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Huang H, Xie C, Xia Z, Sun Z, Chen Y, Gou M, Tang Y, Cui H, Wu X. Multi-omics association study of hexadecane degradation in haloarchaeal strain Halogranum rubrum RO2-11. ENVIRONMENTAL RESEARCH 2024; 252:118751. [PMID: 38522738 DOI: 10.1016/j.envres.2024.118751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/01/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Haloarchaea with the capacity to degrade alkanes is promising to deal with petroleum pollution in hypersaline environments. However, only a limited number of haloarchaeal species are investigated, and their pathway and mechanism for alkane degradation remain unclear. In this study, Halogranum rubrum RO2-11, a haloarchaeal strain, verified the ability to degrade kerosene and hexadecane in 184 g/L NaCl, with 53% and 52% degradation rates after 9 and 4 days, respectively. Genome sequencing and gene annotation indicated that strain RO2-11 possesses a complete potential alkane-degrading pathway, of which alkane hydroxylases may include CYP450, AlmA, and LadA. Transcriptome and metabolome analyses revealed that the upregulation of related genes in TCA cycle, lysine biosynthesis, and acetylation may help improve hexadecane degradation. Additionally, an alternative degrading pathway of hexadecane based on dual-terminal β-oxidation may occur in strain RO2-11. It is likely to be the first report of alkane degradation by the genus Halogranum, which may be helpful for applications of oil-pollution bioremediation under high-salt conditions.
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Affiliation(s)
- HeLang Huang
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China; Chengdu Surveying Geotechnical Research Institute Co. Ltd. of MCC, Chengdu, 610023, China.
| | - CaiYun Xie
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - ZiYuan Xia
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - ZhaoYong Sun
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - YaTing Chen
- Institute for Disaster Management and Reconstruction, Sichuan University, Sichuan, 610207, China.
| | - Min Gou
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - YueQin Tang
- College of Architecture and Environment, Sichuan University, Sichuan, 610065, China.
| | - HengLin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - XiaoLei Wu
- College of Engineering, Peking University, Beijing, 100871, China.
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2
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Chang S, Gui Y, He X, Xue L. Transcriptome analysis of Acinetobacter calcoaceticus HX09 strain with outstanding crude-oil-degrading ability. Braz J Microbiol 2024:10.1007/s42770-024-01392-0. [PMID: 38837015 DOI: 10.1007/s42770-024-01392-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 05/15/2024] [Indexed: 06/06/2024] Open
Abstract
Microbial remediation plays a pivotal role in the elimination of petroleum pollutants, making it imperative to investigate the capabilities of microorganisms in degrading petroleum. The present study describes the isolation of a promising strain, Acinetobacter sp. HX09, from petroleum-contaminated water. GC-MS analysis revealed a remarkable removal efficiency for short and medium-chain alkanes, with a rate of approximately 64% after a 7-days incubation at 30 °C. Transcriptome analysis of HX09 exhibited a predominant upregulation in gene expression levels by the induce of crude oil. Notably, genes such as alkane 1-monooxygenase, dehydrogenases and fatty acid metabolic enzymes exhibited fold changes range from 3.16 to 1.3. Based on the alkB gene sequences in HX09, the Phyre2 algorithm generated a three-dimensional structure that exhibited similarity to segments of acyl coenzyme desaturases and acyl lipid desaturases. Furthermore, three biodegradation-related gene clusters were predicted in HX09 based on the reference genome sequence. These findings contribute to our understanding of the hydrocarbon-degrading mechanisms employed by Acinetobacter species and facilitate the development of effective remediation strategies for crude oil- polluted environments.
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Affiliation(s)
- Sijing Chang
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China.
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China.
| | - Yanwen Gui
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
| | - Xiaoyan He
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
| | - Lingui Xue
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
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Hu X, Zhao S, Li H, Pan Y, Fan Z, Lu J, Li Y, Song G, Zhang H, Liu Q, Bao M. N-alkane shape distinctive microbial patterns in Kuroshio Extension. ENVIRONMENT INTERNATIONAL 2024; 188:108757. [PMID: 38795659 DOI: 10.1016/j.envint.2024.108757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/15/2024] [Accepted: 05/15/2024] [Indexed: 05/28/2024]
Abstract
Marine microorganisms are primary drivers of the elemental cycling. The interaction between heterotrophic prokaryotes and biomarker (n-alkane) in Kuroshio Extension (KE) remains unclear. Here, we categorize KE into three characteristic areas based on ocean temperatures and nutrient conditions: Cold Water Area (CWA), Mixed Area (MA), and Warm Water Area (WWA). A total of 49 samples were collected during two-year voyage to identify the source of n-alkane and associated degrading microorganisms. Total n-alkane concentrations (Σn-Alk) in surface water (SW) spanned from 1,308 ng L-1 to 1,890 ng L-1, it was significantly higher (Tukey-Kramer test, p < 0.05) in MA than CWA and WWA. The Σn-Alk in surface sediments (SS) gradually increased from north to south, ranging from 5,982 ng g-1 to 37,857 ng g-1. Bacteria and algae were the primary sources of n-alkane in both SW and SS. Proteobacteria was the most widely distributed among three areas. The presence of Rhodobacteraceae with alkB was the primary reason affecting n-alkane concentrations in SW. The Gammaproteobacteria with alkB and alkR chiefly affected n-alkane concentrations in SS. In summary, n-alkane s serve as an energy source for particular microorganisms, shaping the unique oceanographic patterns.
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Affiliation(s)
- Xin Hu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Shanshan Zhao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Haoshuai Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Yaping Pan
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Zhongxiang Fan
- Physical Oceanography Laboratory, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Jinren Lu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Yiming Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Guodong Song
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Honghai Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Qian Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Mutai Bao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China.
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Lirette AO, Chen YJ, Freyria NJ, Góngora E, Greer CW, Whyte LG. Characterization of hydrocarbon degraders from Northwest Passage beach sediments and assessment of their ability for bioremediation. Can J Microbiol 2024; 70:163-177. [PMID: 38350082 DOI: 10.1139/cjm-2023-0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Global warming-induced sea ice loss in the Canadian Northwest Passage (NWP) will result in more shipping traffic, increasing the risk of oil spills. Microorganisms inhabiting NWP beach sediments may degrade hydrocarbons, offering a potential bioremediation strategy. In this study, the characterization and genomic analyses of 22 hydrocarbon-biodegradative bacterial isolates revealed that they contained a diverse range of key alkane and aromatic hydrocarbon-degradative genes, as well as cold and salt tolerance genes indicating they are highly adapted to the extreme Arctic environment. Some isolates successfully degraded Ultra Low Sulfur Fuel Oil (ULSFO) at temperatures as low as -5 °C and high salinities (3%-10%). Three isolates were grown in liquid medium containing ULSFO as sole carbon source over 3 months and variation of hydrocarbon concentration was measured at three time points to determine their rate of hydrocarbon biodegradation. Our results demonstrate that two isolates (Rhodococcus sp. R1B_2T and Pseudarthrobacter sp. R2D_1T) possess complete degradation pathways and can grow on alkane and aromatic components of ULSFO under Arctic conditions. Overall, these results demonstrate that diverse hydrocarbon-degrading microorganisms exist in the NWP beach sediments, offering a potential bioremediation strategy in the events of a marine fuel spill reaching the shores of the NWP.
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Affiliation(s)
- Antoine-O Lirette
- Department of Natural Resource Sciences, McGill University, QC, Canada
| | - Ya-Jou Chen
- Department of Natural Resource Sciences, McGill University, QC, Canada
| | | | - Esteban Góngora
- Department of Natural Resource Sciences, McGill University, QC, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, QC, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, QC, Canada
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5
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Okoye AU, Selvarajan R, Chikere CB, Okpokwasili GC, Mearns K. Characterization and identification of long-chain hydrocarbon-degrading bacterial communities in long-term chronically polluted soil in Ogoniland: an integrated approach using culture-dependent and independent methods. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:30867-30885. [PMID: 38622422 PMCID: PMC11096258 DOI: 10.1007/s11356-024-33326-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/11/2024] [Indexed: 04/17/2024]
Abstract
Escalating oil consumption has resulted in an increase in accidental spills of petroleum hydrocarbons, causing severe environmental degradation, notably in vulnerable regions like the Niger Delta. Complex mixture of these hydrocarbons particularly long-chain alkanes presents unique challenges in restoration of polluted environment due to their chemical properties. This study aimed to investigate the long-chain hydrocarbon-degrading bacterial communities within long-term chronically polluted soil in Ogoniland, by utilizing both traditional cultivation methods and modern culture-independent techniques. Results revealed that surface-polluted soil (SPS) and subsurface soil (SPSS) exhibit significantly higher total organic carbon (TOC) ranging from 5.64 to 5.06% and total petroleum hydrocarbons (TPH) levels ranging from 36,775 ppm to 14,087 ppm, compared to unpolluted soil (UPS) with 1.97% TOC and 479 ppm TPH, respectively. Analysis of carbon chain lengths reveals the prevalence of longer-chain alkanes (C20-28) in the surface soil. Culture-dependent methods, utilizing crude oil enrichment (COE) and paraffin wax enrichment (PWE), yield 47 bacterial isolates subjected to a long-chain alkane degradation assay. Twelve bacterial strains demonstrate significant degradation abilities across all enriched media. Three bacterial members, namely Pseudomonas sp. (almA), Marinomonas sp. (almA), and Alteromonas (ladA), exhibit genes responsible for long-chain alkane degradation, demonstrating efficiency between 50 and 80%. Culture-independent analysis reveals that surface SPS samples exhibit greater species richness and diversity compared to subsurface SPSS samples. Proteobacteria dominates as the phylum in both soil sample types, ranging from 22.23 to 82.61%, with Firmicutes (0.2-2.22%), Actinobacteria (0.4-3.02%), and Acidobacteria (0.1-3.53%) also prevalent. Bacterial profiles at genus level revealed that distinct variations among bacterial populations between SPS and SPSS samples comprising number of hydrocarbon degraders and the functional predictions also highlight the presence of potential catabolic genes (nahAa, adh2, and cpnA) in the polluted soil. However, culture-dependent analysis only captured a few of the dominant members found in culture-independent analysis, implying that more specialized media or environments are needed to isolate more bacterial members. The findings from this study contribute valuable information to ecological and biotechnological aspects, aiding in the development of more effective bioremediation applications for restoring oil-contaminated environments.
