria in coastal North Carolina sea water (Beaufort Inlet, USA) with uniformly labeled [(13)C]n-hexadecane. The dominant sequences in clone libraries constructed from (13)C-enriched bacterial DNA (from n-hexadecane enrichments) were identified to belong to the genus Alcanivorax, with ≤98% sequence identity to the closest type strain-thus representing a putative novel phylogenetic taxon within this genus. Unexpectedly, we also identified (13)C-enriched sequences in heavy DNA fractions that were affiliated to the genus Methylophaga. This is a contentious group since, though some of its members have been proposed to degrade hydrocarbons, substantive evidence has not previously confirmed this. We used quantitative PCR primers targeting the 16S rRNA gene of the SIP-identified Alcanivorax and Methylophaga to determine their abundance in incubations amended with unlabeled n-hexadecane. Both showed substantial increases in gene copy number during the experiments. Subsequently, we isolated a strain representing the SIP-identified Methylophaga sequences (99.9% 16S rRNA gene sequence identity) and used it to show, for the first time, direct evidence of hydrocarbon degradation by a cultured Methylophaga sp. This study demonstrates the value of coupling SIP with cultivation methods to identify and expand on the known diversity of hydrocarbon-degrading bacteria in the marine environment.
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Affiliation(s)
- Sara Mishamandani
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina Chapel Hill, NC, USA
| | - Tony Gutierrez
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina Chapel Hill, NC, USA ; Centre for Marine Biodiversity and Biotechnology, School of Life Sciences, Heriot-Watt University Edinburgh, UK
| | - Michael D Aitken
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina Chapel Hill, NC, USA
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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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31
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Fagervold SK, Urios L, Intertaglia L, Batailler N, Lebaron P, Suzuki MT. Pleionea mediterranea gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater. Int J Syst Evol Microbiol 2013; 63:2700-2705. [DOI: 10.1099/ijs.0.045575-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, cream-pigmented, non-motile, non-spore-forming straight rod, strain MOLA115T, was isolated from a coastal water sample from the Mediterranean Sea. On the basis of phylogenetic analysis of the 16S rRNA gene sequences, strain MOLA115T was shown to belong to the
Gammaproteobacteria
, adjacent to members of the genera
Marinicella
,
Arenicella
and
Kangiella
, sharing less than 89 % 16S rRNA gene sequence similarity with strains of all recognized species within the
Gammaproteobacteria
. The only isoprenoid quinone was ubiquinone-8. Polar lipids in strain MOLA115T included phosphatidylethanolamine, an aminolipid, phosphatidylglycerol and an aminophospholipid. Fatty acid analysis revealed iso-C15 : 0 and iso-C17 : 1ω9c to be the dominant components. The DNA G+C content was 44.5 mol%. Based upon the phenotypic and phylogenetic data, we propose that strain MOLA115T should be considered to represent a novel species in a new genus, for which the name Pleionea mediterranea gen. nov., sp. nov. is proposed. The type strain of Pleionea mediterranea is MOLA115T ( = CIP 110343T = DSM 25350T).
