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Guo D, Zhang Y, Dong X, Liu X, Pei Y, Duan J, Guan F. Accelerated deterioration corrosion of X70 steel by oxidation acid-producing process catalyzed by Acinetobacter soli in oil-water environment. Bioelectrochemistry 2023; 154:108539. [PMID: 37579554 DOI: 10.1016/j.bioelechem.2023.108539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/16/2023]
Abstract
Deterioration corrosion occurs between the external surface of oil pipelines and aerobic oil-degrading microorganisms in oil fields. Microorganisms with aerobic oil pollution remediation capabilities may catalyze more serious anaerobic microbial corrosion due to the carbon source supply. In this study, Acinetobacter soli strains were isolated from oil-contaminated environments, and their role in the deterioration corrosion behavior of X70 steel in an oil-water environment was investigated using the EDS multipoint scanning method. The presence of oil controls the deposition of carbon and phosphorus and diffusion of oxygen, leading to significant adhesion attraction and initial growth inhibition of biofilm on the metal surface. A. soli facilitates oxygen transfer and iron ion dissolution, thereby accelerating the pitting corrosion of X70 steel. This corrosion of the X70 steel, in turn, further accelerates the microbial degradation of oil, inhibiting the appearance of calcareous scale in the later stage of corrosion. The corrosion of X70 steel is influenced by microbial degradation, and the specific corrosion behaviors are related to the activity of A. soli in the petroleum environment. This study sheds light on the corrosion mechanisms of X70 steel by A. soli at different stages, providing insights into the interactions between microorganisms, oil pollution, and metal corrosion in oil fields.
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Affiliation(s)
- Ding Guo
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yimeng Zhang
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| | - Xucheng Dong
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xiangju Liu
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yingying Pei
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jizhou Duan
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| | - Fang Guan
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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Vázquez Rosas Landa M, De Anda V, Rohwer RR, Angelova A, Waldram G, Gutierrez T, Baker BJ. Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean. mSystems 2023; 8:e0061923. [PMID: 37702502 PMCID: PMC10654063 DOI: 10.1128/msystems.00619-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/19/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE Petroleum pollution in the ocean has increased because of rapid population growth and modernization, requiring urgent remediation. Our understanding of the metabolic response of native microbial communities to oil spills is not well understood. Here, we explored the baseline hydrocarbon-degrading communities of a subarctic Atlantic region to uncover the metabolic potential of the bacteria that inhabit the surface and subsurface water. We conducted enrichments with a 13C-labeled hydrocarbon to capture the fraction of the community actively using the hydrocarbon. We then combined this approach with metagenomics to identify the metabolic potential of this hydrocarbon-degrading community. This revealed previously undescribed uncultured bacteria with unique metabolic mechanisms involved in aerobic hydrocarbon degradation, indicating that temperature may be pivotal in structuring hydrocarbon-degrading baseline communities. Our findings highlight gaps in our understanding of the metabolic complexity of hydrocarbon degradation by native marine microbial communities.
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Affiliation(s)
- Mirna Vázquez Rosas Landa
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
- Instituto de Ciencias del Mar y Limnologia Universidad Nacional Autónoma de Mexico, Unidad Académica de Ecologia y Biodiversidad Acuática, Mexico City, Mexico
| | - Valerie De Anda
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Robin R. Rohwer
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Angelina Angelova
- School of Engineering and Physical Sciences, Institute of Mechanical, Process and Energy Engineering (IMPEE), Heriot-Watt University, Edinburgh, United Kingdom
| | - Georgia Waldram
- School of Engineering and Physical Sciences, Institute of Mechanical, Process and Energy Engineering (IMPEE), Heriot-Watt University, Edinburgh, United Kingdom
| | - Tony Gutierrez
- School of Engineering and Physical Sciences, Institute of Mechanical, Process and Energy Engineering (IMPEE), Heriot-Watt University, Edinburgh, United Kingdom
| | - Brett J. Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
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García MM, García de Llasera MP. Electrophoretic characterization of cellular and extracellular proteins from Selenastrum capricornutum cultures degrading benzo(a)pyrene and their identification by UPLC-ESI-TOF mass spectrometry. CHEMOSPHERE 2023:139284. [PMID: 37348613 DOI: 10.1016/j.chemosphere.2023.139284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
Selenastrum capricornutum efficiently degrades benzo(a)pyrene (BaP) but few proteins related to BaP degradation have been identified in this microalgae. So far, it has only been suggested that it could degrade BaP via the monooxygenase and/or dioxygenase pathways. To know more about this fact, in this work, cultures of S. capricornutum incubated with BaP were used to obtain the molecular weights (MWs) of proteins existing in its extra- and cellular extracts by electrophoresis and UPLC-ESI(+)-TOF MS analysis. The results of this proteomic approach indicated that BaP markedly induces the MWs: 6-20, 30, 45, and 65 kDa in cells; 6-20, 30.3, 38-45, and 55 kDa in liquid medium. So, these proteins could be related to BaP biodegradation. An identified protein with monooxygenase activity and rubredoxins (Rds) show to be related to BaP degradation: Rds could participate, together with the monooxygenase in the electron transfer during the formation of monohydroxylated-BaP metabolites. Rds may be also associated with a dioxygenase system that degrades BaP to form dihydrodiol-BaP metabolites. A multi-pass membrane protein was identified too, and it can regulate the transport of molecules like enzymes from inside the cell to the outside environment. At the same time, the presence of a dihydrolipoamide acetyltransferase validated the stress caused by the exposure to BaP. It is noteworthy that these findings provide valuable and original information on the characterization of the proteins of S. capricornutum cultures degrading BaP, whose enzymes have so far not been known. It is important to highlight that the functions of the identified proteins can help in understanding the metabolic and environmental behavior of this microalgae, and the extracts containing the degrading enzymes could be utilized in bioremediation applications.
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Affiliation(s)
- Manuel Méndez García
- Facultad de Química, Departamento de Química Analítica, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, D. F., 04510, Mexico
| | - Martha Patricia García de Llasera
- Facultad de Química, Departamento de Química Analítica, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, D. F., 04510, Mexico.
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Xiang W, Hong S, Xue Y, Ma Y. Functional Analysis of Novel alkB Genes Encoding Long-Chain n-Alkane Hydroxylases in Rhodococcus sp. Strain CH91. Microorganisms 2023; 11:1537. [PMID: 37375039 DOI: 10.3390/microorganisms11061537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Rhodococcus sp. strain CH91 is capable of utilizing long-chain n-alkanes as the sole carbon source. Two new genes (alkB1 and alkB2) encoding AlkB-type alkane hydroxylase were predicted by its whole-genome sequence analysis. The purpose of this study was to elucidate the functional role of alkB1 and alkB2 genes in the n-alkane degradation of strain CH91. RT-qPCR analyses revealed that the two genes were induced by n-alkanes ranging from C16 to C36 and the expression of the alkB2 gene was up-regulated much higher than that of alkB1. The knockout of the alkB1 or alkB2 gene in strain CH91 resulted in the obvious reduction of growth and degradation rates on C16-C36 n-alkanes and the alkB2 knockout mutant exhibited lower growth and degradation rate than the alkB1 knockout mutant. When gene alkB1 or alkB2 was heterologously expressed in Pseudomonas fluorescens KOB2Δ1, the two genes could restore its alkane degradation activity. These results demonstrated that both alkB1 and alkB2 genes were responsible for C16-C36 n-alkanes' degradation of strain CH91, and alkB2 plays a more important role than alkB1. The functional characteristics of the two alkB genes in the degradation of a broad range of n-alkanes make them potential gene candidates for engineering the bacteria used for bioremediation of petroleum hydrocarbon contaminations.
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Affiliation(s)
- Wei Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shan Hong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Desmarais M, Fraraccio S, Dolinova I, Ridl J, Strnad H, Kubatova H, Sevcu A, Suman J, Strejcek M, Uhlik O. Genomic analysis of Acinetobacter pittii CEP14 reveals its extensive biodegradation capabilities, including cometabolic degradation of cis-1,2-dichloroethene. Antonie Van Leeuwenhoek 2022; 115:1041-1057. [PMID: 35701646 DOI: 10.1007/s10482-022-01752-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/16/2022] [Indexed: 11/27/2022]
Abstract
Halogenated organic compounds are naturally occurring in subsurface environments; however, accumulation of the degradative intermediate cis-1,2-dichloroethene (cDCE) at soil and groundwater sites contaminated with xenobiotic chlorinated ethenes is a global environmental and public health issue. Identifying microorganisms capable of cDCE degradation in these environments is of interest because of their potential application to bioremediation techniques. In this study, we sequenced, assembled, and analyzed the complete genome of Acinetobacter pittii CEP14, a strain isolated from chloroethene-contaminated groundwater, that has demonstrated the ability for aerobic cometabolic degradation of cDCE in the presence of n-hexane, phenol, and toluene. The A. pittii CEP14 genome consists of a 3.93 Mbp-long chromosome (GenBank accession no. CP084921) with a GC content of 38.9% and three plasmids (GenBank accession no. CP084922, CP084923, and CP084924). Gene function was assigned to 83.4% of the 3,930 coding DNA sequences. Functional annotation of the genome revealed that the CEP14 strain possessed all genetic elements to mediate the degradation of a range of aliphatic and aromatic compounds, including n-hexane and phenol. In addition, it harbors gene clusters involved in cytosol detoxification and oxidative stress resistance, which could play a role in the mitigation of toxic chemical intermediates that can arise during the degradation of cDCE. Gene clusters for heavy metal and antibiotic resistance were also identified in the genome of CEP14. These results suggest that CEP14 may be a versatile degrader of xenobiotic compounds and well-adapted to polluted environments, where a combination of heavy metal and organic compound pollution is often found.
