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Fenibo EO, Selvarajan R, Abia ALK, Matambo T. Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162951. [PMID: 36948313 DOI: 10.1016/j.scitotenv.2023.162951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 05/06/2023]
Abstract
Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Akebe Luther King Abia
- Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa; Environmental Research Foundation, Westville 3630, South Africa
| | - Tonderayi Matambo
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort 1709, South Africa.
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Guo X, Zhang J, Han L, Lee J, Williams SC, Forsberg A, Xu Y, Austin RN, Feng L. Structure and mechanism of the alkane-oxidizing enzyme AlkB. Nat Commun 2023; 14:2180. [PMID: 37069165 PMCID: PMC10110569 DOI: 10.1038/s41467-023-37869-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/03/2023] [Indexed: 04/19/2023] Open
Abstract
Alkanes are the most energy-rich form of carbon and are widely dispersed in the environment. Their transformation by microbes represents a key step in the global carbon cycle. Alkane monooxygenase (AlkB), a membrane-spanning metalloenzyme, converts straight chain alkanes to alcohols in the first step of the microbially-mediated degradation of alkanes, thereby playing a critical role in the global cycling of carbon and the bioremediation of oil. AlkB biodiversity is attributed to its ability to oxidize alkanes of various chain lengths, while individual AlkBs target a relatively narrow range. Mechanisms of substrate selectivity and catalytic activity remain elusive. Here we report the cryo-EM structure of AlkB, which provides a distinct architecture for membrane enzymes. Our structure and functional studies reveal an unexpected diiron center configuration and identify molecular determinants for substrate selectivity. These findings provide insight into the catalytic mechanism of AlkB and shed light on its function in alkane-degrading microorganisms.
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Affiliation(s)
- Xue Guo
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jianxiu Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lei Han
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Juliet Lee
- Department of Chemistry, Barnard College, 3009 Broadway, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Shoshana C Williams
- Department of Chemistry, Barnard College, 3009 Broadway, New York, NY, 10027, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Allison Forsberg
- Department of Chemistry, Barnard College, 3009 Broadway, New York, NY, 10027, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90007, USA
| | - Yan Xu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Liang Feng
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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3
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Dynamics and prevalence of specific hydrocarbonoclastic bacterial population with respect to nutrient treatment levels in crude oil sludge. Arch Microbiol 2022; 204:708. [DOI: 10.1007/s00203-022-03323-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/09/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
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Shapiro TN, Manucharova NA, Lobakova ES. Activity of alkanmonooxygenase alkB gene in strains of hydrocarbon-oxidizing bacteria isolated from petroleum products. Vavilovskii Zhurnal Genet Selektsii 2022; 26:575-582. [PMID: 36313823 PMCID: PMC9556310 DOI: 10.18699/vjgb-22-70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/14/2022] [Accepted: 07/07/2022] [Indexed: 06/16/2023] Open
Abstract
Alkanmonooxygenase enzymes AlkB and Cyp153 are responsible for the aerobic degradation of n-alkanes of petroleum and petroleum products. To prove the usage of n-alkanes from oil and petroleum products by hydrocarbon-oxidizing bacteria isolated from aviation kerosene TS-1 and automobile gasoline AI-95, the detection of the key genes alkB, Alk1, Alk2, Alk3 and Cyp153 encoding alkanmonooxygenases AlkB and Cyp153 (responsible for the oxidation of hydrocarbons with a certain chain length) was carried out. It was found that bacterial strains isolated from TS-1 jet fuel, except Deinococcus sp. Bi7, had at least one of the studied n-alkane degradation genes. The strains Sphingobacterium multivorum Bi2; Alcaligenes faecalis Bi3; Rhodococcus sp. Bi4; Sphingobacterium sp. Bi5; Rhodococcus erythropolis Bi6 contained the alkB gene. In the strains of hydrocarbon-oxidizing bacteria isolated from gasoline AI- 95, this alkanmonooxygenase gene was not detected. Using the real-time PCR method, the activity of the alkB gene in all bacterial strains isolated from petroleum products was analyzed and the number of its copies was determined. By real-time PCR using a primer with a different sequence of nucleotides to detect the alkB gene, its activity was established in all bacterial strains isolated from gasoline AI-95; besides, the strain Paenibacillus agaridevorans Bi11 was assigned to the group with a high level of its activity (1290 copies/ml). According to the assessment of the growth of isolated hydrocarbon-oxidizing bacteria on a solid Evans mineral medium with the addition of the model mixture of hydrocarbons, the strains were divided into three groups. The distributions of strains of hydrocarbon-oxidizing bacteria in the groups based on the activity of the alkB gene and groups formed based on the growth ability and use of the model mixture of hydrocarbons and petroleum products were found to be consistent. The results obtained indicate that we need to use a complex of molecular and physiological methods for a comprehensive analysis of the distribution of the studied genes in bacteria and to assess their activity in the strains of hydrocarbon-oxidizing bacteria capable of biodegradation of petroleum hydrocarbons.