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Affiliation(s)
- Sonja K. Fagervold
- CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66650, Banyuls/Mer, France
- UPMC Université Paris 6, UMS 2348, UMR 7621, Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Laurent Urios
- Université de Pau et des Pays de l’Adour, IPREM UMR 5254, Equipe Environnement et Microbiologie, IBEAS, F-64013 PAU, France
| | - Laurent Intertaglia
- CNRS, UMS 2348, Observatoire Océanologique, F-66650, Banyuls/Mer, France
- UPMC Université Paris 6, UMS 2348, UMR 7621, Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Nicole Batailler
- CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66650, Banyuls/Mer, France
- UPMC Université Paris 6, UMS 2348, UMR 7621, Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Philippe Lebaron
- CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66650, Banyuls/Mer, France
- UPMC Université Paris 6, UMS 2348, UMR 7621, Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Marcelino T. Suzuki
- CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66650, Banyuls/Mer, France
- UPMC Université Paris 6, UMS 2348, UMR 7621, Observatoire Océanologique, F-66650 Banyuls/Mer, France
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32
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Starting Up Microbial Enhanced Oil Recovery. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 142:1-94. [DOI: 10.1007/10_2013_256] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Rocker D, Brinkhoff T, Grüner N, Dogs M, Simon M. Composition of humic acid-degrading estuarine and marine bacterial communities. FEMS Microbiol Ecol 2012; 80:45-63. [PMID: 22133061 DOI: 10.1111/j.1574-6941.2011.01269.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 11/17/2011] [Accepted: 11/21/2011] [Indexed: 11/27/2022] Open
Abstract
We examined the bacterial decomposition of humic acids (HA) in two flow-through culture experiments, one inoculated by marine and one by estuarine bacterial communities. In both experiments, the cultures were fed with HA media of salinities of 28 and 14, close to their ambient and a distinctly different, foreign salinity. HA were decomposed to > 60% of the initial concentration within 70 days, and the foreign salinity yielded the highest decomposition. A detrended correspondence analysis of denaturing gradient gel electrophoresis (DGGE) banding patterns showed that during incubation, the bacterial community composition underwent distinct changes. A phylogenetic analysis of DGGE bands excised and bacteria isolated at the end on HA as the sole carbon source showed that Alphaproteobacteria and Gammaproteobacteria largely dominated the communities in the marine flow-through cultures, whereas Gammaproteobacteria, Actinobacteria and Alphaproteobacteria dominated the estuarine communities. Eleven of 13 isolates obtained from both experiments were able to grow on HA as the sole carbon source, seven on phenol and three, affiliated to the Roseobacter clade, on various aromatic acids. The bacteria retrieved from the flow-through cultures were closely (96-99%) affiliated to organisms capable of degrading humic matter, aromatic and aliphatic compounds and also to other bacteria reported previously from the Wadden Sea and Weser estuary.
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Affiliation(s)
- Dagmar Rocker
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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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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35
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Manilla-Pérez E, Lange AB, Luftmann H, Robenek H, Steinbüchel A. Neutral lipid production in Alcanivorax borkumensis SK2 and other marine hydrocarbonoclastic bacteria. EUR J LIPID SCI TECH 2010. [DOI: 10.1002/ejlt.201000374] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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36
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Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment. Int J Syst Evol Microbiol 2010; 60:1832-1836. [DOI: 10.1099/ijs.0.017194-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, yellow-pigmented, rod-shaped, non-motile bacterium, strain KMM 3895T, was isolated from a marine sandy sample collected offshore from the Sea of Japan. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain KMM 3895T in the class Gammaproteobacteria, forming a separate branch, sharing 89.5 % sequence similarity with Nitrincola lacisaponensis 4CAT and 88–87 % similarity with the other members of the cluster, including members of Kangiella, Spongiibacter, Alcanivorax and Microbulbifer. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and an unknown phospholipid. Fatty acid analysis revealed C16 : 1
ω7, iso-C16 : 0, iso-C18 : 0 and C18 : 1
ω7 as dominant components. The DNA G+C content was determined to be 48.1 mol%. Based on its unique phenotypic characteristics and phylogenetic distance, the marine coastal sediment isolate KMM 3895T should be classified as a representative of a novel genus and species, for which the name Arenicella xantha gen. nov., sp. nov. is proposed. The type strain of Arenicella xantha is KMM 3895T (=NRIC 0759T =JCM 16153T).
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Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV. Marinicella litoralis gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater. Int J Syst Evol Microbiol 2010; 60:1613-1619. [DOI: 10.1099/ijs.0.016147-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, greyish–yellowish-pigmented, stenohaline, rod-shaped, non-motile bacterium, strain KMM 3900T, was isolated from a coastal seawater sample collected from the Sea of Japan. Based on phylogenetic analysis, strain KMM 3900T was positioned within the Gammaproteobacteria on a separate branch adjacent to members of the genera Reinekea and Kangiella, sharing less than 88 % 16S rRNA gene sequence similarity with all recognized species of the Gammaproteobacteria. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown phospholipids. Fatty acid analysis revealed iso-C15 : 0, C16 : 1
ω7c and C16 : 0 as the dominant components. The DNA G+C content was 43.8 mol%. Based on its unique phenotypic characteristics and phylogenetic remoteness, marine isolate KMM 3900T is considered to represent a novel genus and species, for which the name Marinicella litoralis gen. nov., sp. nov. is proposed. The type strain of Marinicella litoralis is KMM 3900T (=NRIC 0758T =JCM 16154T).