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Affiliation(s)
- Miguel Desmarais
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Serena Fraraccio
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Iva Dolinova
- Department of Applied Biology, Advanced Technologies and Innovation Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Institute for Nanomaterials, Technical University of Liberec, Liberec, Czech Republic
- Department of Genetics and Molecular Diagnostics, Regional Hospital Liberec, Liberec, Czech Republic
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hynek Strnad
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Kubatova
- State Office for Nuclear Safety, Prague, Czech Republic
| | - Alena Sevcu
- Department of Applied Biology, Advanced Technologies and Innovation Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Institute for Nanomaterials, Technical University of Liberec, Liberec, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic.
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Qin Y, Wang HH, Zhang HF, Dai WF, Jiao SY, Li BC, Zhang M. The effect of microorganisms on the biomodification of montan resin from lignite. JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION (1995) 2021; 71:1175-1184. [PMID: 34061727 DOI: 10.1080/10962247.2021.1936291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/08/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
Montan resin (MR) is an industrial by-product or solid waste generated during the production of refined montan wax and is not typically reused. In this paper, a bio-modification method using three strains of microorganisms, Acinetobacter venetianus (AV), Pseudomonas aeruginosa (PA), and Phanerochaete chrysosporium (PC), was studied to promote the performance and bio-function of MR so that MR could be recycled. MR can be degraded by these three microorganisms, and their weight loss rates were similar over the treatment period of 15 days. Compared with the original MR, the hydrophilicity of modified MRs was improved, which was related to the increase in apparent oil-water partition coefficients (Kows) and oxygen-containing and hydrophilic groups in modified MRs based on IR and GC-MS analysis. The bio-function of modified MRs by the three strains in terms of promoting maize seed germination and seedling growth was greater compared with untreated MR. Overall, these findings indicate that biomodified MRs might have useful agriculture applications.Implications: An environmentally-friendly method using microorganisms to achieve recycle of solid waste, montan resin (MR) was established in this study. Through this bio-treatment, the performance and bio-function of MR were both improved, that is the appearance and hydrophilicity of modified MRs were better than thoes in before, and the modified MRs treated by three strains showed the better promoting effects on maize seed germination and seedling growth than untreated MR, indicating the modified MRs have the certain potential of agricultural utilization in the future.
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Affiliation(s)
- Yi Qin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Huan-Hong Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Hui-Fen Zhang
- Faculty of Agriculture and Food, Food Security Research Institute of Yunnan Province, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Wei-Feng Dai
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Shi-Yun Jiao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Bao-Cai Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Mi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
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7
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Kong W, Zhao C, Gao X, Wang L, Tian Q, Liu Y, Xue S, Han Z, Chen F, Wang S. Characterization and Transcriptome Analysis of a Long-Chain n-Alkane-Degrading Strain Acinetobacter pittii SW-1. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18126365. [PMID: 34208299 PMCID: PMC8296198 DOI: 10.3390/ijerph18126365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022]
Abstract
Strain sw-1, isolated from 7619-m seawater of the Mariana Trench, was identified as Acinetobacter pittii by 16S rRNA gene and whole-genome sequencing. A. pittii sw-1 was able to efficiently utilize long-chain n-alkanes (C18–C36), but not short- and medium-chain n-alkanes (C8–C16). The degradation rate of C20 was 91.25%, followed by C18, C22, C24, C32, and C36 with the degradation rates of 89.30%, 84.03%, 80.29%, 30.29%, and 13.37%, respectively. To investigate the degradation mechanisms of n-alkanes for this strain, the genome and the transcriptome analyses were performed. Four key alkane hydroxylase genes (alkB, almA, ladA1, and ladA2) were identified in the genome. Transcriptomes of strain sw-1 grown in C20 or CH3COONa (NaAc) as the sole carbon source were compared. The transcriptional levels of alkB and almA, respectively, increased 78.28- and 3.51-fold in C20 compared with NaAc, while ladA1 and ladA2 did not show obvious change. The expression levels of other genes involved in the synthesis of unsaturated fatty acids, permeases, membrane proteins, and sulfur metabolism were also upregulated, and they might be involved in n-alkane uptake. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) confirmed that alkB expression was significantly induced by C20, C24, and C32, and almA induction extent by C24 and C32 was higher than that with C20. Furthermore, ladA2 expression was only induced by C32, and ladA1 expression was not induced by any of n-alkanes. In addition, A. pittii sw-1 could grow with 0%–3% NaCl or 8 out of 10 kinds of the tested heavy metals and degrade n-alkanes at 15 °C. Taken together, these results provide comprehensive insights into the degradation of long-chain n-alkanes by Acinetobacter isolated from the deep ocean environment.
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Affiliation(s)
- Weina Kong
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Cheng Zhao
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Xingwang Gao
- Hulangmao Oil Production Area in No.3 Oil Production Plant of Changqing Oilfield Company, Yan’an 717500, China;
| | - Liping Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Qianqian Tian
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Yu Liu
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Shuwen Xue
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
| | - Zhuang Han
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China;
| | - Fulin Chen
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
- Correspondence: (F.C.); (S.W.)
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (W.K.); (C.Z.); (L.W.); (Q.T.); (Y.L.); (S.X.)
- Correspondence: (F.C.); (S.W.)
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Acinetobacter baumannii: An Ancient Commensal with Weapons of a Pathogen. Pathogens 2021; 10:pathogens10040387. [PMID: 33804894 PMCID: PMC8063835 DOI: 10.3390/pathogens10040387] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter baumannii is regarded as a life-threatening pathogen associated with community-acquired and nosocomial infections, mainly pneumonia. The rise in the number of A. baumannii antibiotic-resistant strains reduces effective therapies and increases mortality. Bacterial comparative genomic studies have unraveled the innate and acquired virulence factors of A. baumannii. These virulence factors are involved in antibiotic resistance, environmental persistence, host-pathogen interactions, and immune evasion. Studies on host–pathogen interactions revealed that A. baumannii evolved different mechanisms to adhere to in order to invade host respiratory cells as well as evade the host immune system. In this review, we discuss current data on A. baumannii genetic features and virulence factors. An emphasis is given to the players in host–pathogen interaction in the respiratory tract. In addition, we report recent investigations into host defense systems using in vitro and in vivo models, providing new insights into the innate immune response to A. baumannii infections. Increasing our knowledge of A. baumannii pathogenesis may help the development of novel therapeutic strategies based on anti-adhesive, anti-virulence, and anti-cell to cell signaling pathways drugs.
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Li H, Zhang D, Luo J, Jones KC, Martin FL. Applying Raman Microspectroscopy to Evaluate the Effects of Nutrient Cations on Alkane Bioavailability to Acinetobacter baylyi ADP1. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15800-15810. [PMID: 33274919 DOI: 10.1021/acs.est.0c04944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Contamination with petroleum hydrocarbons causes extensive damage to ecological systems. On oil-contaminated sites, alkanes are major components; many indigenous bacteria can access and/or degrade alkanes. However, their ability to do so is affected by external properties of the soil, including nutrient cations. This study used Raman microspectroscopy to study how nutrient cations affect alkanes' bioavailability to Acinetobacter baylyi ADP1 (a known degrader). Treated with Na, K, Mg, and Ca at 10 mM, A. baylyi was exposed to seven n-alkanes (decane, dodecane, tetradecane, hexadecane, nonadecane, eicosane, and tetracosane) and one alkane mixture (mineral oil). Raman spectral analysis indicated that bioavailability of alkanes varied with carbon chain lengths, and additional cations altered the bacterial response to n-alkanes. Sodium significantly increased the bacterial affinity toward decane and dodecane, and K and Mg enhanced the bioavailability of tetradecane and hexadecane. In contrast, the bacterial response was inhibited by Ca for all alkanes. Similar results were observed in mineral oil exposure. Our study employed Raman spectral assay to offer a deep insight into how nutrient cations affect the bioavailability of alkanes, suggesting that nutrient cations can play a key role in influencing the harmful effects of hydrocarbons and could be optimized to enhance the bioremediation strategy.