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Affiliation(s)
- T N Shapiro
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
| | - N A Manucharova
- Lomonosov Moscow State University, Faculty of Soil Science, Moscow, Russia
| | - E S Lobakova
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
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Sah D, Rai JPN, Ghosh A, Chakraborty M. A review on biosurfactant producing bacteria for remediation of petroleum contaminated soils. 3 Biotech 2022; 12:218. [PMID: 35965658 PMCID: PMC9365905 DOI: 10.1007/s13205-022-03277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/21/2022] [Indexed: 11/01/2022] Open
Abstract
The discharge of potentially toxic petroleum hydrocarbons into the environment has been a matter of concern, as these organic pollutants accumulate in many ecosystems due to their hydrophobicity and low bioavailability. Petroleum hydrocarbons are neurotoxic and carcinogenic organic pollutants, extremely harmful to human and environmental health. Traditional treatment methods for removing hydrocarbons from polluted areas, including various mechanical and chemical strategies, are ineffective and costly. However, many indigenous microorganisms in soil and water can utilise hydrocarbon compounds as sources of carbon and energy and hence, can be employed to degrade hydrocarbon contaminants. Therefore, bioremediation using bacteria that degrade petroleum hydrocarbons is commonly viewed as an environmentally acceptable and effective method. The efficacy of bioremediation can be boosted further by using potential biosurfactant-producing microorganisms, as biosurfactants reduce surface tension, promote emulsification and micelle formation, making hydrocarbons bio-available for microbial breakdown. Further, introducing nanoparticles can improve the solubility of hydrophobic hydrocarbons as well as microbial synthesis of biosurfactants, hence establishing a favourable environment for microbial breakdown of these chemicals. The review provides insights into the role of microbes in the bioremediation of soils contaminated with petroleum hydrocarbons and emphasises the significance of biosurfactants and potential biosurfactant-producing bacteria. The review partly focusses on how nanotechnology is being employed in different critical bioremediation processes.
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Affiliation(s)
- Diksha Sah
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - J. P. N. Rai
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Ankita Ghosh
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Moumita Chakraborty
- Department of Environmental Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
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Zhang Y, Yang Q, Ling J, Zhang Y, Zhou W, Ahmad M, Lin X, Lin L, Peng Q, Dong J. The diversity of alkane-degrading bacterial communities in seagrass ecosystem of the South China Sea. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1799-1807. [PMID: 34264477 DOI: 10.1007/s10646-021-02450-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Seagrass meadows are one of the most important marine ecosystems. Alkanes are the common hydrocarbon contaminants that can affect seagrass growth. In this study, a large spatial-scale investigation has been carried out on the alkane-degrading bacterial community structure in the rhizosphere and non-rhizosphere sediments of two seagrass species (Thalassia hemprichii and Halophila ovalis). AlkB gene was employed as a biomarker gene to study the alkane-degrading bacterial community structure. The results showed that the alpha diversity of the alkane-degrading bacterial community in T. hemprichii non-rhizosphere sediments was higher than that of its rhizosphere sediments. However, the alpha diversity of the alkane-degrading bacterial community in H. ovalis rhizosphere sediments was higher than that of its non-rhizosphere sediments in the open sea, but the result was contrast in the coast area. In addition, the alpha diversity of alkane-degrading bacterial communities in the coast area was higher than that of far away from the coast in the T. hemprichii rhizosphere and non-rhizosphere sediments. The phylogenetic analysis result revealed that the alkB sequences from the seagrass ecosystem were mainly affiliated with the class Alphaproteobacteria, and had the two novel lineages. Genus Agrobacterium was the most predominant alkane-degrading bacteria. These results contributed to disclose the geographical distribution pattern of alkane-degrading bacteria in the seagrass ecosystem of the South China Sea.