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Affiliation(s)
- Amara Ukamaka Okoye
- Department of Microbiology, Faculty of Science, University of Port Harcourt, Port Harcourt, 500272, Nigeria
| | - Ramganesh Selvarajan
- Department of Environmental Science, Florida Campus, University of South Africa, Roodepoort, 1709, South Africa.
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
| | - Chioma Blaise Chikere
- Department of Microbiology, Faculty of Science, University of Port Harcourt, Port Harcourt, 500272, Nigeria
- Department of Environmental Science, Florida Campus, University of South Africa, Roodepoort, 1709, South Africa
| | | | - Kevin Mearns
- Department of Environmental Science, Florida Campus, University of South Africa, Roodepoort, 1709, South Africa
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Vigneron A, Guyoneaud R, Goñi-Urriza M. Genome-Centric Metatranscriptomics Reveals Multiple Co-occurring Routes for Hydrocarbon Degradation in Chronically Contaminated Marine Microbial Mats. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1551-1562. [PMID: 38197744 DOI: 10.1021/acs.est.3c08386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Long-term hydrocarbon pollution is a devious threat to aquatic and marine ecosystems. However, microbial responses to chronic pollution remain poorly understood. Combining genome-centric metagenomic and metatranscriptomic analyses of microbial mat samples that experienced chronic hydrocarbon pollution for more than 80 years, we analyzed the transcriptomic activity of alkane and aromatic hydrocarbon degradation pathways at the population level. Consistent with the fluctuating and stratified redox conditions of the habitat, both aerobic and anaerobic hydrocarbon degradation pathways were expressed by taxonomically and metabolically contrasted lineages including members of Bacteroidiales, Desulfobacteraceae, Pseudomonadales; Alcanivoraceae and Halieaceae populations with (photo)-heterotrophic, sulfur- and organohalide-based metabolisms, providing evidence for the co-occurrence and activity of aerobic and anaerobic hydrocarbon degradation pathways in shallow marine microbial mats. In addition, our results suggest that aerobic alkane degradation in long-term pollution involved bacterial families that are naturally widely distributed in marine habitats, but hydrocarbon concentration and composition were found to be a strong structuring factor of their intrafamily diversity and transcriptomic activities.
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Affiliation(s)
- Adrien Vigneron
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Marisol Goñi-Urriza
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
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Ru J, Xue J, Sun J, Cova L, Deng L. Unveiling the hidden role of aquatic viruses in hydrocarbon pollution bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132299. [PMID: 37597386 DOI: 10.1016/j.jhazmat.2023.132299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/28/2023] [Accepted: 08/12/2023] [Indexed: 08/21/2023]
Abstract
Hydrocarbon pollution poses substantial environmental risks to water and soil. Bioremediation, which utilizes microorganisms to manage pollutants, offers a cost-effective solution. However, the role of viruses, particularly bacteriophages (phages), in bioremediation remains unexplored. This study examines the diversity and activity of hydrocarbon-degradation genes encoded by environmental viruses, focusing on phages, within public databases. We identified 57 high-quality phage-encoded auxiliary metabolic genes (AMGs) related to hydrocarbon degradation, which we refer to as virus-encoded hydrocarbon degradation genes (vHYDEGs). These genes are encoded by taxonomically diverse aquatic phages and highlight the under-characterized global virosphere. Six protein families involved in the initial alkane hydroxylation steps were identified. Phylogenetic analyses revealed the diverse evolutionary trajectories of vHYDEGs across habitats, revealing previously unknown biodegraders linked evolutionarily with vHYDEGs. Our findings suggest phage AMGs may contribute to alkane and aromatic hydrocarbon degradation, participating in the initial, rate-limiting hydroxylation steps, thereby aiding hydrocarbon pollution bioremediation and promoting their propagation. To support future research, we developed vHyDeg, a database containing identified vHYDEGs with comprehensive annotations, facilitating the screening of hydrocarbon degradation AMGs and encouraging their bioremediation applications.
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Affiliation(s)
- Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jianfeng Sun
- Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Linda Cova
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising 85354, Germany.
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Hsueh SW, Jian YH, Fugmann SD, Yang SY. Polystyrene-colonizing bacteria are enriched for long-chain alkane degradation pathways. PLoS One 2023; 18:e0292137. [PMID: 37788234 PMCID: PMC10547174 DOI: 10.1371/journal.pone.0292137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023] Open
Abstract
One of the most promising strategies for the management of plastic waste is microbial biodegradation, but efficient degraders for many types of plastics are still lacking, including those for polystyrene (PS). Genomics has emerged as a powerful tool for mining environmental microbes that may have the ability to degrade different types of plastics. In this study, we use 16S rRNA sequencing to analyze the microbiomes for multiple PS samples collected from sites with different vegetation in Taiwan to reveal potential common properties between species that exhibit growth advantages on PS surfaces. Phylum enrichment analysis identified Cyanobacteria and Deinococcus-Thermus as being the most over-represented groups on PS, and both phyla include species known to reside in extreme environments and could encode unique enzymes that grant them properties suitable for colonization on PS surfaces. Investigation of functional enrichment using reference genomes of PS-enriched species highlighted carbon metabolic pathways, especially those related to hydrocarbon degradation. This is corroborated by the finding that genes encoding long-chain alkane hydroxylases such as AlmA are more prevalent in the genomes of PS-associated bacteria. Our analyses illustrate how plastic in the environment support the colonization by different microbes compared to surrounding soil. In addition, our results point to the possibility that alkane hydroxylases could confer growth advantages of microbes on PS.
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Affiliation(s)
- Shu Wei Hsueh
- Department and Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - You-Hua Jian
- Department and Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Sebastian D. Fugmann
- Department and Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Department of Nephrology, Linkou Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
| | - Shu Yuan Yang
- Department and Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
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Dai X, Lv J, Fu P, Guo S. Microbial remediation of oil-contaminated shorelines: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:93491-93518. [PMID: 37572250 DOI: 10.1007/s11356-023-29151-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023]
Abstract
Frequent marine oil spills have led to increasingly serious oil pollution along shorelines. Microbial remediation has become a research hotspot of intertidal oil pollution remediation because of its high efficiency, low cost, environmental friendliness, and simple operation. Many microorganisms are able to convert oil pollutants into non-toxic substances through their growth and metabolism. Microorganisms use enzymes' catalytic activities to degrade oil pollutants. However, microbial remediation efficiency is affected by the properties of the oil pollutants, microbial community, and environmental conditions. Feasible field microbial remediation technologies for oil spill pollution in the shorelines mainly include the addition of high-efficiency oil degrading bacteria (immobilized bacteria), nutrients, biosurfactants, and enzymes. Limitations to the field application of microbial remediation technology mainly include slow start-up, rapid failure, long remediation time, and uncontrolled environmental impact. Improving the environmental adaptability of microbial remediation technology and developing sustainable microbial remediation technology will be the focus of future research. The feasibility of microbial remediation techniques should also be evaluated comprehensively.
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Affiliation(s)
- Xiaoli Dai
- Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing, 10089, China.
| | - Jing Lv
- China University of Petroleum-Beijing, Beijing, 102249, China
| | - Pengcheng Fu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Hainan, 570228, China
| | - Shaohui Guo
- China University of Petroleum-Beijing, Beijing, 102249, China
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Viggor S, Jõesaar M, Peterson C, Teras R, Kivisaar M. Potential of Indigenous Strains Isolated from the Wastewater Treatment Plant of a Crude Oil Refinery. Microorganisms 2023; 11:microorganisms11030752. [PMID: 36985325 PMCID: PMC10051678 DOI: 10.3390/microorganisms11030752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Contamination of the environment with crude oil or other fuels is an enormous disaster for all organisms. The microbial communities for bioremediation have been an effective tool for eliminating pollution. This study aimed to determine individual cultures’ and a strain mixture’s ability to utilize alkanes (single alkanes and crude oil). The proper study of pure cultures is necessary to design synergistically working consortia. The Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13 strains isolated from a wastewater treatment plant of a crude oil refinery can grow in media containing various aromatic and aliphatic hydrocarbons. The genome of the strain ICP1 contains four genes encoding alkane hydroxylases, whose transcription depended on the length of the alkane in the media. We observed that the hydrophobic cells of the strain ICP1 adhered to hydrophobic substrates, and their biofilm formation increased the bioavailability and biodegradation of the hydrocarbons. Although strain ICTN13 also has one alkane hydroxylase-encoding gene, the growth of the strain in a minimal medium containing alkanes was weak. Importantly, the growth of the mixture of strains in the crude oil-containing medium was enhanced compared with that of the single strains, probably due to the specialization in the degradation of different hydrocarbon classes and co-production of biosurfactants.