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Affiliation(s)
- Lyudmila A. Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Galina M. Frolova
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Valery V. Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
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38
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Lange AB, Tenberge KB, Robenek H, Steinbüchel A. Cell surface analysis of the lipid-discharging obligate hydrocarbonoclastic species of the genus Alcanivorax. EUR J LIPID SCI TECH 2010. [DOI: 10.1002/ejlt.201000048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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39
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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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40
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Analysis of lipid export in hydrocarbonoclastic bacteria of the genus Alcanivorax: identification of lipid export-negative mutants of Alcanivorax borkumensis SK2 and Alcanivorax jadensis T9. J Bacteriol 2009; 192:643-56. [PMID: 19933359 DOI: 10.1128/jb.00700-09] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Triacylglycerols (TAGs), wax esters (WEs), and polyhydroxyalkanoates (PHAs) are the major hydrophobic compounds synthesized in bacteria and deposited as cytoplasmic inclusion bodies when cells are cultivated under imbalanced growth conditions. The intracellular occurrence of these compounds causes high costs for downstream processing. Alcanivorax species are able to produce extracellular lipids when the cells are cultivated on hexadecane or pyruvate as the sole carbon source. In this study, we developed a screening procedure to isolate lipid export-negative transposon-induced mutants of bacteria of the genus Alcanivorax for identification of genes required for lipid export by employing the dyes Nile red and Solvent Blue 38. Three transposon-induced mutants of A. jadensis and seven of A. borkumensis impaired in lipid secretion were isolated. All isolated mutants were still capable of synthesizing and accumulating these lipids intracellularly and exhibited no growth defect. In the A. jadensis mutants, the transposon insertions were mapped in genes annotated as encoding a putative DNA repair system specific for alkylated DNA (Aj17), a magnesium transporter (Aj7), and a transposase (Aj5). In the A. borkumensis mutants, the insertions were mapped in genes encoding different proteins involved in various transport processes, like genes encoding (i) a heavy metal resistance (CZCA2) in mutant ABO_6/39, (ii) a multidrug efflux (MATE efflux) protein in mutant ABO_25/21, (iii) an alginate lyase (AlgL) in mutants ABO_10/30 and ABO_19/48, (iv) a sodium-dicarboxylate symporter family protein (GltP) in mutant ABO_27/29, (v) an alginate transporter (AlgE) in mutant ABO_26/1, or (vi) a two-component system protein in mutant ABO_27/56. Site-directed MATE, algE, and algL gene disruption mutants, which were constructed in addition, were also unable to export neutral lipids and confirmed the phenotype of the transposon-induced mutants. The putative localization of the different gene products and their possible roles in lipid excretion are discussed. Beside this, the composition of the intra- and extracellular lipids in the wild types and mutants were analyzed in detail.
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Nakano M, Okunishi S, Tanaka R, Maeda H. Denitrifying activity and homologous enzyme analysis of Alcanivorax dieselolei strain N1203. Biocontrol Sci 2009; 14:97-105. [PMID: 19785282 DOI: 10.4265/bio.14.97] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
An Alcanivorax dieselolei strain, termed strain N1203, was isolated from the consortia of ammonia-oxidizing bacteria (AOB) combined with denitrifying bacteria from our previous study and was shown to have ability to reduce nitrate to nitrite to either nitrous oxide or molecular nitrogen. Analysis of 16S rRNA gene sequences established strain N1203 as a member of the species Alcanivorax dieselolei. In addition, the ability of strain N1203 to utilize various organic substrates as the sole carbon source, supplemented with carbohydrates, amino acids, and n-alkane compounds, was investigated, and this strain was found to have a narrow substrate range of growth such as grycerol, succinate, ethanol and n-alkane hydrocarbon. Furthermore, N1203's stepwise denitrifying activity, utilizing succinate and hexadecane as sole carbon sources, was measured. Gene fragments of nirK and qnorB genes, which are involved in denitrifying activities, were obtained, cloned and sequenced. Phylogenetic analysis for these two genes showed that both the nirK and qnorB sequences, although found in separate branches within clusters, formed subclusters branching from uncultured environmental clones. This demonstrated the typical uniqueness of these genes from any cultivated denitrifiers. Thus, strain N1203 is novel type of denitrifying bacteria that demonstrated denitrifying activities when cultivated using succinate as the sole carbon source.