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Affiliation(s)
- Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Yanying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Ocean School, Yantai University, Yantai, 264005, China
| | - Weiguo Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Manzoor Ahmad
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangcheng Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liyun Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuying Peng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, 572000, China.
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7
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Lee YY, Seo Y, Ha M, Lee J, Yang H, Cho KS. Dynamics of bacterial functional genes and community structures during rhizoremediation of diesel-contaminated compost-amended soil. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2021; 56:1107-1120. [PMID: 34554047 DOI: 10.1080/10934529.2021.1965817] [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: 03/11/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The objective of this study was to characterize the effects of organic soil amendment (compost) on bacterial populations associated with petroleum hydrocarbon (PH) degradation and nitrous oxide (N2O) dynamics via pot experiments. Soil was artificially contaminated with diesel oil at total petroleum hydrocarbon (TPH) concentration of 30,000 mg·kg-soil-1 and compost was mixed with the contaminated soil at a 1:9 ratio (w/w). Maize seedlings were planted in each pot and a total of ten pots with two treatments (compost-amended and unamended) were prepared. The pot experiment was conducted for 85 days. The compost-amended soil had a significantly higher TPH removal efficiency (51.1%) than unamended soil (21.4%). Additionally, the relative abundance of the alkB gene, which is associated with PH degradation, was higher in the compost-amended soil than in the unamended soil. Similarly, cnorB and nosZ (which are associated with nitric oxide (NO) and N2O reduction, respectively) were also highly upregulated in the compost-amended soil. Moreover, the compost-amended soil exhibited higher richness and evenness indices, indicating that bacterial diversity was higher in the amended soil than in the unamended soil. Therefore, our findings may contribute to the development of strategies to enhance remediation efficiency and greenhouse gas mitigation during the rhizoremediation of diesel-contaminated soils.
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Affiliation(s)
- Yun-Yeong Lee
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Yoonjoo Seo
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Minyoung Ha
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jiho Lee
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Hyoju Yang
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
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8
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Christian WC, Butler TM, Ghannam RB, Webb PN, Techtmann SM. Phylogeny and diversity of alkane-degrading enzyme gene variants in the laurentian great lakes and western atlantic. FEMS Microbiol Lett 2021; 367:5974522. [PMID: 33354724 DOI: 10.1093/femsle/fnaa182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/09/2020] [Indexed: 11/14/2022] Open
Abstract
Many aquatic environments are at risk for oil contamination and alkanes are one of the primary constituents of oil. The alkane hydroxylase (AlkB) is a common enzyme used by microorganisms to initiate the process of alkane-degradation. While many aspects of alkane bioremediation have been studied, the diversity and evolution of genes involved in hydrocarbon degradation from environmental settings is relatively understudied. The majority of work done to-date has focused on the marine environment. Here we sought to better understand the phylogenetic diversity of alkB genes across marine and freshwater settings using culture-independent methods. We hypothesized that there would be distinct phylogenetic diversity of alkB genes in freshwater relative to the marine environment. Our results confirm that alkB has distinct variants based on environment while our diversity analyses demonstrate that freshwater and marine alkB communities have unique responses to oil amendments. Our results also demonstrate that in the marine environment, depth is a key factor impacting diversity of alkB genes.