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Affiliation(s)
- Signe Viggor
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia
- Correspondence:
| | - Merike Jõesaar
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia
| | - Celeste Peterson
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia
- Institute of Biomedicine and Translational Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia
| | - Riho Teras
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia
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Perera M, Wijesundera S, Wijayarathna CD, Seneviratne G, Jayasena S. Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis. Front Microbiol 2022; 13:898456. [PMID: 36110294 PMCID: PMC9468676 DOI: 10.3389/fmicb.2022.898456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Efficient degradation of alkanes in crude oil by the isolated Aspergillus flavus MM1 alluded to the presence of highly active alkane-degrading enzymes in this fungus. A long-chain alkane-degrading, LadA-like enzyme family in A. flavus was identified, and possible substrate-binding modes were analyzed using a computational approach. By analyzing publicly available protein databases, we identified six uncharacterized proteins in A. flavus NRRL 3357, of which five were identified as class LadAα and one as class LadAβ, which are eukaryotic homologs of bacterial long-chain alkane monooxygenase (LadA). Computational models of A. flavus LadAα homologs (Af1-Af5) showed overall structural similarity to the bacterial LadA and the unique sequence and structural elements that bind the cofactor Flavin mononucleotide (FMN). A receptor-cofactor-substrate docking protocol was established and validated to demonstrate the substrate binding in the A. flavus LadAα homologs. The modeled Af1, Af3, Af4, and Af5 captured long-chain n-alkanes inside the active pocket, above the bound FMN. Isoalloxazine ring of reduced FMN formed a π–alkyl interaction with the terminal carbon atom of captured alkanes, C16–C30, in Af3–Af5 and C16–C24 in Af1. Our results confirmed the ability of identified A. flavus LadAα monooxygenases to bind long-chain alkanes inside the active pocket. Hence A. flavus LadAα monooxygenases potentially initiate the degradation of long-chain alkanes by oxidizing bound long-chain alkanes into their corresponding alcohol.
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Affiliation(s)
- Madushika Perera
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Sulochana Wijesundera
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | | | | | - Sharmila Jayasena
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
- *Correspondence: Sharmila Jayasena,
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12
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Tourova TP, Sokolova DS, Semenova EM, Ershov AP, Grouzdev DS, Nazina TN. Genomic and Physiological Characterization of Halophilic Bacteria of the Genera Halomonas and Marinobacter from Petroleum Reservoirs. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722300038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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13
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Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice. Microorganisms 2022; 10:microorganisms10020328. [PMID: 35208784 PMCID: PMC8879337 DOI: 10.3390/microorganisms10020328] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
The anthropogenic release of oil hydrocarbons into the cold marine environment is an increasing concern due to the elevated usage of sea routes and the exploration of new oil drilling sites in Arctic areas. The aim of this study was to evaluate prokaryotic community structures and the genetic potential of hydrocarbon degradation in the metagenomes of seawater, sea ice, and crude oil encapsulating the sea ice of the Norwegian fjord, Ofotfjorden. Although the results indicated substantial differences between the structure of prokaryotic communities in seawater and sea ice, the crude oil encapsulating sea ice (SIO) showed increased abundances of many genera-containing hydrocarbon-degrading organisms, including Bermanella, Colwellia, and Glaciecola. Although the metagenome of seawater was rich in a variety of hydrocarbon degradation-related functional genes (HDGs) associated with the metabolism of n-alkanes, and mono- and polyaromatic hydrocarbons, most of the normalized gene counts were highest in the clean sea ice metagenome, whereas in SIO, these counts were the lowest. The long-chain alkane degradation gene almA was detected from all the studied metagenomes and its counts exceeded ladA and alkB counts in both sea ice metagenomes. In addition, almA was related to the most diverse group of prokaryotic genera. Almost all 18 good- and high-quality metagenome-assembled genomes (MAGs) had diverse HDGs profiles. The MAGs recovered from the SIO metagenome belonged to the abundant taxa, such as Glaciecola, Bermanella, and Rhodobacteracea, in this environment. The genera associated with HDGs were often previously known as hydrocarbon-degrading genera. However, a substantial number of new associations, either between already known hydrocarbon-degrading genera and new HDGs or between genera not known to contain hydrocarbon degraders and multiple HDGs, were found. The superimposition of the results of comparing HDG associations with taxonomy, the HDG profiles of MAGs, and the full genomes of organisms in the KEGG database suggest that the found relationships need further investigation and verification.
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14
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Cabral L, Giovanella P, Pellizzer EP, Teramoto EH, Kiang CH, Sette LD. Microbial communities in petroleum-contaminated sites: Structure and metabolisms. CHEMOSPHERE 2022; 286:131752. [PMID: 34426136 DOI: 10.1016/j.chemosphere.2021.131752] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.
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Affiliation(s)
- Lucélia Cabral
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Patricia Giovanella
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Elisa Pais Pellizzer
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Elias Hideo Teramoto
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Laboratório de Estudos de Bacias (LEBAC), Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Chang Hung Kiang
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Laboratório de Estudos de Bacias (LEBAC), Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Lara Durães Sette
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil.
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15
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Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature. Microorganisms 2021; 9:microorganisms9122425. [PMID: 34946026 PMCID: PMC8707851 DOI: 10.3390/microorganisms9122425] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
The development of oil exploration activities and an increase in shipping in Arctic areas have increased the risk of oil spills in this cold marine environment. The objective of this experimental study was to assess the effect of biostimulation on microbial community abundance, structure, dynamics, and metabolic potential for oil hydrocarbon degradation in oil-contaminated Arctic seawater. The combination of amplicon-based and shotgun sequencing, together with the integration of genome-resolved metagenomics and omics data, was applied to assess microbial community structure and metabolic properties in naphthenic crude oil-amended microcosms. The comparison of estimates for oil-degrading microbial taxa obtained with different sequencing and taxonomic assignment methods showed substantial discrepancies between applied methods. Consequently, the data acquired with different methods was integrated for the analysis of microbial community structure, and amended with quantitative PCR, producing a more objective description of microbial community dynamics and evaluation of the effect of biostimulation on particular microbial taxa. Implementing biostimulation of the seawater microbial community with the addition of nutrients resulted in substantially elevated prokaryotic community abundance (103-fold), a distinctly different bacterial community structure from that in the initial seawater, 1.3-fold elevation in the normalized abundance of hydrocarbon degradation genes, and 12% enhancement of crude oil biodegradation. The bacterial communities in biostimulated microcosms after four months of incubation were dominated by Gammaproteobacterial genera Pseudomonas, Marinomonas, and Oleispira, which were succeeded by Cycloclasticus and Paraperlucidibaca after eight months of incubation. The majority of 195 compiled good-quality metagenome-assembled genomes (MAGs) exhibited diverse hydrocarbon degradation gene profiles. The results reveal that biostimulation with nutrients promotes naphthenic oil degradation in Arctic seawater, but this strategy alone might not be sufficient to effectively achieve bioremediation goals within a reasonable timeframe.
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16
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Jagtap CB, Ram RM, Tiwari OK, Titus S, Lodha T. Genome sequence of an obligate hydrocarbonoclastic bacterium Alcanivorax marinus NMRL4 isolated from oil polluted seawater of the Arabian Sea. Mar Genomics 2021; 60:100875. [PMID: 34627547 DOI: 10.1016/j.margen.2021.100875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 11/28/2022]
Abstract
Alcanivorax belongs to the hydrocarbonoclastic group of bacteria that are known for their preferential growth on alkanes and other related compounds. Here we report the genomic features of Alcanivorax marinus strain NMRL4 (=MCC 4632) isolated from oil polluted seawater of the Arabian Sea. Its 4,062,055 bp genome with 66.1% GC content encodes for 3935 coding sequences. The genome annotations of strain NMRL4 revealed the presence of multiple hydrocarbon degradation genes suggestive of its wider hydrocarbon substrate range. The strain encodes for three alkane monooxygenases, two cytochrome P450 and two flavin binding monooxygenases for degradation of short and long-chain alkanes. The genome shows capabilities for scavenging of nutrients, biofilm formation at oil-water interfaces, chemotaxis, motility and habitat specific adaptation. The genomic insights showed that the strain NMRL4 is an ideal candidate for bioremediation of pollutant petroleum hydrocarbons from the marine environment.