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Affiliation(s)
- Miyo Nakano
- Marine Microbiology, Faculty of Bioresources, Mie University, Kurimamachiya-cho 1577, Tsu, Mie 514-8507, Japan
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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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43
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Olivera NL, Nievas ML, Lozada M, del Prado G, Dionisi HM, Siñeriz F. Isolation and characterization of biosurfactant-producing Alcanivorax strains: hydrocarbon accession strategies and alkane hydroxylase gene analysis. Res Microbiol 2009; 160:19-26. [DOI: 10.1016/j.resmic.2008.09.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 09/04/2008] [Accepted: 09/29/2008] [Indexed: 11/27/2022]
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44
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Kanoh K, Adachi K, Katsuta A, Shizuri Y. Structural Determination and Proposed Biosynthesis of Alcanivorone, a Novel α-Pyrone Produced by Alcanivorax jadensis. J Antibiot (Tokyo) 2008; 61:70-4. [DOI: 10.1038/ja.2008.112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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45
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Kim H, Choo YJ, Cho JC. Litoricolaceae fam. nov., to include Litoricola lipolytica gen. nov., sp. nov., a marine bacterium belonging to the order Oceanospirillales. Int J Syst Evol Microbiol 2007; 57:1793-1798. [PMID: 17684259 DOI: 10.1099/ijs.0.65059-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile, chemoheterotrophic, facultatively aerobic, short-rod-shaped bacterium, designated IMCC1097(T), was isolated from coastal seawater (10 m depth) of the East Sea, Korea. The temperature, pH and NaCl ranges for growth were 15-30 degrees C, pH 5.0-10.0 and 1.5-10 % NaCl. The colonies of the strain were very small, having a mean diameter of 0.05 mm. 16S rRNA gene sequence data indicated that the strain was most closely related to genera within the class Gammaproteobacteria. Members of the most closely related genera showed less than 90 % sequence similarity and included Saccharospirillum (89.3 %), Oleiphilus (88.7 %), Reinekea (88.2 %), Alcanivorax (86.4-87.6 %) and Zooshikella (87.6 %), which represent five different families of the order Oceanospirillales. Phylogenetic analyses showed that this marine strain represented a distinct phylogenetic lineage in the order Oceanospirillales and could not be assigned to any of the defined families in the order. The predominant fatty acids were C(16 : 1) omega 7c and/or iso-C(15 : 0) 2-OH, C(18 : 1) omega 7c and C(10 : 0) 3-OH, and the DNA G+C content was 57.9 mol%. These chemotaxonomic properties, together with phenotypic characteristics, served to differentiate the strain from phylogenetically closely related genera. The very low sequence similarities (<90 %) and distant relationships between IMCC1097(T) and members of the order Oceanospirillales suggested that the strain merited classification within a novel genus within a novel family in the order. On the basis of taxonomic evidence collected in this study, a novel genus and species are proposed, Litoricola lipolytica gen. nov., sp. nov., within a new family Litoricolaceae fam. nov. Strain IMCC1097(T) (=KCCM 42360(T) =NBRC 102074(T)) is the type strain of Litoricola lipolytica.