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Affiliation(s)
- William C Christian
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive Houghton MI 49931 USA
| | - Timothy M Butler
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive Houghton MI 49931 USA
| | - Ryan B Ghannam
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive Houghton MI 49931 USA
| | - Paige N Webb
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive Houghton MI 49931 USA
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive Houghton MI 49931 USA
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Affiliation(s)
- Judith Münch
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West seventh Avenue, Tianjin 300308, China
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
- Institute of Chemistry, MartinLuther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120, Halle, Saale, Germany
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10
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Lee YY, Seo Y, Ha M, Lee J, Yang H, Cho KS. Evaluation of rhizoremediation and methane emission in diesel-contaminated soil cultivated with tall fescue (Festuca arundinacea). ENVIRONMENTAL RESEARCH 2021; 194:110606. [PMID: 33345896 DOI: 10.1016/j.envres.2020.110606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/24/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
Rhizoremediation, CH4 emission, and bacterial community dynamics were evaluated in diesel-contaminated soil cultivated with tall fescue via a pot experiment. At the beginning of the experiment, total petroleum hydrocarbons (TPHs) removal efficiency was 30.2% in tall fescue-cultivated soil, which was significantly higher than that of unplanted soil (19.4%). However, when compost was added as a soil amendment, TPHs removal efficiency increased to 39.2% in tall fescue-cultivated soil. Interestingly, potential CH4 emissions were more affected by the initial diesel concentration than by compost addition or tall fescue planting. Specifically, the potential CH4 emission was approximately 3.8 times higher in the treatment with the highest initial diesel concentration (T-WC38) than that of the treatment with the lowest initial diesel concentration (T-WC5). Functional gene analysis revealed that TPHs removal had a linear correlation with the alkB/16S gene ratio, whereas potential CH4 emission had a linear correlation with pmoA gene copy numbers. Initial diesel concentrations in soil also affected bacterial community structures and the genera Rhizobium, Halothiobacillus, and Geobacter were found to be positively linked to diesel-contaminated soil rhizoremediation. Therefore, this study provides useful insights into the development of strategies to enhance rhizoremediation efficiency and CH4 emission mitigation in diesel-contaminated soils.
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Affiliation(s)
- Yun-Yeong Lee
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Yoonjoo Seo
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Minyoung Ha
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jiho Lee
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Hyoju Yang
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea.
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11
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Seo Y, Cho KS. Effects of Plant and Soil Amendment on Remediation Performance and Methane Mitigation in Petroleum-Contaminated Soil. J Microbiol Biotechnol 2021; 31:104-114. [PMID: 33144544 PMCID: PMC9705697 DOI: 10.4014/jmb.2006.06023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
Petroleum-contaminated soil is considered among the most important potential anthropogenic atmospheric methane sources. Additionally, various rhizoremediation factors can affect methane emissions by altering soil ecosystem carbon cycles. Nonetheless, greenhouse gas emissions from soil have not been given due importance as a potentially relevant parameter in rhizoremediation techniques. Therefore, in this study we sought to investigate the effects of different plant and soil amendments on both remediation efficiencies and methane emission characteristics in dieselcontaminated soil. An indoor pot experiment consisting of three plant treatments (control, maize, tall fescue) and two soil amendments (chemical nutrient, compost) was performed for 95 days. Total petroleum hydrocarbon (TPH) removal efficiency, dehydrogenase activity, and alkB (i.e., an alkane compound-degrading enzyme) gene abundance were the highest in the tall fescue and maize soil system amended with compost. Compost addition enhanced both the overall remediation efficiencies, as well as pmoA (i.e., a methane-oxidizing enzyme) gene abundance in soils. Moreover, the potential methane emission of diesel-contaminated soil was relatively low when maize was introduced to the soil system. After microbial community analysis, various TPH-degrading microorganisms (Nocardioides, Marinobacter, Immitisolibacter, Acinetobacter, Kocuria, Mycobacterium, Pseudomonas, Alcanivorax) and methane-oxidizing microorganisms (Methylocapsa, Methylosarcina) were observed in the rhizosphere soil. The effects of major rhizoremediation factors on soil remediation efficiency and greenhouse gas emissions discussed herein are expected to contribute to the development of sustainable biological remediation technologies in response to global climate change.