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Affiliation(s)
- C B Jagtap
- Department of Marine Biotechnology, Naval Materials Research Laboratory (NMRL), Ambernath 421 506, India.
| | - R Mohan Ram
- Department of Marine Biotechnology, Naval Materials Research Laboratory (NMRL), Ambernath 421 506, India
| | - O K Tiwari
- Department of Marine Biotechnology, Naval Materials Research Laboratory (NMRL), Ambernath 421 506, India
| | - S Titus
- Department of Marine Biotechnology, Naval Materials Research Laboratory (NMRL), Ambernath 421 506, India
| | - T Lodha
- National Center for Microbial Resource (NCMR), National Centre for Cell Science, Pune, India.
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17
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Xu A, Zhang X, Wu S, Xu N, Huang Y, Yan X, Zhou J, Cui Z, Dong W. Pollutant Degrading Enzyme: Catalytic Mechanisms and Their Expanded Applications. Molecules 2021; 26:4751. [PMID: 34443339 PMCID: PMC8401168 DOI: 10.3390/molecules26164751] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/03/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
The treatment of environmental pollution by microorganisms and their enzymes is an innovative and socially acceptable alternative to traditional remediation approaches. Microbial biodegradation is often characterized with high efficiency as this process is catalyzed via degrading enzymes. Various naturally isolated microorganisms were demonstrated to have considerable ability to mitigate many environmental pollutants without external intervention. However, only a small fraction of these strains are studied in detail to reveal the mechanisms at the enzyme level, which strictly limited the enhancement of the degradation efficiency. Accordingly, this review will comprehensively summarize the function of various degrading enzymes with an emphasis on catalytic mechanisms. We also inspect the expanded applications of these pollutant-degrading enzymes in industrial processes. An in-depth understanding of the catalytic mechanism of enzymes will be beneficial for exploring and exploiting more degrading enzyme resources and thus ameliorate concerns associated with the ineffective biodegradation of recalcitrant and xenobiotic contaminants with the help of gene-editing technology and synthetic biology.
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Affiliation(s)
- Anming Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Xiaoxiao Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Shilei Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Ning Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.H.); (X.Y.)
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.H.); (X.Y.)
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.H.); (X.Y.)
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
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18
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Kalami R, Pourbabaee AA. Investigating the potential of bioremediation in aged oil-polluted hypersaline soils in the south oilfields of Iran. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:517. [PMID: 34309727 DOI: 10.1007/s10661-021-09304-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
To date, studies for bioremediation of oil-polluted hypersaline soils have been neglected or limited to specific spots. Hence, in this study, ten samples of oil field soils in the Khuzestan province of Iran were collected to evaluate bioremediation's feasibility. These samples were analyzed for their physicochemical properties as well as the most probable number of total and hydrocarbon-degrading bacteria. Thirty-nine hydrocarbon-degrading bacteria were isolated from these soils over a 1-month incubation in an MSM medium enriched with diesel oil as the sole source of carbon. As revealed by 16S-rRNA analysis, the identified strains belonged to the genera Ochrobactrum, Microbacterium, and Bacillus with a high frequency of Ochrobactrum species. Additionally, by using degenerate primers, the third group of alkB gene was detected in Ochrobactrum and Microbacterium isolates through the touchdown nested PCR method for the first time. Ochrobactrum species possessing the alkB gene showed the highest population, and therefore, the highest adaptation to harsh environmental conditions. Most isolates showed outstanding results in the ability to grow with crude and diesel oil and tolerate high salt percentages, biosurfactant production, and emulsification activity, which are considered the most effective factors in bioremediation of such environments. Considering the soil analysis, limiting factors in bioremediation like available phosphorous, and the abundance of bacteria with remediation traits in these soils, these extremely polluted environments can be refined.
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Affiliation(s)
- Reyhaneh Kalami
- Department of Soil Science, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran
| | - Ahmad-Ali Pourbabaee
- Department of Soil Science, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran.
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19
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Microbial production and consumption of hydrocarbons in the global ocean. Nat Microbiol 2021; 6:489-498. [PMID: 33526885 DOI: 10.1038/s41564-020-00859-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/17/2020] [Indexed: 01/30/2023]
Abstract
Seeps, spills and other oil pollution introduce hydrocarbons into the ocean. Marine cyanobacteria also produce hydrocarbons from fatty acids, but little is known about the size and turnover of this cyanobacterial hydrocarbon cycle. We report that cyanobacteria in an oligotrophic gyre mainly produce n-pentadecane and that microbial hydrocarbon production exhibits stratification and diel cycling in the sunlit surface ocean. Using chemical and isotopic tracing we find that pentadecane production mainly occurs in the lower euphotic zone. Using a multifaceted approach, we estimate that the global flux of cyanobacteria-produced pentadecane exceeds total oil input in the ocean by 100- to 500-fold. We show that rapid pentadecane consumption sustains a population of pentadecane-degrading bacteria, and possibly archaea. Our findings characterize a microbial hydrocarbon cycle in the open ocean that dwarfs oil input. We hypothesize that cyanobacterial hydrocarbon production selectively primes the ocean's microbiome with long-chain alkanes whereas degradation of other petroleum hydrocarbons is controlled by factors including proximity to petroleum seepage.
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20
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Hou L, Majumder ELW. Potential for and Distribution of Enzymatic Biodegradation of Polystyrene by Environmental Microorganisms. MATERIALS (BASEL, SWITZERLAND) 2021; 14:503. [PMID: 33494256 PMCID: PMC7864516 DOI: 10.3390/ma14030503] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 11/16/2022]
Abstract
Polystyrene (PS) is one of the main polymer types of plastic wastes and is known to be resistant to biodegradation, resulting in PS waste persistence in the environment. Although previous studies have reported that some microorganisms can degrade PS, enzymes and mechanisms of microorganism PS biodegradation are still unknown. In this study, we summarized microbial species that have been identified to degrade PS. By screening the available genome information of microorganisms that have been reported to degrade PS for enzymes with functional potential to depolymerize PS, we predicted target PS-degrading enzymes. We found that cytochrome P4500s, alkane hydroxylases and monooxygenases ranked as the top potential enzyme classes that can degrade PS since they can break C-C bonds. Ring-hydroxylating dioxygenases may be able to break the side-chain of PS and oxidize the aromatic ring compounds generated from the decomposition of PS. These target enzymes were distributed in Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, suggesting a broad potential for PS biodegradation in various earth environments and microbiomes. Our results provide insight into the enzymatic degradation of PS and suggestions for realizing the biodegradation of this recalcitrant plastic.
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Affiliation(s)
| | - Erica L.-W. Majumder
- Department of Chemistry, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA;
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21
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Multispecies Diesel Fuel Biodegradation and Niche Formation Are Ignited by Pioneer Hydrocarbon-Utilizing Proteobacteria in a Soil Bacterial Consortium. Appl Environ Microbiol 2020; 87:AEM.02268-20. [PMID: 33067200 DOI: 10.1128/aem.02268-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/12/2020] [Indexed: 11/20/2022] Open
Abstract
A soil bacterial consortium that was grown on diesel fuel and consisted of more than 10 members from different genera was maintained through repetitive subculturing and was utilized as a practical model to investigate a bacterial community that was continuously exposed to petroleum hydrocarbons. Through metagenomics analyses, consortium member isolation, growth assays, and metabolite identification which supported the linkage of genomic data and functionality, two pioneering genera, Sphingobium and Pseudomonas, whose catabolic capabilities were differentiated, were found to be responsible for the creation of specialized ecological niches that were apparently occupied by other bacterial members for survival within the consortium. Coexisting genera Achromobacter and Cupriavidus maintained their existence in the consortium through metabolic dependencies by utilizing hydrocarbon biotransformation products of pioneer metabolism, which was confirmed through growth tests and identification of biotransformation products of the isolated strains. Pioneering Sphingobium and Pseudomonas spp. utilized relatively water-insoluble hydrocarbon parent compounds and facilitated the development of a consortium community structure that resulted in the creation of niches in response to diesel fuel exposure which were created through the production of more-water-soluble biotransformation products available to cocolonizers. That these and other organisms were still present in the consortium after multiple transfers spanning 15 years provided evidence for these ecological niches. Member survival through occupation of these niches led to robustness of each group within the multispecies bacterial community. Overall, these results contribute to our understanding of the complex ecological relationships that may evolve during prokaryotic hydrocarbon pollutant biodegradation.IMPORTANCE There are few metagenome studies that have explored soil consortia maintained on a complex hydrocarbon substrate after the community interrelationships were formed. A soil bacterial consortium maintained on diesel fuel was utilized as a practical model to investigate bacterial community relationships through metagenomics analyses, consortium member isolation, growth assays, and metabolite identification, which supported the linkage of genomic data and functionality. Two pioneering genera were responsible for the biodegradation of aromatics and alkanes by initiating biotransformation and thereby created specialized niches that were populated by other members. A model that represents these relationships was constructed, which contributes to our understanding of the complex ecological relationships that evolve during prokaryotic hydrocarbon pollutant biodegradation.