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Affiliation(s)
- Hanbing Li
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, U.K
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, U.K
- School of Environment, Tsinghua University, Beijing 100086, China
| | - Jun Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Kevin C Jones
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, U.K
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
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Beraud-Martínez LK, Gómez-Gil B, Franco-Nava MÁ, Almazán-Rueda P, Betancourt-Lozano M. A metagenomic assessment of microbial communities in anaerobic bioreactors and sediments: Taxonomic and functional relationships. Anaerobe 2020; 68:102296. [PMID: 33207267 DOI: 10.1016/j.anaerobe.2020.102296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/20/2020] [Accepted: 11/11/2020] [Indexed: 02/04/2023]
Abstract
The present study used metagenomic sequencing, metagenome assembly and physical-chemical analysis to describe taxonomically and functionally 3 anaerobic bioreactors treating manure (LI), brewery (BR) and cornmeal (CO) wastes, and an anaerobic estuarine sediment (ES). Proteobacteria, Firmicutes, Euryarchaeota and Bacteroidetes were the most abundant Phyla in all metagenomes. A bacteria/archaea ratio of 3.4 was found in the industrial full-scale anaerobic bioreactors BR and CO, while ratios greater than 10 were found for LI and ES. Canonical correspondence analysis showed that environmental variables such as chemical oxygen demand, lipid content, and ammonium nitrogen influenced the ordination of taxonomic groups. Mesotoga prima was linked to high-temperature conditions, particularly in the BR bioreactor, along with the presence of heat shock proteins genes. Likewise, the hydrogenotrophic methanogen, Methanoregula formicica, was associated with high ammonium concentration in LI bioreactor. The interactions of microbes with specific methanogenic pathways were identified using Clusters of Orthologous Groups (COG) functions, while metagenome-assembled genomes (MAGs) further confirmed relationships between taxa and functions. Our results provide valuable information to understand microbial processes in anaerobic environments.
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Affiliation(s)
- Liov Karel Beraud-Martínez
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Unit for Aquaculture, Avenida Sábalo-Cerritos SS/n, Mazatlán, Sinaloa, 82112, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Unit for Aquaculture, Avenida Sábalo-Cerritos SS/n, Mazatlán, Sinaloa, 82112, Mexico
| | - Miguel Ángel Franco-Nava
- Tecnológico Nacional de México, Campus Mazatlán. Calle Corsario 1 No. 203 Col. Urías, A.P. 757, Mazatlán, Sinaloa, 82070, Mexico
| | - Pablo Almazán-Rueda
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Unit for Aquaculture, Avenida Sábalo-Cerritos SS/n, Mazatlán, Sinaloa, 82112, Mexico
| | - Miguel Betancourt-Lozano
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Unit for Aquaculture, Avenida Sábalo-Cerritos SS/n, Mazatlán, Sinaloa, 82112, Mexico.
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11
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Ho MT, Li MSM, McDowell T, MacDonald J, Yuan ZC. Characterization and genomic analysis of a diesel-degrading bacterium, Acinetobacter calcoaceticus CA16, isolated from Canadian soil. BMC Biotechnol 2020; 20:39. [PMID: 32711499 PMCID: PMC7477861 DOI: 10.1186/s12896-020-00632-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 07/16/2020] [Indexed: 12/18/2022] Open
Abstract
Background With the high demand for diesel across the world, environmental decontamination from its improper usage, storage and accidental spills becomes necessary. One highly environmentally friendly and cost-effective decontamination method is to utilize diesel-degrading microbes as a means for bioremediation. Here, we present a newly isolated and identified strain of Acinetobacter calcoaceticus (‘CA16’) as a candidate for the bioremediation of diesel-contaminated areas. Results Acinetobacter calcoaceticus CA16 was able to survive and grow in minimal medium with diesel as the only source of carbon. We determined through metabolomics that A. calcoaceticus CA16 appears to be efficient at diesel degradation. Specifically, CA16 is able to degrade 82 to 92% of aliphatic alkane hydrocarbons (CnHn + 2; where n = 12–18) in 28 days. Several diesel-degrading genes (such as alkM and xcpR) that are present in other microbes were also found to be activated in CA16. Conclusions The results presented here suggest that Acinetobacter strain CA16 has good potential in the bioremediation of diesel-polluted environments.
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Affiliation(s)
- Margaret T Ho
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Michelle S M Li
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada
| | - Tim McDowell
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, N5V 4T3, Canada
| | - Jacqueline MacDonald
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada
| | - Ze-Chun Yuan
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada. .,London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, N5V 4T3, Canada.
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12
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Xu A, Wang D, Ding Y, Zheng Y, Wang B, Wei Q, Wang S, Yang L, Ma LZ. Integrated Comparative Genomic Analysis and Phenotypic Profiling of Pseudomonas aeruginosa Isolates From Crude Oil. Front Microbiol 2020; 11:519. [PMID: 32300337 PMCID: PMC7145413 DOI: 10.3389/fmicb.2020.00519] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/10/2020] [Indexed: 11/22/2022] Open
Abstract
Pseudomonas aeruginosa is an environmental microorganism that can thrive in diverse ecological niches including plants, animals, water, soil, and crude oil. It also one of the microorganism widely used in tertiary recovery of crude oil and bioremediation. However, the genomic information regarding the mechanisms of survival and adapation of this bacterium in crude oil is still limited. In this study, three Pseudomonads strains (named as IMP66, IMP67, and IMP68) isolated from crude oil were taken for whole-genome sequencing by using a hybridized PacBio and Illumina approach. The phylogeny analysis showed that the three strains were all P. aeruginosa species and clustered in clade 1, the group with PAO1 as a representitive. Subsequent comparative genomic analysis revealed a high degree of individual genomic plasticity, with a probable alkane degradation genomic island, one type I-F CRISPR-Cas system and several prophages integrated into their genomes. Nine genes encoding alkane hydroxylases (AHs) homologs were found in each strain, which might enable these strains to degrade alkane in crude oil. P. aeruginosa can produce rhamnolipids (RLs) biosurfactant to emulsify oil, which enables their survival in crude oil enviroments. Our previous report showed that IMP67 and IMP68 were high RLs producers, while IMP66 produced little RLs. Genomic analysis suggested that their RLs yield was not likely due to differences at genetic level. We then further analyzed the quorum sensing (QS) signal molecules that regulate RLs synthesis. IMP67 and IMP68 produced more N-acyl-homoserine lactones (AHLs) signal molecules than that of PAO1 and IMP66, which could explain their high RLs yield. This study provides evidence for adaptation of P. aeruginosa in crude oil and proposes the potential application of IMP67 and IMP68 in microbial-enhanced oil recovery and bioremediation.
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Affiliation(s)
- Anming Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yichen Ding
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Jurong West, Singapore
| | - Yaqian Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bo Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qing Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shiwei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Luyan Z Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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13
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Gibu N, Kasai D, Ikawa T, Akiyama E, Fukuda M. Characterization and Transcriptional Regulation of n-Alkane Hydroxylase Gene Cluster of Rhodococcus jostii RHA1. Microorganisms 2019; 7:microorganisms7110479. [PMID: 31652785 PMCID: PMC6921075 DOI: 10.3390/microorganisms7110479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 11/16/2022] Open
Abstract
Gram-positive actinomycete Rhodococcus jostii RHA1 is able to grow on C10 to C19 n-alkanes as a sole source of carbon and energy. To clarify, the n-alkane utilization pathway-a cluster of 5 genes (alkBrubA1A2BalkU) which appeared to be involved in n-alkane degradation-was identified and the transcriptional regulation of these genes was characterized. Reverse transcription-PCR analyses revealed that these genes constituted an operon and were transcribed in the presence of n-alkane. Inactivation of alkB led to the absence of the ability to utilize n-undecane. The alkB mutation resulted in reduction of growth rates on C10 and C12 n-alkanes; however, growths on C13 to C19 n-alkanes were not affected by this mutation. These results suggested that alkB was essential for the utilization of C10 to C12 n-alkanes. Inactivation of alkU showed the constitutive expression of alkB. Purified AlkU is able to bind to the putative promoter region of alkB, suggesting that AlkU played a role in repression of the transcription of alk operon. The results of this study indicated that alkB was involved in the medium-chain n-alkanes degradation of strain RHA1 and the transcription of alk operon was negatively regulated by alkU-encoded regulator. This report is important to understand the n-alkane degradation pathway of R. jostii, including the transcriptional regulation of alk gene cluster.