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Affiliation(s)
- Hana Kim
- Division of Biology and Ocean Sciences, Inha University, Namgu, Incheon 402-751, Republic of Korea
| | - Yoe-Jin Choo
- Division of Biology and Ocean Sciences, Inha University, Namgu, Incheon 402-751, Republic of Korea
| | - Jang-Cheon Cho
- Division of Biology and Ocean Sciences, Inha University, Namgu, Incheon 402-751, Republic of Korea
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46
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Rivas R, García-Fraile P, Peix A, Mateos PF, Martínez-Molina E, Velázquez E. Alcanivorax balearicus sp. nov., isolated from Lake Martel. Int J Syst Evol Microbiol 2007; 57:1331-1335. [PMID: 17551053 DOI: 10.1099/ijs.0.64912-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated MACL04(T) was isolated from Lake Martel, a subterraneous saline lake in Mallorca (Spain). The complete 16S rRNA gene sequence of this strain showed nearly 100 % similarity to that of Alcanivorax dieselolei B-5(T). Despite this high similarity, strain MACL04(T) showed phenotypic, chemotaxonomic and molecular differences with respect to A. dieselolei, indicating that strain MACL04(T) represents a separate species. Cells of strain MACL04(T) were motile by means of a single polar or subpolar flagellum and colonies formed on media containing 1 % (v/v) Tween 20 were opaque and mucoid, with blue-green iridescence. The generation time of strain MACL04(T) in this medium was approximately half that of A. dieselolei B-5(T) and strain MACL04(T) did not produce lipases after incubation for 5 days. Strain MACL04(T) did not require NaCl for growth and grew in the presence of up to 15 % (w/v) NaCl. The strain was able to use alkanes as a sole carbon source; however, glucose could also be used, albeit weakly, as a carbon source. Several amino acids and organic acids were used as carbon sources. Strain MACL04(T) produced acid in media containing pyruvate as the sole carbon source. The major fatty acids were C(19 : 0) cyclo omega8c and C(16 : 0). The fatty acid C(16 : 1)omega8c, present in strain MACL04(T), was not detected in the recognized Alcanivorax species. The sequences of the large and short 16S-23S intergenic spacer regions showed similarities of 97.2 and 98.8 % (ungapped) with respect to A. dieselolei B-5(T). Partial sequences of gyrB and alkb genes showed 94.0 % similarity between strain MACL04(T) and A. dieselolei B-5(T). The G+C content of strain MACL04(T) was 62.8 mol%. The data from this polyphasic study indicate that strain MACL04(T) represents a novel species of the genus Alcanivorax, for which the name Alcanivorax balearicus sp. nov. is proposed. The type strain is MACL04(T) (=LMG 22508(T)=CECT 5683(T)).
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MESH Headings
- Alcanivoraceae/classification
- Alcanivoraceae/drug effects
- Alcanivoraceae/isolation & purification
- Alcanivoraceae/physiology
- Alkanes/metabolism
- Amino Acids/metabolism
- Anti-Bacterial Agents/pharmacology
- Bacterial Proteins/genetics
- Bacterial Typing Techniques
- Base Composition
- Carboxylic Acids/metabolism
- DNA Gyrase/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Fatty Acids/analysis
- Flagella/physiology
- Genes, rRNA
- Lipase/analysis
- Locomotion
- Mixed Function Oxygenases/genetics
- Molecular Sequence Data
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Saline Solution, Hypertonic/pharmacology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Spain
- Water Microbiology
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Affiliation(s)
- Raúl Rivas
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent KL, Ledeganckstraat 35, B-9000 Gent, Belgium
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
| | | | - Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
| | - Pedro F Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
| | | | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
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Yakimov MM, Timmis KN, Golyshin PN. Obligate oil-degrading marine bacteria. Curr Opin Biotechnol 2007; 18:257-66. [PMID: 17493798 DOI: 10.1016/j.copbio.2007.04.006] [Citation(s) in RCA: 442] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 03/18/2007] [Accepted: 04/30/2007] [Indexed: 11/17/2022]
Abstract
Over the past few years, a new and ecophysiologically unusual group of marine hydrocarbon-degrading bacteria - the obligate hydrocarbonoclastic bacteria (OHCB) - has been recognized and shown to play a significant role in the biological removal of petroleum hydrocarbons from polluted marine waters. The introduction of oil or oil constituents into seawater leads to successive blooms of a relatively limited number of indigenous marine bacterial genera--Alcanivorax, Marinobacter, Thallassolituus, Cycloclasticus, Oleispira and a few others (the OHCB)--which are present at low or undetectable levels before the polluting event. The types of OHCB that bloom depend on the latitude/temperature, salinity, redox and other prevailing physical-chemical factors. These blooms result in the rapid degradation of many oil constituents, a process that can be accelerated further by supplementation with limiting nutrients. Genome sequencing and functional genomic analysis of Alcanivorax borkumensis, the paradigm of OHCB, has provided significant insights into the genomic basis of the efficiency and versatility of its hydrocarbon utilization, the metabolic routes underlying its special hydrocarbon diet, and its ecological success. These and other studies have revealed the potential of OHCB for multiple biotechnological applications that include not only oil pollution mitigation, but also biopolymer production and biocatalysis.