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22
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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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Okoye A, Chikere C, Okpokwasili G. Isolation and Characterization of Hexadecane Degrading Bacteria from Oil- polluted soil in Gio Community, Niger Delta, Nigeria. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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24
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Cao Y, Zhang B, Zhu Z, Song X, Cai Q, Chen B, Dong G, Ye X. Microbial eco-physiological strategies for salinity-mediated crude oil biodegradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138723. [PMID: 32334234 DOI: 10.1016/j.scitotenv.2020.138723] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 05/26/2023]
Abstract
Salinity variability strongly affects the behaviors of oil degrading bacteria for spilled oil biodegradation in the marine environment. However, limited studies explored the strategies of microbes on salinity-mediated crude oil biodegradation. In this study, a halotolerant bio-emulsifier producer, Exiguobacterium sp. N41P, was examined as a model strain for Alaska North Slope (ANS) crude oil (0.5%, v/v) biodegradation. Results indicated that Exiguobacterium sp. N41P could tolerant a wide range of salinity (0-120 g/L NaCl) and achieve the highest degradation efficiency under the salinity of 15 g/L NaCl due to the highest biofilm formation ability. Moreover, increased salinity induced decreased cell surface hydrophobicity and a migration of microbial growth from oil phase to aqueous phase, leading to limited bio-emulsifier productivity and depressed degradation of insoluble long-chain n-alkanes while enhancing the degradation of relative soluble naphthalene. Research findings illustrated the microbial eco-physiological mechanism for spilled oil biodegradation under diverse salinities and advanced the understanding of sophisticated marine crude oil biodegradation process.
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Affiliation(s)
- Yiqi Cao
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Baiyu Zhang
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada.
| | - Zhiwen Zhu
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Xing Song
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Qinhong Cai
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Bing Chen
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Guihua Dong
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Xudong Ye
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
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25
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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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26
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Li AZ, Han XB, Zhang MX, Zhou Y, Chen M, Yao Q, Zhu HH. Culture-Dependent and -Independent Analyses Reveal the Diversity, Structure, and Assembly Mechanism of Benthic Bacterial Community in the Ross Sea, Antarctica. Front Microbiol 2019; 10:2523. [PMID: 31787942 PMCID: PMC6856632 DOI: 10.3389/fmicb.2019.02523] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/21/2019] [Indexed: 11/22/2022] Open
Abstract
The benthic bacterial community in Antarctic continental shelf ecosystems are not well-documented. We collected 13 surface sediments from the Ross Sea, a biological hotspot in high-latitude maritime Antarctica undergoing rapid climate change and possible microflora shift, and aimed to study the diversity, structure and assembly mechanism of benthic bacterial community using both culture-dependent and -independent approaches. High-throughput sequencing of 16S rRNA gene amplicons revealed 370 OTUs distributed in 21 phyla and 284 genera. The bacterial community was dominated by Bacteroidetes, Gamma- and Alphaproteobacteria, and constituted by a compact, conserved and positively-correlated group of anaerobes and other competitive aerobic chemoheterotrophs. Null-model test based on βNTI and RCBray indicated that stochastic processes, including dispersal limitation and undominated fractions, were the main forces driving community assembly. On the other hand, environmental factors, mainly temperature, organic matter and chlorophyll, were significantly correlated with bacterial richness, diversity and community structure. Moreover, metabolic and physiological features of the prokaryotic taxa were mapped to evaluate the adaptive mechanisms and functional composition of the benthic bacterial community. Our study is helpful to understand the structural and functional aspects, as well as the ecological and biogeochemical role of the benthic bacterial community in the Ross Sea.
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Affiliation(s)
- An-Zhang Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xi-Bin Han
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Ming-Xia Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yang Zhou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meng Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qing Yao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Grass Science, Guangdong Engineering Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Hong-Hui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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27
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Li YP, Pan JC, Ma YL. Elucidation of multiple alkane hydroxylase systems in biodegradation of crude oil
n
‐alkane pollution by
Pseudomonas aeruginosa
DN1. J Appl Microbiol 2019; 128:151-160. [DOI: 10.1111/jam.14470] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 09/17/2019] [Accepted: 09/22/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Y. P. Li
- Shaanxi Provincial Key Laboratory of Biotechnology Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Science Northwest University Xi’an, Shaanxi China
| | - J. C. Pan
- Shaanxi Provincial Key Laboratory of Biotechnology Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Science Northwest University Xi’an, Shaanxi China
| | - Y. L. Ma
- Shaanxi Provincial Key Laboratory of Biotechnology Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Science Northwest University Xi’an, Shaanxi China
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28
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Walter JM, Bagi A, Pampanin DM. Insights into the Potential of the Atlantic Cod Gut Microbiome as Biomarker of Oil Contamination in the Marine Environment. Microorganisms 2019; 7:microorganisms7070209. [PMID: 31336609 PMCID: PMC6680985 DOI: 10.3390/microorganisms7070209] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Microorganisms are widespread in all environments, including in and on animal bodies. The gut microbiome has an essential influence on fish health, and is affected by several persistent and harmful organic and inorganic contaminants. Considering the shifts in gut microbiota composition observed in those studies, we hypothesized that certain microbial groups in the gut can serve as indicators of pollution. To test this hypothesis, we explored the possibility of identifying key microbial players that indicate environmental contamination. METHODS Published 16S rRNA gene amplicon sequencing data generated from the gut microbiota of Atlantic cod caught in geographically different Norwegian waters were used for bacterial diversity comparison. RESULTS Different microbiomes were identified between the northern Norway and southern Norway samples. Several bacterial genera previously identified as polycyclic aromatic hydrocarbon degraders were present only in the samples collected in the southern Norway area, suggesting fish contamination with oil-related compounds. CONCLUSIONS The results contribute to the identification of bacterial taxa present in the Atlantic cod gut that indicate fish exposure to contaminants in the marine environment.
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Affiliation(s)
- Juline M Walter
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, NO-4036 Stavanger, Norway
| | - Andrea Bagi
- NORCE Norwegian Research Centre AS, 5008 Bergen, Norway
| | - Daniela M Pampanin
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, NO-4036 Stavanger, Norway.
- NORCE Norwegian Research Centre AS, 5008 Bergen, Norway.
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29
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Culturable hydrocarbonoclastic marine bacterial isolates from Indonesian seawater in the Lombok Strait and Indian Ocean. Heliyon 2019; 5:e01594. [PMID: 31111106 PMCID: PMC6512556 DOI: 10.1016/j.heliyon.2019.e01594] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/20/2019] [Accepted: 04/25/2019] [Indexed: 11/23/2022] Open
Abstract
Purpose The study aims to isolate the culturable marine bacteria and to assess their potential as the bioremediation agent for petroleum hydrocarbons contamination in marine environment. Methods Bacteria isolates were obtained by repetitive streaks to obtain purified bacteria on Zobell marine agar plates before further analysis and culture through direct visualization on agar plates. Identification were conducted using 16S rDNA sequence which are compared using NCBI BLAST and, combined with phenotypic and phylogenetic data. The potential use of the selected bacteria was tested by culturing them with two carbon sources i.e., glucose and crude oil. Result Fifty-one culturable marine hydrocarbonoclastic bacteria were isolated from the Lombok Strait (LS-3, LS-13, LS-14, LS-15, LS-16 and LS-20) and Indian Ocean (IO-1, IO-6, IO-8, IO-19, IO-24 and IO-25). Twelve isolates were found to degrade crude oil efficiently at a >2% concentration and to grow with crude oil as their sole carbon and energy source. These 12 strains belong to the genus Bacillus, which is well known to produce surface active agents, and the oil displacement assay indicated the production of these agents by these strains. Within the genera Bacillus, five species (Bacillus flexus, B. methylotrophicus, B. aquimaris, B. horikoshii, and B. thioparans) were represented by the 12 identified strains. Conclusion Selected strains from the Lombok Strait and Indian Ocean were capable of degrading crude oil (2% v/v) by 43.9-71.9% over 14 days. These results are important for marine bioremediation in Indonesia, which often faces risks of oil spill contamination and disaster.
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30
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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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31
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Ji N, Wang X, Yin C, Peng W, Liang R. CrgA Protein Represses AlkB2 Monooxygenase and Regulates the Degradation of Medium-to-Long-Chain n-Alkanes in Pseudomonas aeruginosa SJTD-1. Front Microbiol 2019; 10:400. [PMID: 30915046 PMCID: PMC6422896 DOI: 10.3389/fmicb.2019.00400] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/15/2019] [Indexed: 11/13/2022] Open
Abstract
AlkB monooxygenases in bacteria are responsible for the hydroxylation of medium- and long-chain n-alkanes. In this study, one CrgA protein of Pseudomonas aeruginosa SJTD-1, a member of LysR family, was proved to regulate AlkB2 monooxygenase and the degradation of medium-to-long-chain n-alkanes (C14-C20) by directly binding to the upstream of alkB2 gene. Two specific sites for CrgA binding were found in the promoter region of alkB2 gene, and the imperfect mirror repeat (IIR) structure was proved critical for CrgA recognition and binding. Hexadecyl CoA and octadecyl CoA could effectively release the CrgA binding and start the transcription of alkB2 gene, implying a positive regulation of metabolic intermediate. In the presence of medium-to-long-chain n-alkanes (C14-C20), deletion of crgA gene could enhance the transcription and expression of AlkB2 monooxygenase significantly; and in n-octadecane culture, strain S1ΔalkB1&crgA grew more vigorously than strain S1 ΔalkB1 &crgA . Almost no regulation of CrgA protein was observed to alkB1 gene in vitro and in vivo. Therefore, CrgA acted as a negative regulator for the medium-to-long-chain n-alkane utilization in P. aeruginosa SJTD-1. The work will promote the regulation mechanism study of n-alkane degradation in bacteria and help the bioremediation method development for petroleum pollution.