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Affiliation(s)
- Namiko Gibu
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
| | - Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan.
| | - Takumi Ikawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
| | - Emiko Akiyama
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
| | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
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14
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Gregson BH, Metodieva G, Metodiev MV, McKew BA. Differential protein expression during growth on linear versus branched alkanes in the obligate marine hydrocarbon-degrading bacterium Alcanivorax borkumensis SK2 T. Environ Microbiol 2019; 21:2347-2359. [PMID: 30951249 PMCID: PMC6850023 DOI: 10.1111/1462-2920.14620] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/19/2019] [Indexed: 02/02/2023]
Abstract
Alcanivorax borkumensis SK2T is an important obligate hydrocarbonoclastic bacterium (OHCB) that can dominate microbial communities following marine oil spills. It possesses the ability to degrade branched alkanes which provides it a competitive advantage over many other marine alkane degraders that can only degrade linear alkanes. We used LC–MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on linear (n‐C14) or branched (pristane) alkanes. During growth on n‐C14, A. borkumensis expressed a complete pathway for the terminal oxidation of n‐alkanes to their corresponding acyl‐CoA derivatives including AlkB and AlmA, two CYP153 cytochrome P450s, an alcohol dehydrogenase and an aldehyde dehydrogenase. In contrast, during growth on pristane, an alternative alkane degradation pathway was expressed including a different cytochrome P450, an alcohol oxidase and an alcohol dehydrogenase. A. borkumensis also expressed a different set of enzymes for β‐oxidation of the resultant fatty acids depending on the growth substrate utilized. This study significantly enhances our understanding of the fundamental physiology of A. borkumensis SK2T by identifying the key enzymes expressed and involved in terminal oxidation of both linear and branched alkanes. It has also highlights the differential expression of sets of β‐oxidation proteins to overcome steric hinderance from branched substrates.
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Affiliation(s)
- Benjamin H Gregson
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Gergana Metodieva
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Metodi V Metodiev
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
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15
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Acinetobacter baumannii OxyR Regulates the Transcriptional Response to Hydrogen Peroxide. Infect Immun 2018; 87:IAI.00413-18. [PMID: 30297527 DOI: 10.1128/iai.00413-18] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/03/2018] [Indexed: 12/21/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative opportunistic pathogen that causes diverse infections, including pneumonia, bacteremia, and wound infections. Due to multiple intrinsic and acquired antimicrobial-resistance mechanisms, A. baumannii isolates are commonly multidrug resistant, and infections are notoriously difficult to treat. The World Health Organization recently highlighted carbapenem-resistant A. baumannii as a "critical priority" for the development of new antimicrobials because of the risk to human health posed by this organism. Therefore, it is important to discover the mechanisms used by A. baumannii to survive stresses encountered during infection in order to identify new drug targets. In this study, by use of in vivo imaging, we identified hydrogen peroxide (H2O2) as a stressor produced in the lung during A. baumannii infection and defined OxyR as a transcriptional regulator of the H2O2 stress response. Upon exposure to H2O2, A. baumannii differentially transcribes several hundred genes. However, the transcriptional upregulation of genes predicted to detoxify hydrogen peroxide is abolished in an A. baumannii strain in which the transcriptional regulator oxyR is genetically inactivated. Moreover, inactivation of oxyR in both antimicrobial-susceptible and multidrug-resistant A. baumannii strains impairs growth in the presence of H2O2 OxyR is a direct regulator of katE and ahpF1, which encode the major H2O2-degrading enzymes in A. baumannii, as confirmed through measurement of promoter binding by recombinant OxyR in electromobility shift assays. Finally, an oxyR mutant is less fit than wild-type A. baumannii during infection of the murine lung. This work reveals a mechanism used by this important human pathogen to survive H2O2 stress encountered during infection.
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16
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Draft Genome Sequence of n-Alkane-Utilizing Acinetobacter sp. Strain BS1, Isolated from Ethane Oxidation Culture. GENOME ANNOUNCEMENTS 2018; 6:6/22/e00465-18. [PMID: 29853505 PMCID: PMC5981037 DOI: 10.1128/genomea.00465-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft whole-genome sequence of a bacterial strain, Acinetobacter sp. strain BS1, isolated from black soil during ethane oxidation culture. Medium- or long-chain alkane oxidation-related genes were identified; however, the short-chain alkane monooxygenase was not detected.
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17
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Liu YF, Galzerani DD, Mbadinga SM, Zaramela LS, Gu JD, Mu BZ, Zengler K. Metabolic capability and in situ activity of microorganisms in an oil reservoir. MICROBIOME 2018; 6:5. [PMID: 29304850 PMCID: PMC5756336 DOI: 10.1186/s40168-017-0392-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/19/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy. RESULTS Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach. Almost complete genome sequences obtained by differential binning highlight the distinct capability of different community members to degrade hydrocarbons under oxic or anoxic condition. Transcriptomic data delineate active members of the community and give insights that Acinetobacter species completely oxidize alkanes into carbon dioxide with the involvement of oxygen, and Archaeoglobus species mainly ferment alkanes to generate acetate which could be consumed by Methanosaeta species. Furthermore, nutritional requirements based on amino acid and vitamin auxotrophies suggest a complex network of interactions and dependencies among active community members that go beyond classical syntrophic exchanges; this network defines community composition and microbial ecology in oil reservoirs undergoing secondary recovery. CONCLUSION Our data expand current knowledge of the metabolic potential and role in hydrocarbon metabolism of individual members of thermophilic microbial communities from an oil reservoir. The study also reveals potential metabolic exchanges based on vitamin and amino acid auxotrophies indicating the presence of complex network of interactions between microbial taxa within the community.
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Affiliation(s)
- Yi-Fan Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, 130 Meilong Road, Xuhui District, Shanghai, 200237, People's Republic of China
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0760, USA
| | - Daniela Domingos Galzerani
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0760, USA
| | - Serge Maurice Mbadinga
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, 130 Meilong Road, Xuhui District, Shanghai, 200237, People's Republic of China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, 200237, People's Republic of China
| | - Livia S Zaramela
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0760, USA
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, 130 Meilong Road, Xuhui District, Shanghai, 200237, People's Republic of China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, 200237, People's Republic of China.
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0760, USA.
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0436, USA.
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18
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Kothari A, Charrier M, Wu YW, Malfatti S, Zhou CE, Singer SW, Dugan L, Mukhopadhyay A. Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization. FEMS Microbiol Lett 2016; 363:fnw224. [PMID: 27664055 PMCID: PMC5074533 DOI: 10.1093/femsle/fnw224] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2016] [Indexed: 02/04/2023] Open
Abstract
The hydrocarbonoclastic bacterium Acinetobacter venetianus RAG-1 has attracted substantial attention due to its powerful oil-degrading capabilities and its potential to play an important ecological role in the cleanup of alkanes. In this study, we compare the transcriptome of the strain RAG-1 grown in dodecane, the corresponding alkanol (dodecanol), and sodium acetate for the characterization of genes involved in dodecane uptake and utilization. Comparison of the transcriptional responses of RAG-1 grown on dodecane led to the identification of 1074 genes that were differentially expressed relative to sodium acetate. Of these, 622 genes were upregulated when grown in dodecane. The highly upregulated genes were involved in alkane catabolism, along with stress response. Our data suggest AlkMb to be primarily involved in dodecane oxidation. Transcriptional response of RAG-1 grown on dodecane relative to dodecanol also led to the identification of permease, outer membrane protein and thin fimbriae coding genes potentially involved in dodecane uptake. This study provides the first model for key genes involved in alkane uptake and metabolism in A. venetianus RAG-1. Analysis of the transcriptome of the oil-degrading bacterium Acinetobacter venetianus RAG-1 helps in identification of genes that are involved in uptake and metabolism of alkanes, thus helping in bioremediation.