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48
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Kalscheuer R, Stöveken T, Malkus U, Reichelt R, Golyshin PN, Sabirova JS, Ferrer M, Timmis KN, Steinbüchel A. Analysis of storage lipid accumulation in Alcanivorax borkumensis: Evidence for alternative triacylglycerol biosynthesis routes in bacteria. J Bacteriol 2006; 189:918-28. [PMID: 17122340 PMCID: PMC1797296 DOI: 10.1128/jb.01292-06] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine hydrocarbonoclastic bacteria, like Alcanivorax borkumensis, play a globally important role in bioremediation of petroleum oil contamination in marine ecosystems. Accumulation of storage lipids, serving as endogenous carbon and energy sources during starvation periods, might be a potential adaptation mechanism for coping with nutrient limitation, which is a frequent stress factor challenging those bacteria in their natural marine habitats. Here we report on the analysis of storage lipid biosynthesis in A. borkumensis strain SK2. Triacylglycerols (TAGs) and wax esters (WEs), but not poly(hydroxyalkanoic acids), are the principal storage lipids present in this and other hydrocarbonoclastic bacterial species. Although so far assumed to be a characteristic restricted to gram-positive actinomycetes, substantial accumulation of TAGs corresponding to a fatty acid content of more than 23% of the cellular dry weight is the first characteristic of large-scale de novo TAG biosynthesis in a gram-negative bacterium. The acyltransferase AtfA1 (ABO_2742) exhibiting wax ester synthase/acyl-coenzyme A:diacylglycerol acyltransferase (WS/DGAT) activity plays a key role in both TAG and WE biosynthesis, whereas AtfA2 (ABO_1804) was dispensable for storage lipid formation. However, reduced but still substantial residual TAG levels in atfA1 and atfA2 knockout mutants compellingly indicate the existence of a yet unknown WS/DGAT-independent alternative TAG biosynthesis route. Storage lipids of A. borkumensis were enriched in saturated fatty acids and accumulated as insoluble intracytoplasmic inclusions exhibiting great structural variety. Storage lipid accumulation provided only a slight growth advantage during short-term starvation periods but was not required for maintaining viability and long-term persistence during extended starvation phases.
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Affiliation(s)
- Rainer Kalscheuer
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Corrensstrasse 3, D-48149 Münster, Germany
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49
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Characterization of hydrocarbonoclastic bacterial communities from mangrove sediments in Guanabara Bay, Brazil. Res Microbiol 2006; 157:752-62. [DOI: 10.1016/j.resmic.2006.03.005] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Revised: 02/22/2006] [Accepted: 03/20/2006] [Indexed: 11/23/2022]
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50
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Abstract
Hundreds of millions of litres of petroleum enter the environment from both natural and anthropogenic sources every year. The input from natural marine oil seeps alone would be enough to cover all of the world's oceans in a layer of oil 20 molecules thick. That the globe is not swamped with oil is testament to the efficiency and versatility of the networks of microorganisms that degrade hydrocarbons, some of which have recently begun to reveal the secrets of when and how they exploit hydrocarbons as a source of carbon and energy.
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Affiliation(s)
- Ian M Head
- School of Civil Engineering and Geosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, UK.
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