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Affiliation(s)
- Nannan Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuli Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chong Yin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanli Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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32
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Tolmie C, Smit MS, Opperman DJ. Native roles of Baeyer–Villiger monooxygenases in the microbial metabolism of natural compounds. Nat Prod Rep 2019; 36:326-353. [DOI: 10.1039/c8np00054a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Baeyer–Villiger monooxygenases function in the primary metabolism of atypical carbon sources, as well as the synthesis of complex microbial metabolites.
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Affiliation(s)
- Carmien Tolmie
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
| | - Martha S. Smit
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
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33
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Yang R, Zhang G, Li S, Moazeni F, Li Y, Wu Y, Zhang W, Chen T, Liu G, Zhang B, Wu X. Degradation of crude oil by mixed cultures of bacteria isolated from the Qinghai-Tibet plateau and comparative analysis of metabolic mechanisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:1834-1847. [PMID: 30456621 DOI: 10.1007/s11356-018-3718-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/08/2018] [Indexed: 06/09/2023]
Abstract
This study investigates the biodegradation of crude oil by a mixed culture of bacteria isolated from the Qinghai-Tibet plateau using gas chromatography-mass spectrometer (GC-MS) and the gravimetric method. The results showed that a mixed culture has a stronger ability to degrade hydrocarbon than pure cultures. Once both Nocardia soli Y48 and Rhodococcus erythropolis YF28-1 (8) were present in a culture, the culture demonstrated the highest crude oil removal efficiency of almost 100% after 10 days of incubation at 20 °C. Moreover, further analysis of the degradation mechanisms used by the above strains, which revealed utilization of different n-alkane substrates, indicated the diversity of evolution and variations in different strains, as well as the importance of multiple metabolic mechanisms for alkane degradation. Therefore, it is concluded that a mixed culture of Y48 and YF28-1 (8) strains can provide a more effective method for bioremediation of hydrocarbon-contaminated soil in permafrost regions.
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Affiliation(s)
- Ruiqi Yang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Shiweng Li
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Faegheh Moazeni
- School of Science Engineering and Technology, Penn State Harrisburg University, Middletown, PA, 17057, USA
| | - Yunshi Li
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Yongna Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China.
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China.
| | - Binglin Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
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Gregson BH, Metodieva G, Metodiev MV, Golyshin PN, McKew BA. Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1. Front Microbiol 2018; 9:3130. [PMID: 30619200 PMCID: PMC6304351 DOI: 10.3389/fmicb.2018.03130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 02/02/2023] Open
Abstract
The marine obligate hydrocarbonoclastic bacterium Thalassolituus oleivorans MIL-1 metabolizes a broad range of aliphatic hydrocarbons almost exclusively as carbon and energy sources. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on medium- (n-C14) or long-chain (n-C28) alkanes. During growth on n-C14, T. oleivorans expresses an alkane monooxygenase system involved in terminal oxidation including two alkane 1-monooxygenases, a ferredoxin, a ferredoxin reductase and an aldehyde dehydrogenase. In contrast, during growth on long-chain alkanes (n-C28), T. oleivorans may switch to a subterminal alkane oxidation pathway evidenced by significant upregulation of Baeyer-Villiger monooxygenase and an esterase, proteins catalyzing ketone and ester metabolism, respectively. The metabolite (primary alcohol) generated from terminal oxidation of an alkane was detected during growth on n-C14 but not on n-C28 also suggesting alternative metabolic pathways. Expression of both active and passive transport systems involved in uptake of long-chain alkanes was higher when compared to the non-hydrocarbon control, including a TonB-dependent receptor, a FadL homolog and a specialized porin. Also, an inner membrane transport protein involved in the export of an outer membrane protein was expressed. This study has demonstrated the substrate range of T. oleivorans is larger than previously reported with growth from n-C10 up to n-C32. It has also greatly enhanced our understanding of the fundamental physiology of T. oleivorans, a key bacterium that plays a significant role in natural attenuation of marine oil pollution, by identifying key enzymes expressed during the catabolism of n-alkanes.
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Affiliation(s)
- Benjamin H Gregson
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Gergana Metodieva
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Metodi V Metodiev
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Bangor, United Kingdom.,School of Natural Sciences, College of Environmental Sciences and Engineering, Bangor University, Bangor, United Kingdom
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
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35
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Characterization of a biosurfactant-producing Leclercia sp. B45 with new transcriptional patterns of alkB gene. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1409-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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36
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Meng L, Bao M, Sun P. Construction of long-chain alkane degrading bacteria and its application in bioremediation of crude oil pollution. Int J Biol Macromol 2018; 119:524-532. [DOI: 10.1016/j.ijbiomac.2018.07.137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 01/02/2023]
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37
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Kim HS, Dong K, Kim J, Lee SS. Characteristics of crude oil-degrading bacteria Gordonia iterans isolated from marine coastal in Taean sediment. Microbiologyopen 2018; 8:e00754. [PMID: 30338941 PMCID: PMC6562140 DOI: 10.1002/mbo3.754] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/18/2018] [Accepted: 09/20/2018] [Indexed: 01/01/2023] Open
Abstract
Crude oil is a major pollutant of marine and coastal ecosystems, and it causes environmental problems more seriously. It is believed ultimate and complete degradation is accomplished mainly by microorganisms. In this study, we aim to search out for bacterial strains with high ability in degrading crude oil. From sediments contaminated by the petroleum spilled in 2007, an accident in Taean, South Korea, we isolated thirty‐one bacterial strains in total with potential application in crude oil contamination remediation. In terms of removal percentage after 7 days, one of the strains, Co17, showed the highest removal efficiency with 84.2% of crude oil in Bushnell‐Haas media. The Co17 strain even exhibited outstanding ability removing crude oil at a high salt concentration. Through the whole genome sequencing annotation results, many genes related with n‐alkane degradation in the genome of Gordonia sp. Co17, revealed alkane‐1‐monooxygenase, alcohol dehydrogenase, and Baeyer–Villiger monooxygenase. Specially, for confirmation of gene‐level, alkB gene encoding alkane hydroxylase (alkane‐1‐monooxygenase) was found in the strain Co17. The expression of alkB upregulated 125‐fold after 18 hr accompany with the removal of n‐alkanes of 48.9%. We therefore propose the strain Gordonia iterans Co17, isolated from crude oil‐contaminated marine sediment, could be used to offer a new strategy for bioremediation with high efficiency.
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Affiliation(s)
- Hyun-Sook Kim
- Department of Biological Engineering, Kyonggi University, Suwon-si, Korea
| | - Ke Dong
- Department of Life Science, Kyonggi University, Suwon-si, Korea
| | - Jinsoo Kim
- Department of Life Science, Kyonggi University, Suwon-si, Korea
| | - Sang-Seob Lee
- Department of Biological Engineering, Kyonggi University, Suwon-si, Korea.,Department of Life Science, Kyonggi University, Suwon-si, Korea
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Promoting the treatment of crude oil alkane pollution through the study of enzyme activity. Int J Biol Macromol 2018; 119:708-716. [PMID: 30055278 DOI: 10.1016/j.ijbiomac.2018.07.160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/25/2018] [Accepted: 07/25/2018] [Indexed: 11/22/2022]
Abstract
Microbes appear to play a key role in bioremediation of petroleum hydrocarbons pollution and little attention has been paid to the enzyme activity in the process of alkane bioremediation. Oil field bacterium identified as Pseudomonas synxantha LSH-7' was chosen as the tested strain. Periodically collected samples were analyzed by GC-FID (Gas Chromatography- Flame Ionization Detector) and RT-qPCR (Quantitative-Real-Time-PCR). GC-FID results showed this bacterial strain has great degradation ability on crude oil n-alkanes and RT-qPCR data indicated the differences between the three genes expression including AlkB-, Cytochromes P450-, and almA- related when grown on different-chain alkanes. Meanwhile, enzyme activity like alkane hydroxylase, alcohol dehydrogenase, dehydrogenase, protease, phosphatase, catalase and lipase were measured. Extracellular alkane hydroxylase was induced in a higher degree than intracellular in the early incubation time, alcohol dehydrogenase increased/decreased along with alkane hydroxylase, and the pH of the medium obviously decreased. Other enzymes were also described including dehydrogenase activity that reached a highest point that was slower than alcohol dehydrogenase, protease activity started multiplying after a period of culture while biomass was immediately increased, catalase activity dramatically enhanced in the presence of alkanes, phosphatase activity was closely linked to pH approximately but lipase activity was found to be moderate.