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Affiliation(s)
- Ankita Kothari
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8099, USA
| | - Marimikel Charrier
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8099, USA
| | - Yu-Wei Wu
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8099, USA.,Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei 110, Taiwan Biosciences
| | - Stephanie Malfatti
- Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550-5507, USA
| | - Carol E Zhou
- Computing Applications and Research Department, Lawrence Livermore National Laboratory, Livermore, CA 94550-9234, USA
| | - Steven W Singer
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8099, USA
| | - Larry Dugan
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei 110, Taiwan Biosciences.,Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550-5507, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8099, USA
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19
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Genomic and phenotypic characterization of the species Acinetobacter venetianus. Sci Rep 2016; 6:21985. [PMID: 26902269 PMCID: PMC4763211 DOI: 10.1038/srep21985] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/01/2016] [Indexed: 11/10/2022] Open
Abstract
Crude oil is a complex mixture of hydrocarbons and other organic compounds that can produce serious environmental problems and whose removal is highly demanding in terms of human and technological resources. The potential use of microbes as bioremediation agents is one of the most promising fields in this area. Members of the species Acinetobacter venetianus have been previously characterized for their capability to degrade n-alkanes and thus may represent interesting model systems to implement this process. Although a preliminary experimental characterization of the overall hydrocarbon degradation capability has been performed for five of them, to date, the genetic/genomic features underlying such molecular processes have not been identified. Here we have integrated genomic and phenotypic information for six A. venetianus strains, i.e. VE-C3, RAG-1T, LUH 13518, LUH 7437, LUH 5627 and LUH 8758. Besides providing a thorough description of the A. venetianus species, these data were exploited to infer the genetic features (presence/absence patterns of genes) and the short-term evolutionary events possibly responsible for the variability in n-alkane degradation efficiency of these strains, including the mechanisms of interaction with the fuel droplet and the subsequent catabolism of this pollutant.
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20
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Kurth D, Belfiore C, Gorriti MF, Cortez N, Farias ME, Albarracín VH. Genomic and proteomic evidences unravel the UV-resistome of the poly-extremophile Acinetobacter sp. Ver3. Front Microbiol 2015; 6:328. [PMID: 25954258 PMCID: PMC4406064 DOI: 10.3389/fmicb.2015.00328] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/01/2015] [Indexed: 12/20/2022] Open
Abstract
Ultraviolet radiation can damage biomolecules, with detrimental or even lethal effects for life. Even though lower wavelengths are filtered by the ozone layer, a significant amount of harmful UV-B and UV-A radiation reach Earth's surface, particularly in high altitude environments. high-altitude Andean lakes (HAALs) are a group of disperse shallow lakes and salterns, located at the Dry Central Andes region in South America at altitudes above 3,000 m. As it is considered one of the highest UV-exposed environments, HAAL microbes constitute model systems to study UV-resistance mechanisms in environmental bacteria at various complexity levels. Herein, we present the genome sequence of Acinetobacter sp. Ver3, a gammaproteobacterium isolated from Lake Verde (4,400 m), together with further experimental evidence supporting the phenomenological observations regarding this bacterium ability to cope with increased UV-induced DNA damage. Comparison with the genomes of other Acinetobacter strains highlighted a number of unique genes, such as a novel cryptochrome. Proteomic profiling of UV-exposed cells identified up-regulated proteins such as a specific cytoplasmic catalase, a putative regulator, and proteins associated to amino acid and protein synthesis. Down-regulated proteins were related to several energy-generating pathways such as glycolysis, beta-oxidation of fatty acids, and electronic respiratory chain. To the best of our knowledge, this is the first report on a genome from a polyextremophilic Acinetobacter strain. From the genomic and proteomic data, an "UV-resistome" was defined, encompassing the genes that would support the outstanding UV-resistance of this strain.
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Affiliation(s)
- Daniel Kurth
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Carolina Belfiore
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Marta F Gorriti
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Néstor Cortez
- Centro Científico Tecnológico, IBR - CONICET, Universidad Nacional de Rosario Rosario, Argentina
| | - María E Farias
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Virginia H Albarracín
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina ; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán Argentina
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21
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Jung J, Park W. Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives. Appl Microbiol Biotechnol 2015; 99:2533-48. [PMID: 25693672 DOI: 10.1007/s00253-015-6439-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 01/11/2023]
Abstract
Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.
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Affiliation(s)
- Jaejoon Jung
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
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Singh S, Joshi P, Chopade BA. Pathway Analysis of Acinetobacter baylyi: A Combined Bioinformatic and Genomics Approach. Chem Biol Drug Des 2011; 78:893-905. [DOI: 10.1111/j.1747-0285.2011.01191.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Comparative genomic analysis of Acinetobacter oleivorans DR1 to determine strain-specific genomic regions and gentisate biodegradation. Appl Environ Microbiol 2011; 77:7418-24. [PMID: 21856821 DOI: 10.1128/aem.05231-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The comparative genomics of Acinetobacter oleivorans DR1 assayed with A. baylyi ADP1, A. calcoaceticus PHEA-2, and A. baumannii ATCC 17978 revealed that the incorporation of phage-related genomic regions and the absence of transposable elements have contributed to the large size (4.15 Mb) of the DR1 genome. A horizontally transferred genomic region and a higher proportion of transcriptional regulator- and signal peptide-coding genes were identified as characteristics of the DR1 genome. Incomplete glucose metabolism, metabolic pathways of aromatic compounds, biofilm formation, antibiotics and metal resistance, and natural competence genes were conserved in four compared genomes. Interestingly, only strain DR1 possesses gentisate 1,2-dioxygenase (nagI) and grows on gentisate, whereas other species cannot. Expression of the nagI gene was upregulated during gentisate utilization, and four downstream open reading frames (ORFs) were cotranscribed, supporting the notion that gentisate metabolism is a unique characteristic of strain DR1. The genomic analysis of strain DR1 provides additional insights into the function, ecology, and evolution of Acinetobacter species.
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Di Capua C, Bortolotti A, Farías ME, Cortez N. UV-resistant Acinetobacter sp. isolates from Andean wetlands display high catalase activity. FEMS Microbiol Lett 2011; 317:181-9. [DOI: 10.1111/j.1574-6968.2011.02231.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Fuangthong M, Julotok M, Chintana W, Kuhn K, Rittiroongrad S, Vattanaviboon P, Mongkolsuk S. Exposure of Acinetobacter baylyi ADP1 to the biocide chlorhexidine leads to acquired resistance to the biocide itself and to oxidants. J Antimicrob Chemother 2010; 66:319-22. [DOI: 10.1093/jac/dkq435] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Li C, Wang H, Zhou L, Zhang Y, Song F, Zhang J. Quantitative measurement of pH influence on SalR regulated gene expression in Acinetobacter baylyi ADP1. J Microbiol Methods 2009; 79:8-12. [DOI: 10.1016/j.mimet.2009.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 07/08/2009] [Accepted: 07/08/2009] [Indexed: 10/20/2022]
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Kato T, Miyanaga A, Kanaya S, Morikawa M. Gene cloning and characterization of an aldehyde dehydrogenase from long-chain alkane-degrading Geobacillus thermoleovorans B23. Extremophiles 2009; 14:33-9. [PMID: 19787414 DOI: 10.1007/s00792-009-0285-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 09/15/2009] [Indexed: 12/01/2022]
Abstract
Geobacillus thermoleovorans B23 is capable of degrading long-chain alkanes at 70 degrees C. Bt-aldh, an aldehyde dehydrogenase gene in B23, was located in the upstream region of p21 whose expression level was dramatically increased when alkane degradation was started (Kato et al. 2009, BMC Microbiol 9:60). Like p21, transcription level of Bt-aldh was also increased upon alkane degradation. Bt-Aldh (497 aa, MW = 53,886) was overproduced in Escherichia coli, purified, and characterized biochemically. Bt-Aldh acted as an octamer, required NAD(+) as a coenzyme, and showed high activity against aliphatic long-chain aldehydes such as tetradecanal. The optimum condition for activity was 50-55 degrees C and pH 10.0. The activity was elevated to two- to threefold in the presence of 2 mM Ba(2+), Ca(2+), or Sr(2+), while Mg(2+) and Zn(2+) inhibited the enzyme activity. Bt-Aldh represents thermophilic aldehyde dehydrogenases responsible for degradation of long-chain alkanes.
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Affiliation(s)
- Tomohisa Kato
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
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de Berardinis V, Durot M, Weissenbach J, Salanoubat M. Acinetobacter baylyi ADP1 as a model for metabolic system biology. Curr Opin Microbiol 2009; 12:568-76. [PMID: 19709925 DOI: 10.1016/j.mib.2009.07.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 07/15/2009] [Indexed: 01/20/2023]
Abstract
Information produced by the annotation of an 'average bacterial genome' can be separated into three parts. One-third represents what we know, another third what we think we know, and the last third what we know we do not know. Knowledge of metabolism is also described by this three thirds rule. Understanding how a cell operates will require a better knowledge of the two ignored thirds of its parts. Moreover, metabolism needs to be further investigated using organisms whose life styles are different from those of model organisms. In this short review, we present Acinetobacter baylyi ADP1 as an environmental model especially suitable for large-scale genetic manipulation. Resources have been constructed in the past few years that can form the basis for diverse metabolic studies: the genome sequence, a single gene mutant collection, and a genome-scale metabolic model.