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Sun JQ, Xu L, Liu XY, Zhao GF, Cai H, Nie Y, Wu XL. Functional Genetic Diversity and Culturability of Petroleum-Degrading Bacteria Isolated From Oil-Contaminated Soils. Front Microbiol 2018; 9:1332. [PMID: 29973925 PMCID: PMC6019457 DOI: 10.3389/fmicb.2018.01332] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/31/2018] [Indexed: 12/18/2022] Open
Abstract
In this study, we compared the culturability of aerobic bacteria isolated from long-term oil-contaminated soils via enrichment and direct-plating methods; bacteria were cultured at 30°C or ambient temperatures. Two soil samples were collected from two sites in the Shengli oilfield located in Dongying, China. One sample (S0) was close to the outlet of an oil-production water treatment plant, and the other sample (S1) was located 500 m downstream of the outlet. In total, 595 bacterial isolates belonging to 56 genera were isolated, distributed in Actinobacteria, Firmicutes, Bacterioidetes, and Proteobacteria. It was interesting that Actinobacteria and Firmicutes were not detected from the 16S rRNA gene clone library. The results suggested the activation of rare species during culture. Using the enrichment method, 239 isolates (31 genera) and 96 (22 genera) isolates were obtained at ambient temperatures and 30°C, respectively, from S0 soil. Using the direct-plating method, 97 isolates (15 genera) and 163 isolates (20 genera) were obtained at ambient temperatures and 30°C, respectively, from two soils. Of the 595 isolates, 244 isolates (41.7% of total isolates) could degrade n-hexadecane. A greater number of alkane-degraders was isolated at ambient temperatures using the enrichment method, suggesting that this method could significantly improve bacterial culturability. Interestingly, the proportion of alkane degrading isolates was lower in the isolates obtained using enrichment method than that obtained using direct-plating methods. Considering the greater species diversity of isolates obtained via the enrichment method, this technique could be used to increase the diversity of the microbial consortia. Furthermore, phenol hydroxylase genes (pheN), medium-chain alkane monooxygenases genes (alkB and CYP153A), and long-chain alkane monooxygenase gene (almA) were detected in 60 isolates (11 genotypes), 91 isolates (27 genotypes) and 93 isolates (24 genotypes), and 34 isolates (14 genotypes), respectively. This study could provide new insights into microbial resources from oil fields or other environments, and this information will be beneficial for bioremediation of petroleum contamination and for other industrial applications.
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Affiliation(s)
- Ji-Quan Sun
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
| | - Lian Xu
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
| | - Xue-Ying Liu
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
| | - Gui-Fang Zhao
- School of Environment, Tsinghua University, Beijing, China
| | - Hua Cai
- School of Environment, Tsinghua University, Beijing, China
| | - Yong Nie
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
| | - Xiao-Lei Wu
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
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Kadri T, Rouissi T, Magdouli S, Brar SK, Hegde K, Khiari Z, Daghrir R, Lauzon JM. Production and characterization of novel hydrocarbon degrading enzymes from Alcanivorax borkumensis. Int J Biol Macromol 2018; 112:230-240. [DOI: 10.1016/j.ijbiomac.2018.01.177] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 01/26/2018] [Accepted: 01/27/2018] [Indexed: 11/16/2022]
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Park C, Park W. Survival and Energy Producing Strategies of Alkane Degraders Under Extreme Conditions and Their Biotechnological Potential. Front Microbiol 2018; 9:1081. [PMID: 29910779 PMCID: PMC5992423 DOI: 10.3389/fmicb.2018.01081] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/07/2018] [Indexed: 11/17/2022] Open
Abstract
Many petroleum-polluted areas are considered as extreme environments because of co-occurrence of low and high temperatures, high salt, and acidic and anaerobic conditions. Alkanes, which are major constituents of crude oils, can be degraded under extreme conditions, both aerobically and anaerobically by bacteria and archaea of different phyla. Alkane degraders possess exclusive metabolic pathways and survival strategies, which involve the use of protein and RNA chaperones, compatible solutes, biosurfactants, and exopolysaccharide production for self-protection during harsh environmental conditions such as oxidative and osmotic stress, and ionic nutrient-shortage. Recent findings suggest that the thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus uses a novel alkylsuccinate synthase for long-chain alkane degradation, and the thermophilic Candidatus Syntrophoarchaeum butanivorans anaerobically oxidizes butane via alkyl-coenzyme M formation. In addition, gene expression data suggest that extremophiles produce energy via the glyoxylate shunt and the Pta-AckA pathway when grown on a diverse range of alkanes under stress conditions. Alkane degraders possess biotechnological potential for bioremediation because of their unusual characteristics. This review will provide genomic and molecular insights on alkane degraders under extreme conditions.
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Affiliation(s)
- Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
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Shift in microbial group during remediation by enhanced natural attenuation (RENA) of a crude oil-impacted soil: a case study of Ikarama Community, Bayelsa, Nigeria. 3 Biotech 2017; 7:152. [PMID: 28597163 DOI: 10.1007/s13205-017-0782-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/15/2017] [Indexed: 10/19/2022] Open
Abstract
Acute and chronic pollution of environments with crude oil does not bode well for biota living within the vicinity of polluted environments. This is due to environmental and public health concerns on the negative impact of crude oil pollution on living organisms. Enhancing microbial activities by adding nutrients and other amendments had proved effective in pollutant removal during bioremediation. This study was carried out to determine how microbial group respond during remediation by enhanced natural attenuation (RENA) during a field-scale bioremediation. Crude oil-polluted soil samples were collected (before, during, and after remediation) from a site undergoing remediation by enhanced natural attenuation (RENA) at Ikarama Community, Bayelsa State, Nigeria, and were analyzed for total petroleum hydrocarbon (TPH), polyaromatic hydrocarbon (PAH), and a shift in microbial community. The gas chromatography-flame ionization detector (GC-FID) results showed that the pollutant concentrations (TPH and PAH) reduced by 98 and 85%, respectively, after the remediation. Culturable hydrocarbon utilizing bacteria (CHUB) was highest (8.3 × 104 cfu/g) for sample collected during the remediation studies, whilst sample collected after remediation had low CHUB (6.1 × 104 cfu/g) compared to that collected before remediation (7.7 × 104 cfu/g). Analysis of 16S rRNA of the isolated CHUB showed they belonged to eight bacterial genera namely: Achromobacter, Alcaligenes, Azospirillus, Bacillus, Lysinibacillus, Ochrobactrum, Proteus, and Pusillimonas, with Alcaligenes as the dominant genus. In this study, it was observed that the bacterial community shifted from mixed group (Gram-positive and -negative) before and during the remediation, to only the latter group after the remediation studies. The betaproteobacteria groups were the dominant isolated bacterial phylotype. This study showed that RENA is an effective method of reducing pollutant concentration in crude oil-polluted sites, and could be applied to other polluted sites in the Niger Delta region of Nigeria to mitigate the devastating effects of crude oil pollution.
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Long H, Wang Y, Chang S, Liu G, Chen T, Huo G, Zhang W, Wu X, Tai X, Sun L, Zhang B. Diversity of crude oil-degrading bacteria and alkane hydroxylase (alkB) genes from the Qinghai-Tibet Plateau. ENVIRONMENTAL MONITORING AND ASSESSMENT 2017; 189:116. [PMID: 28220441 DOI: 10.1007/s10661-017-5798-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 01/23/2017] [Indexed: 06/06/2023]
Abstract
The aim of this study was to survey the response of the microbial community to crude oil and the diversity of alkane hydroxylase (alkB) genes in soil samples from the Qinghai-Tibet Plateau (QTP). The enrichment cultures and clone libraries were used. Finally, 53 isolates and 94 alkB sequences were obtained from 10 pristine soil samples after enrichment at 10 °C with crude oil as sole carbon source. The isolates fell into the phyla Proteobacteria, Actinobacteria, and Bacteroidetes, with the dominance of Pseudomonas and Acinetobacter. The composition of degraders was different from polar habitats where Acinetobacter sp. is not a predominant responder of alkane degradative microbial communities. Phylogenetic analysis showed that the alkB genes from isolates and enrichment communities formed eight clusters and mainly related with alkB genes of Pseudomonas, Rhodococcus, and Acinetobacter. The alkB gene diversity in the QTP was lower than marine environments and polar soil samples. In particular, a total of 10 isolates exhibiting vigorous growth with crude oil could detect no crude oil degradation-related gene sequences, such as alkB, P450, almA, ndoB, and xylE genes. The Shannon-Wiener index of the alkB clone libraries from the QTP ranged from 1.00 to 2.24 which is similar with polar pristine soil samples but lower than that of contaminated soils. These results indicated that the Pseudomonas, Acinetobacter, and Rhodococcus genera are the candidate for in situ bioremediation, and the environment of QTP may be still relatively uncontaminated by crude oil.
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Affiliation(s)
- Haozhi Long
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
| | - Yilin Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China
| | - Sijing Chang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
- State Key Laboratory of Cryospheric Sciences, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China.
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China.
- State Key Laboratory of Cryospheric Sciences, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China.
| | - Guanghua Huo
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
| | - Xisheng Tai
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
| | - Likun Sun
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
| | - Baogui Zhang
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
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Barbato M, Scoma A, Mapelli F, De Smet R, Banat IM, Daffonchio D, Boon N, Borin S. Hydrocarbonoclastic Alcanivorax Isolates Exhibit Different Physiological and Expression Responses to n-dodecane. Front Microbiol 2016; 7:2056. [PMID: 28066376 PMCID: PMC5174103 DOI: 10.3389/fmicb.2016.02056] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/07/2016] [Indexed: 12/28/2022] Open
Abstract
Autochthonous microorganisms inhabiting hydrocarbon polluted marine environments play a fundamental role in natural attenuation and constitute promising resources for bioremediation approaches. Alcanivorax spp. members are ubiquitous in contaminated surface waters and are the first to flourish on a wide range of alkanes after an oil-spill. Following oil contamination, a transient community of different Alcanivorax spp. develop, but whether they use a similar physiological, cellular and transcriptomic response to hydrocarbon substrates is unknown. In order to identify which cellular mechanisms are implicated in alkane degradation, we investigated the response of two isolates belonging to different Alcanivorax species, A. dieselolei KS 293 and A. borkumensis SK2 growing on n-dodecane (C12) or on pyruvate. Both strains were equally able to grow on C12 but they activated different strategies to exploit it as carbon and energy source. The membrane morphology and hydrophobicity of SK2 changed remarkably, from neat and hydrophilic on pyruvate to indented and hydrophobic on C12, while no changes were observed in KS 293. In addition, SK2 accumulated a massive amount of intracellular grains when growing on pyruvate, which might constitute a carbon reservoir. Furthermore, SK2 significantly decreased medium surface tension with respect to KS 293 when growing on C12, as a putative result of higher production of biosurfactants. The transcriptomic responses of the two isolates were also highly different. KS 293 changes were relatively balanced when growing on C12 with respect to pyruvate, giving almost the same amount of upregulated (28%), downregulated (37%) and equally regulated (36%) genes, while SK2 transcription was upregulated for most of the genes (81%) when growing on pyruvate when compared to C12. While both strains, having similar genomic background in genes related to hydrocarbon metabolism, retained the same capability to grow on C12, they nevertheless presented very different physiological, cellular and transcriptomic landscapes.
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Affiliation(s)
- Marta Barbato
- Centre for Microbial Ecology and Technology, Ghent UniversityGhent, Belgium; Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Alberto Scoma
- Centre for Microbial Ecology and Technology, Ghent University Ghent, Belgium
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy
| | - Rebecca De Smet
- Department of Medical and Forensic Pathology, University of Ghent Ghent, Belgium
| | - Ibrahim M Banat
- School of Biomedical Sciences, University of Ulster Coleraine, UK
| | - Daniele Daffonchio
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Nico Boon
- Centre for Microbial Ecology and Technology, Ghent University Ghent, Belgium
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy
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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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Bonin P, Vieira C, Grimaud R, Militon C, Cuny P, Lima O, Guasco S, Brussaard CPD, Michotey V. Substrates specialization in lipid compounds and hydrocarbons of Marinobacter genus. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15347-15359. [PMID: 25561256 DOI: 10.1007/s11356-014-4009-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 12/15/2014] [Indexed: 06/04/2023]
Abstract
The impact of petroleum contamination and of burrowing macrofauna on abundances of Marinobacter and denitrifiers was tested in marine sediment mesocoms after 3 months incubation. Quantification of this genus by qPCR with a new primer set showed that the main factor favoring Marinobacter abundance was hydrocarbon amendment followed by macrofauna presence. In parallel, proportion of nosZ-harboring bacteria increased in the presence of marcrofauna. Quantitative finding were explained by physiological data from a set of 34 strains and by genomic analysis of 16 genomes spanning 15 different Marinobacter-validated species (Marinobacter hydrocarbonoclasticus, Marinobacter daeopensis, Marinobacter santoriniensis, Marinobacter pelagius, Marinobacter flavimaris, Marinobacter adhaerens, Marinobacter xestospongiae, Marinobacter algicola, Marinobacter vinifirmus, Marinobacter maritimus, Marinobacter psychrophilus, Marinobacter lipoliticus, Marinobacter manganoxydans, Marinobacter excellens, Marinobacter nanhaiticus) and 4 potential novel ones. Among the 105 organic electron donors tested in physiological analysis, Marinobacter pattern appeared narrow for almost all kinds of organic compounds except lipid ones. Strains of this set could oxidize a very large spectrum of lipids belonging to glycerolipids, branched, fatty acyls, and aromatic hydrocarbon classes. Physiological data were comforted by genomic analysis, and genes of alkane 1-monooxygenase, haloalkane dehalogenase, and flavin-binding monooxygenase were detected in most genomes. Denitrification was assessed for several strains belonging to M. hydrocarbonoclasticus, M. vinifirmus, Marinobacter maritinus, and M. pelagius species indicating the possibility to use nitrate as alternative electron acceptor. Higher occurrence of Marinobacter in the presence of petroleum appeared to be the result of a broader physiological trait allowing this genus to use lipids including hydrocarbon as principal electron donors.
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Affiliation(s)
- Patricia Bonin
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France
| | - Christophe Vieira
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France
- Sorbonne Universités, UPMC Univ Paris 06, IFD, 4 Place Jussieu, 75252, Paris cedex 05, France
| | - Régis Grimaud
- Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Equipe Environnement et Microbiologie, UMR 5254, CNRS, IBEAS, Université de Pau et des Pays de l'Adour, Pau, France
| | - Cécile Militon
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France
| | - Philippe Cuny
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France
| | - Oscar Lima
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France
- Ecosystèmes, Biodiversité, Evolution (ECOBIO), CNRS : UMR6553 - Université de Rennes 1 - INEE - Observatoire des Sciences de l'Univers de Rennes, Rennes, France
| | - Sophie Guasco
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France
| | - Corina P D Brussaard
- Department of Biological Oceanography, Royal Netherlands Institute for Sea Research, NL-1790, Den Burg, AB, Netherlands
| | - Valérie Michotey
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France.
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Tsuboi S, Yamamura S, Nakajima-Kambe T, Iwasaki K. Diversity of alkane hydroxylase genes on the rhizoplane of grasses planted in petroleum-contaminated soils. SPRINGERPLUS 2015; 4:526. [PMID: 26405645 PMCID: PMC4575313 DOI: 10.1186/s40064-015-1312-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 09/07/2015] [Indexed: 11/10/2022]
Abstract
The study investigated the diversity and genotypic features of alkane hydroxylase genes on rhizoplanes of grasses planted in artificial petroleum-contaminated soils to acquire new insights into the bacterial communities responsible for petroleum degradation in phytoremediation. Four types of grass (Cynodon dactylon, two phenotypes of Zoysia japonica, and Z. matrella) were used. The concentrations of total petroleum hydrocarbon effectively decreased in the grass-planted systems compared with the unplanted system. Among the representative alkane hydroxylase genes alkB, CYP153, almA and ladA, the first two were detected in this study, and the genotypes of both genes were apparently different among the systems studied. Their diversity was also higher on the rhizoplanes of the grasses than in unplanted oil-contaminated soils. Actinobacteria-related genes in particular were among the most diverse alkane hydroxylase genes on the rhizoplane in this study, indicating that they are one of the main contributors to degrading alkanes in oil-contaminated soils during phytoremediation. Actinobacteria-related alkB genes and CYP153 genes close to the genera Parvibaculum and Aeromicrobium were found in significant numbers on the rhizoplanes of grasses. These results suggest that the increase in diversity and genotype differences of the alkB and CYP153 genes are important factors affecting petroleum hydrocarbon-degrading ability during phytoremediation.
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Affiliation(s)
- Shun Tsuboi
- National Institute for Environmental Studies (NIES), Center for Regional Environmental Research, 16-2 Onogawa, Tsukuba, 305-8506 Japan ; National Institute for Environmental Studies (NIES), Center for Environmental Biology and Ecosystem Studies, 16-2 Onogawa, Tsukuba, 305-8506 Japan
| | - Shigeki Yamamura
- National Institute for Environmental Studies (NIES), Center for Regional Environmental Research, 16-2 Onogawa, Tsukuba, 305-8506 Japan
| | - Toshiaki Nakajima-Kambe
- Faculty of Life and Environmental Sciences (Bioindustrial Sciences), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Japan
| | - Kazuhiro Iwasaki
- National Institute for Environmental Studies (NIES), Center for Regional Environmental Research, 16-2 Onogawa, Tsukuba, 305-8506 Japan
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The long-chain alkane metabolism network of Alcanivorax dieselolei. Nat Commun 2014; 5:5755. [DOI: 10.1038/ncomms6755] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 11/05/2014] [Indexed: 11/08/2022] Open
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Mounier J, Camus A, Mitteau I, Vaysse PJ, Goulas P, Grimaud R, Sivadon P. The marine bacteriumMarinobacter hydrocarbonoclasticusSP17 degrades a wide range of lipids and hydrocarbons through the formation of oleolytic biofilms with distinct gene expression profiles. FEMS Microbiol Ecol 2014; 90:816-31. [DOI: 10.1111/1574-6941.12439] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 10/05/2014] [Accepted: 10/06/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
- Julie Mounier
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
| | - Arantxa Camus
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
| | - Isabelle Mitteau
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
| | - Pierre-Joseph Vaysse
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
| | - Philippe Goulas
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
| | - Régis Grimaud
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
| | - Pierre Sivadon
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
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