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Phrommanich S, Suanjit S, Upatham S, Grams SV, Kruatrachue M, Pokethitiyook P, Korge G, Hofmann A. Quantitative detection of the oil-degrading bacterium Acinetobacter sp. strain MUB1 by hybridization probe based real-time PCR. Microbiol Res 2009; 164:486-92. [PMID: 17459684 DOI: 10.1016/j.micres.2007.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 03/13/2007] [Accepted: 03/13/2007] [Indexed: 10/23/2022]
Abstract
Quantitative detection of the oil-degrading bacterium Acinetobacter sp. strain MUB1 was performed using the SoilMaster() DNA Extraction Kit (Epicentre, Madison, Wisconsin) and hybridization probe based real-time PCR. The detection target was the alkane hydroxylase gene (alkM). Standard curve construction showed a linear relation between log values of cell concentrations and real-time PCR threshold cycles over five orders of magnitude between 5.4+/-3.0x10(6) and 5.4+/-3.0x10(2)CFUml(-1) cell suspension. The detection limit was about 540CFUml(-1), which was ten times more sensitive than conventional PCR. The quantification of Acinetobacter sp. strain MUB1 cells in soil samples resulted in 46.67%, 82.41%, and 87.59% DNA recovery with a detection limit of 5.4+/-3.0x10(4)CFUg(-1) dry soil. In this study, a method was developed for the specific, sensitive, and rapid quantification of the Acinetobacter sp. strain MUB1 in soil samples.
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Affiliation(s)
- Seksan Phrommanich
- Biological Science Graduate Program, Faculty of Science, Burapha University, Bangsaen, Chonburi, Thailand.
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Bordenave S, Goñi-Urriza MS, Caumette P, Duran R. Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat. Appl Environ Microbiol 2007; 73:6089-97. [PMID: 17704271 PMCID: PMC2075027 DOI: 10.1128/aem.01352-07] [Citation(s) in RCA: 114] [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
The effects of petroleum contamination on the bacterial community of a pristine microbial mat from Salins-de-Giraud (Camargue, France) have been investigated. Mats were maintained as microcosms and contaminated with no. 2 fuel oil from the wreck of the Erika. The evolution of the complex bacterial community was monitored by combining analyses based on 16S rRNA genes and their transcripts. 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) analyses clearly showed the effects of the heavy fuel oil after 60 days of incubation. At the end of the experiment, the initial community structure was recovered, illustrating the resilience of this microbial ecosystem. In addition, the responses of the metabolically active bacterial community were evaluated by T-RFLP and clone library analyses based on 16S rRNA. Immediately after the heavy fuel oil was added to the microcosms, the structure of the active bacterial community was modified, indicating a rapid microbial mat response. Members of the Gammaproteobacteria were initially dominant in the contaminated microcosms. Pseudomonas and Acinetobacter were the main genera representative of this class. After 90 days of incubation, the Gammaproteobacteria were superseded by "Bacilli" and Alphaproteobacteria. This study shows the major changes that occur in the microbial mat community at different time periods following contamination. At the conclusion of the experiment, the RNA approach also demonstrated the resilience of the microbial mat community in resisting environmental stress resulting from oil pollution.
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Affiliation(s)
- Sylvain Bordenave
- Equipe Environnement et Microbiologie, IPREM UMR5254, IBEAS, Université de Pau, BP1155, 64013 Pau Cedex, France
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Wentzel A, Ellingsen TE, Kotlar HK, Zotchev SB, Throne-Holst M. Bacterial metabolism of long-chain n-alkanes. Appl Microbiol Biotechnol 2007; 76:1209-21. [PMID: 17673997 DOI: 10.1007/s00253-007-1119-1] [Citation(s) in RCA: 207] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2007] [Revised: 07/10/2007] [Accepted: 07/11/2007] [Indexed: 10/23/2022]
Abstract
Degradation of alkanes is a widespread phenomenon in nature, and numerous microorganisms, both prokaryotic and eukaryotic, capable of utilizing these substrates as a carbon and energy source have been isolated and characterized. In this review, we summarize recent advances in the understanding of bacterial metabolism of long-chain n-alkanes. Bacterial strategies for accessing these highly hydrophobic substrates are presented, along with systems for their enzymatic degradation and conversion into products of potential industrial value. We further summarize the current knowledge on the regulation of bacterial long-chain n-alkane metabolism and survey progress in understanding bacterial pathways for utilization of n-alkanes under anaerobic conditions.
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Affiliation(s)
- Alexander Wentzel
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Saelandsvei 6/8, 7491 Trondheim, Norway.
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Young DM, Parke D, Ornston LN. OPPORTUNITIES FOR GENETIC INVESTIGATION AFFORDED BYACINETOBACTER BAYLYI, A NUTRITIONALLY VERSATILE BACTERIAL SPECIES THAT IS HIGHLY COMPETENT FOR NATURAL TRANSFORMATION. Annu Rev Microbiol 2005; 59:519-51. [PMID: 16153178 DOI: 10.1146/annurev.micro.59.051905.105823] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genetic and physiological properties of Acinetobacter baylyi strain ADP1 make it an inviting subject for investigation of the properties underlying its nutritional versatility. The organism possesses a relatively small genome in which genes for most catabolic functions are clustered in several genetic islands that, unlike pathogenicity islands, give little evidence of horizontal transfer. Coupling mutagenic polymerase chain reaction to natural transformation provides insight into how structure influences function in transporters, transcriptional regulators, and enzymes. With appropriate selection, mutants in which such molecules have acquired novel function may be obtained. The extraordinary competence of A. baylyi for natural transformation and the ease with which it expresses heterologous genes make it a promising platform for construction of novel metabolic systems. Steps toward this goal should take into account the complexity of existing pathways in which transmembrane trafficking plays a significant role.
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Affiliation(s)
- David M Young
- 1Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
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van Beilen JB, Marín MM, Smits THM, Röthlisberger M, Franchini AG, Witholt B, Rojo F. Characterization of two alkane hydroxylase genes from the marine hydrocarbonoclastic bacterium Alcanivorax borkumensis. Environ Microbiol 2004; 6:264-73. [PMID: 14871210 DOI: 10.1111/j.1462-2920.2004.00567.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The marine gamma-Proteobacterium Alcanivorax borkumensis is highly specialized in the assimilation of aliphatic hydrocarbons, and makes up a large part of the biomass in oil-polluted marine environments. In addition to the previously identified alkane hydroxylase AlkB1, a second alkane hydroxylase (AlkB2) showing 65% identity to the Pseudomonas aeruginosa AlkB2 alkane hydroxylase was identified. Unlike alkB1, alkB2 is not flanked by genes involved in alkane metabolism. Heterologous expression of the A. borkumensis AP1 alkB1 and alkB2 genes showed that they encode functional alkane hydroxylases with substrate ranges similar to those of their P. putida and P. aeruginosa homologues. The transcription initiation sites and levels of the alkB1, alkB2 and alkS mRNA transcripts were determined. Expression of both alkB1 and alkB2 was induced by alkanes, but transcripts corresponding to alkB1 were much more abundant than those of alkB2. An inverted repeat similar to the binding site for the P. putida GPo1 transcriptional activator AlkS was present upstream of the promoters for alkB1 and alkB2, although that of alkB2 was less well conserved, and only the transcriptional fusion of promoter PalkB1 to the reporter gene lacZ efficiently responded to n-octane. Contrary to what has been found for the P. putida GPo1 alkane degradation pathway, expression of the A. borkumensis AP1 alkS gene was not induced by alkanes, and an AlkS binding site was not present upstream of the promoter for alkS. This indicates that, in spite of the clear similarities, the A. borkumensis alk-genes are regulated by a strategy different from that of the P. putida GPo1 alk genes.
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MESH Headings
- Alkanes/metabolism
- Artificial Gene Fusion
- Biodegradation, Environmental
- Cloning, Molecular
- Cytochrome P-450 CYP4A/genetics
- Cytochrome P-450 CYP4A/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- Gene Expression Regulation, Bacterial
- Genes, Bacterial/genetics
- Genes, Bacterial/physiology
- Genes, Reporter
- Halomonadaceae/enzymology
- Halomonadaceae/genetics
- Molecular Sequence Data
- Promoter Regions, Genetic
- Pseudomonas/genetics
- Pseudomonas/growth & development
- Pseudomonas/metabolism
- RNA, Messenger/analysis
- RNA, Messenger/biosynthesis
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Repetitive Sequences, Nucleic Acid
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology
- Substrate Specificity
- Transcription Initiation Site
- Water Pollution, Chemical
- beta-Galactosidase/genetics
- beta-Galactosidase/metabolism
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Affiliation(s)
- Jan B van Beilen
- Institute of Biotechnology, Swiss Federal Institute of Technology (ETH), ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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Abstract
Recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. The physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. New molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystems. By establishing conditions which maximize rates and extents of microbial growth, hydrocarbon access, and transformation, highly accelerated and bioreactor-based petroleum waste degradation processes have been implemented. Biofilters capable of removing and biodegrading volatile petroleum contaminants in air streams with short substrate-microbe contact times (<60 s) are being used effectively. Microbes are being injected into partially spent petroleum reservoirs to enhance oil recovery. However, these microbial processes have not exhibited consistent and effective performance, primarily because of our inability to control conditions in the subsurface environment. Microbes may be exploited to break stable oilfield emulsions to produce pipeline quality oil. There is interest in replacing physical oil desulfurization processes with biodesulfurization methods through promotion of selective sulfur removal without degradation of associated carbon moieties. However, since microbes require an environment containing some water, a two-phase oil-water system must be established to optimize contact between the microbes and the hydrocarbon, and such an emulsion is not easily created with viscous crude oil. This challenge may be circumvented by application of the technology to more refined gasoline and diesel substrates, where aqueous-hydrocarbon emulsions are more easily generated. Molecular approaches are being used to broaden the substrate specificity and increase the rates and extents of desulfurization. Bacterial processes are being commercialized for removal of H(2)S and sulfoxides from petrochemical waste streams. Microbes also have potential for use in removal of nitrogen from crude oil leading to reduced nitric oxide emissions provided that technical problems similar to those experienced in biodesulfurization can be solved. Enzymes are being exploited to produce added-value products from petroleum substrates, and bacterial biosensors are being used to analyze petroleum-contaminated environments.
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Affiliation(s)
- Jonathan D Van Hamme
- Department of Biological Sciences, The University College of the Cariboo, Kamloops, British Columbia V2C 5N3
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Abstract
The enzymological and genetic aspects of microbial metabolism of hydrocarbons have been extensively revealed. Such molecular information is useful for understanding the bioremediation of oil spill environments and production of hydrocarbon-specific fine chemicals.
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Affiliation(s)
- Takeru Ishige
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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Del Carmen Vargas M, Encarnación S, Dávalos A, Reyes-Pérez A, Mora Y, García-de Los Santos A, Brom S, Mora J. Only one catalase, katG, is detectable in Rhizobium etli, and is encoded along with the regulator OxyR on a plasmid replicon. MICROBIOLOGY (READING, ENGLAND) 2003; 149:1165-1176. [PMID: 12724378 DOI: 10.1099/mic.0.25909-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The plasmid-borne Rhizobium etli katG gene encodes a dual-function catalase-peroxidase (KatG) (EC 1.11.1.7) that is inducible and heat-labile. In contrast to other rhizobia, katG was shown to be solely responsible for catalase and peroxidase activity in R. etli. An R. etli mutant that did not express catalase activity exhibited increased sensitivity to hydrogen peroxide (H(2)O(2)). Pre-exposure to a sublethal concentration of H(2)O(2) allowed R. etli to adapt and survive subsequent exposure to higher concentrations of H(2)O(2). Based on a multiple sequence alignment with other catalase-peroxidases, it was found that the catalytic domains of the R. etli KatG protein had three large insertions, two of which were typical of KatG proteins. Like the katG gene of Escherichia coli, the R. etli katG gene was induced by H(2)O(2) and was important in sustaining the exponential growth rate. In R. etli, KatG catalase-peroxidase activity is induced eightfold in minimal medium during stationary phase. It was shown that KatG catalase-peroxidase is not essential for nodulation and nitrogen fixation in symbiosis with Phaseolus vulgaris, although bacteroid proteome analysis indicated an alternative compensatory mechanism for the oxidative protection of R. etli in symbiosis. Next to, and divergently transcribed from the catalase promoter, an ORF encoding the regulator OxyR was found; this is the first plasmid-encoded oxyR gene described so far. Additionally, the katG promoter region contained sequence motifs characteristic of OxyR binding sites, suggesting a possible regulatory mechanism for katG expression.
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Affiliation(s)
- María Del Carmen Vargas
- Programa de Ingeniería Metabólica, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, CP62210, Mexico
| | - Sergio Encarnación
- Programa de Ingeniería Metabólica, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, CP62210, Mexico
| | - Araceli Dávalos
- Programa de Ingeniería Metabólica, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, CP62210, Mexico
| | - Agustín Reyes-Pérez
- Programa de Ingeniería Metabólica, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, CP62210, Mexico
| | - Yolanda Mora
- Programa de Ingeniería Metabólica, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, CP62210, Mexico
| | - Alejandro García-de Los Santos
- Programa de Genética Molecular de Plásmidos Bacterianos, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, CP62210, Mexico
| | - Susana Brom
- Programa de Genética Molecular de Plásmidos Bacterianos, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, CP62210, Mexico
| | - Jaime Mora
- Programa de Ingeniería Metabólica, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, CP62210, Mexico
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Whyte LG, Smits THM, Labbé D, Witholt B, Greer CW, van Beilen JB. Gene cloning and characterization of multiple alkane hydroxylase systems in Rhodococcus strains Q15 and NRRL B-16531. Appl Environ Microbiol 2002; 68:5933-42. [PMID: 12450813 PMCID: PMC134402 DOI: 10.1128/aem.68.12.5933-5942.2002] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2002] [Accepted: 08/30/2002] [Indexed: 11/20/2022] Open
Abstract
The alkane hydroxylase systems of two Rhodococcus strains (NRRL B-16531 and Q15, isolated from different geographical locations) were characterized. Both organisms contained at least four alkane monooxygenase gene homologs (alkB1, alkB2, alkB3, and alkB4). In both strains, the alkB1 and alkB2 homologs were part of alk gene clusters, each encoding two rubredoxins (rubA1 and rubA2; rubA3 and rubA4), a putative TetR transcriptional regulatory protein (alkU1; alkU2), and, in the alkB1 cluster, a rubredoxin reductase (rubB). The alkB3 and alkB4 homologs were found as separate genes which were not part of alk gene clusters. Functional heterologous expression of some of the rhodococcal alk genes (alkB2, rubA2, and rubA4 [NRRL B-16531]; alkB2 and rubB [Q15]) was achieved in Escherichia coli and Pseudomonas expression systems. Pseudomonas recombinants containing rhodococcal alkB2 were able to mineralize and grow on C(12) to C(16) n-alkanes. All rhodococcal alkane monooxygenases possessed the highly conserved eight-histidine motif, including two apparent alkane monooxygenase signature motifs (LQRH[S/A]DHH and NYXEHYG[L/M]), and the six hydrophobic membrane-spanning regions found in all alkane monooxygenases related to the Pseudomonas putida GPo1 alkane monooxygenase. The presence of multiple alkane hydroxylases in the two rhodococcal strains is reminiscent of other multiple-degradative-enzyme systems reported in Rhodococcus.
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Affiliation(s)
- L G Whyte
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada H4P 2R2
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Vangnai AS, Arp DJ, Sayavedra-Soto LA. Two distinct alcohol dehydrogenases participate in butane metabolism by Pseudomonas butanovora. J Bacteriol 2002; 184:1916-24. [PMID: 11889098 PMCID: PMC134940 DOI: 10.1128/jb.184.7.1916-1924.2002] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2001] [Accepted: 01/11/2002] [Indexed: 11/20/2022] Open
Abstract
The involvement of two primary alcohol dehydrogenases, BDH and BOH, in butane utilization in Pseudomonas butanovora (ATCC 43655) was demonstrated. The genes coding for BOH and BDH were isolated and characterized. The deduced amino acid sequence of BOH suggests a 67-kDa alcohol dehydrogenase containing pyrroloquinoline quinone (PQQ) as cofactor and in the periplasm (29-residue leader sequence). The deduced amino acid sequence of BDH is consistent with a 70.9-kDa, soluble, periplasmic (37-residue leader sequence) alcohol dehydrogenase containing PQQ and heme c as cofactors. BOH and BDH mRNAs were induced whenever the cell's 1-butanol oxidation activity was induced. When induced with butane, the gene for BOH was expressed earlier than the gene for BDH. Insertional disruption of bdh or boh affected adversely, but did not eliminate, butane utilization by P. butanovora. The P. butanovora mutant with both genes boh and bdh inactivated was unable to grow on butane or 1-butanol. These cells, when grown in citrate and incubated in butane, developed butane oxidation capability and accumulated 1-butanol. The enzyme activity of BOH was characterized in cell extracts of the P. butanovora strain with bdh disrupted. Unlike BDH, BOH oxidized 2-butanol. The results support the involvement of two distinct NAD(+)-independent, PQQ-containing alcohol dehydrogenases, BOH (a quinoprotein) and BDH (a quinohemoprotein), in the butane oxidation pathway of P. butanovora.
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Affiliation(s)
- Alisa S Vangnai
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-2902, USA
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Coulter ED, Kurtz DM. A role for rubredoxin in oxidative stress protection in Desulfovibrio vulgaris: catalytic electron transfer to rubrerythrin and two-iron superoxide reductase. Arch Biochem Biophys 2001; 394:76-86. [PMID: 11566030 DOI: 10.1006/abbi.2001.2531] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Desulfovibrio vulgaris rubredoxin, which contains a single [Fe(SCys)4] site, is shown to be a catalytically competent electron donor to two enzymes from the same organism, namely, rubrerythrin and two-iron superoxide reductase (a.k.a. rubredoxin oxidoreductase or desulfoferrodoxin). These two enzymes have been implicated in catalytic reduction of hydrogen peroxide and superoxide, respectively, during periods of oxidative stress in D. vulgaris, but their proximal electron donors had not been characterized. We further demonstrate the incorrectness of a previous report that rubredoxin is not an electron donor to the superoxide reductase and describe convenient assays for demonstrating the catalytic competence of all three proteins in their respective functions. Rubrerythrin is shown to be an efficient rubredoxin peroxidase in which the rubedoxin:hydrogen peroxide redox stoichiometry is 2:1 mol:mol. Using spinach ferredoxin-NADP+ oxidoreductase (FNR) as an artificial, but proficient, NADPH:rubredoxin reductase, rubredoxin was further found to catalyze rapid and complete reduction of all Fe3+ to Fe2+ in rubrerythrin by NADPH under anaerobic conditions. The combined system, FNR/rubredoxin/rubrerythrin, was shown to function as a catalytically competent NADPH peroxidase. Another small rubredoxin-like D. vulgaris protein, Rdl, could not substitute for rubredoxin as a peroxidase substrate of rubrerythrin. Similarly, D. vulgaris rubredoxin was demonstrated to efficiently catalyze reduction of D. vulgaris two-iron superoxide reductase and, when combined with FNR, to function as an NADPH:superoxide oxidoreductase. We suggest that, during periods of oxidative stress, rubredoxin could divert electron flow from the electron transport chain of D. vulgaris to rubrerythrin and superoxide reductase, thereby simultaneously protecting autoxidizable redox enzymes and lowering intracellular hydrogen peroxide and superoxide levels.
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Affiliation(s)
- E D Coulter
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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Marín MM, Smits TH, van Beilen JB, Rojo F. The alkane hydroxylase gene of Burkholderia cepacia RR10 is under catabolite repression control. J Bacteriol 2001; 183:4202-9. [PMID: 11418560 PMCID: PMC95309 DOI: 10.1128/jb.183.14.4202-4209.2001] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In many microorganisms the first step for alkane degradation is the terminal oxidation of the molecule by an alkane hydroxylase. We report the characterization of a gene coding for an alkane hydroxylase in a Burkholderia cepacia strain isolated from an oil-contaminated site. The protein encoded showed similarity to other known or predicted bacterial alkane hydroxylases, although it clustered on a separate branch together with the predicted alkane hydroxylase of a Mycobacterium tuberculosis strain. Introduction of the cloned B. cepacia gene into an alkane hydroxylase knockout mutant of Pseudomonas fluorescens CHAO restored its ability to grow on alkanes, which confirms that the gene analyzed encodes a functional alkane hydroxylase. The gene, which was named alkB, is not linked to other genes of the alkane oxidation pathway. Its promoter was identified, and its expression was analyzed under different growth conditions. Transcription was induced by alkanes of chain lengths containing 12 to at least 30 carbon atoms as well as by alkanols. Although the gene was efficiently expressed during exponential growth, transcription increased about fivefold when cells approached stationary phase, a characteristic not shared by the few alkane degraders whose regulation has been studied. Expression of the alkB gene was under carbon catabolite repression when cells were cultured in the presence of several organic acids and sugars or in a complex (rich) medium. The catabolic repression process showed several characteristics that are clearly different from what has been observed in other alkane degradation pathways.
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Affiliation(s)
- M M Marín
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Benndorf D, Loffhagen N, Babel W. Protein synthesis patterns in Acinetobacter calcoaceticus induced by phenol and catechol show specificities of responses to chemostress. FEMS Microbiol Lett 2001; 200:247-52. [PMID: 11425483 DOI: 10.1111/j.1574-6968.2001.tb10723.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The proteins induced in Acinetobacter calcoaceticus by the potentially toxic growth substrates phenol and catechol were analyzed by 2D-electrophoresis of cell extracts and compared with those induced by heat shock and oxidative stress. Although both aromatic compounds are quite similar, the only difference being that catechol has an additional hydroxyl group, the responses obtained differed considerably. Phenol has greater lipophilicity and mainly induced heat shock proteins, whereas catechol, which causes the production of reactive oxygen species, predominantly induced oxidative stress proteins. Furthermore, some special proteins were induced by phenol or catechol, which might be useful as biomarkers for chemostress, and could be involved in the catalytic degradation of potentially toxic compounds.
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Affiliation(s)
- D Benndorf
- Umweltforschungszentrum Leipzig-Halle GmbH, Sektion Umweltmikrobiologie, Permoserstr. 15, 04318, Leipzig, Germany
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Koma D, Hasumi F, Yamamoto E, Ohta T, Chung SY, Kubo M. Biodegradation of long-chain n-paraffins from waste oil of car engine by Acinetobacter sp. J Biosci Bioeng 2001. [DOI: 10.1016/s1389-1723(01)80120-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Kato T, Haruki M, Imanaka T, Morikawa M, Kanaya S. Isolation and characterization of long-chain-alkane degrading Bacillus thermoleovorans from deep subterranean petroleum reservoirs. J Biosci Bioeng 2001. [DOI: 10.1016/s1389-1723(01)80113-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kim JA, Mayfield J. Identification of Brucella abortus OxyR and its role in control of catalase expression. J Bacteriol 2000; 182:5631-3. [PMID: 10986275 PMCID: PMC111015 DOI: 10.1128/jb.182.19.5631-5633.2000] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the cloning and sequencing of the Brucella abortus oxyR homolog and provide evidence that the transcription product of this gene binds to the B. abortus catalase promoter region. A gene replacement/deletion Brucella oxyR mutant exhibits increased sensitivity to prolonged exposure to H(2)O(2) and is unable to adapt to H(2)O(2) in the environment.
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Affiliation(s)
- J A Kim
- Department of Zoology and Genetics, Iowa State University, Ames, Iowa 50011, USA
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Rocha ER, Owens G, Smith CJ. The redox-sensitive transcriptional activator OxyR regulates the peroxide response regulon in the obligate anaerobe Bacteroides fragilis. J Bacteriol 2000; 182:5059-69. [PMID: 10960088 PMCID: PMC94652 DOI: 10.1128/jb.182.18.5059-5069.2000] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The peroxide response-inducible genes ahpCF, dps, and katB in the obligate anaerobe Bacteroides fragilis are controlled by the redox-sensitive transcriptional activator OxyR. This is the first functional oxidative stress regulator identified and characterized in anaerobic bacteria. oxyR and dps were found to be divergently transcribed, with an overlap in their respective promoter regulatory regions. B. fragilis OxyR and Dps proteins showed high identity to homologues from a closely related anaerobe, Porphyromonas gingivalis. Northern blot analysis revealed that oxyR was expressed as a monocistronic 1-kb mRNA and that dps mRNA was approximately 500 bases in length. dps mRNA was induced over 500-fold by oxidative stress in the parent strain and was constitutively induced in the peroxide-resistant mutant IB263. The constitutive peroxide response in strain IB263 was shown to have resulted from a missense mutation at codon 202 (GAT to GGT) of the oxyR gene [oxyR(Con)] with a predicted D202G substitution in the OxyR protein. Transcriptional fusion analysis revealed that deletion of oxyR abolished the induction of ahpC and katB following treatment with hydrogen peroxide or oxygen exposure. However, dps expression was induced approximately fourfold by oxygen exposure in DeltaoxyR strains but not by hydrogen peroxide. This indicates that dps expression is also under the control of an oxygen-dependent OxyR-independent mechanism. Complementation of DeltaoxyR mutant strains with wild-type oxyR and oxyR(Con) restored the inducible peroxide response and the constitutive response of the ahpCF, katB, and dps genes, respectively. However, overexpression of OxyR abolished the catalase activity but not katB expression, suggesting that higher levels of intracellular OxyR may be involved in other physiological processes. Analysis of oxyR expression in the parents and in DeltaoxyR and overexpressing oxyR strains by Northern blotting and oxyR'::xylB fusions revealed that B. fragilis OxyR does not control its own expression.
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Affiliation(s)
- E R Rocha
- Department of Microbiology and Immunology, East Carolina University School of Medicine, Greenville, North Carolina 27858-4354, USA
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