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Affiliation(s)
- Yoonjoo Seo
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea,Corresponding author Phone: +82-2-3277-2393 Fax: +82-2-3277-3275 E-mail:
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Phulpoto IA, Hu B, Wang Y, Ndayisenga F, Li J, Yu Z. Effect of natural microbiome and culturable biosurfactants-producing bacterial consortia of freshwater lake on petroleum-hydrocarbon degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141720. [PMID: 32882554 DOI: 10.1016/j.scitotenv.2020.141720] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
Freshwater lake ecosystem is a reservior of valuable microbial diversity. It needs to be explored for addressing key environmental issues like petroleum-hydrocarbon contamination. In this work, the microbial communities (pre and post enriched with petroleum-hydrocarbons) from different layers of freshwater lake, i.e. surface water, sediments and deepwater, were explored through metagenomic and culture-dependent approaches. A total of 41 bacterial phyla were retrieved from pre-enriched samples, which were significantly reduced in enriched samples where Proteobacteria were dominant (87% to 100%) followed by Bacteroidetes (7.37%) and Verrucomicrobia (3.06%). The most dominant hydrocarbon-degrading genera were extensively verified as Pseudomonas (48.65%), Acinetobacter (45.38%), Stenotrophomonas (3.16%) and Brevundimonas (2.07%) in surface water (S1WCC); Acinetobacter (62.46%), Aeromonas (10.7%), Sphingobacterium (5.20%) and Pseudomonas (4.23%) in sediment (S2MCC); and Acinetobacter (46.57%), Pseudomonas (13.10%), Comamonas (12.93%), Flavobacterium (12.18%) and Enterobacter (9.62%) in deep water (S4WCC). Additionally, the maximum biodegradation of petroleum-hydrocarbons (i.e. used engine oil or UEO) was achieved by microbiome of S2MCC (67.60 ± 0.08%) followed by S4WCC (59.70 ± 0.12%), whereas only 36.80 ± 0.10% degradation was achieved by S1WCC microbiome. On the other hand, UEO degradation by cultivable biosurfactant-producing single cultures such as Pseudomonas sp. S2WE, Pseudomonas sp. S2WG, Pseudomonas sp. S2MS, Ochrobactrum sp. S1MM and Bacillus nealsonii S2MT showed 31.10 ± 0.08% to 40.50 ± 0.11% biodegradation. Comparatively, the biodegradation efficiency was found higher (i.e. 42.20 ± 0.12% to 56.10 ± 0.12%) in each consortia comprising of two, three, four, and five bacterial cultures. Conclusively, the isolated culturable biosurfactants-producing bacterial consortium of freshwater lake demonstrated >80% contribution in the total petroleum-hydrocarbons degradation by the natural microbiome of the ecosystem.
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Affiliation(s)
- Irfan Ali Phulpoto
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China
| | - Bowen Hu
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China
| | - Yanfen Wang
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, No. 380 Huaibei Town, Huairou District, Beijing 101408, PR China
| | - Fabrice Ndayisenga
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China
| | - Jinmei Li
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China.
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Knapik K, Bagi A, Krolicka A, Baussant T. Metatranscriptomic Analysis of Oil-Exposed Seawater Bacterial Communities Archived by an Environmental Sample Processor (ESP). Microorganisms 2020; 8:E744. [PMID: 32429288 PMCID: PMC7284936 DOI: 10.3390/microorganisms8050744] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 11/17/2022] Open
Abstract
The use of natural marine bacteria as "oil sensors" for the detection of pollution events can be suggested as a novel way of monitoring oil occurrence at sea. Nucleic acid-based devices generically called genosensors are emerging as potentially promising tools for in situ detection of specific microbial marker genes suited for that purpose. Functional marker genes are particularly interesting as targets for oil-related genosensing but their identification remains a challenge. Here, seawater samples, collected in tanks with oil addition mimicking a realistic oil spill scenario, were filtered and archived by the Environmental Sample Processor (ESP), a fully robotized genosensor, and the samples were then used for post-retrieval metatranscriptomic analysis. After extraction, RNA from ESP-archived samples at start, Day 4 and Day 7 of the experiment was used for sequencing. Metatranscriptomics revealed that several KEGG pathways were significantly enriched in samples exposed to oil. However, these pathways were highly expressed also in the non-oil-exposed water samples, most likely as a result of the release of natural organic matter from decaying phytoplankton. Temporary peaks of aliphatic alcohol and aldehyde dehydrogenases and monoaromatic ring-degrading enzymes (e.g., ben, box, and dmp clusters) were observed on Day 4 in both control and oil-exposed and non-exposed tanks. Few alkane 1-monooxygenase genes were upregulated on oil, mostly transcribed by families Porticoccaceae and Rhodobacteraceae, together with aromatic ring-hydroxylating dioxygenases, mostly transcribed by Rhodobacteraceae. Few transcripts from obligate hydrocarbonoclastic genera of Alcanivorax, Oleispira and Cycloclasticus were significantly enriched in the oil-treated exposed tank in comparison to control the non-exposed tank, and these were mostly transporters and genes involved in nitrogen and phosphorous acquisition. This study highlights the importance of seasonality, i.e., phytoplankton occurrence and senescence leading to organic compound release which can be used preferentially by bacteria over oil compounds, delaying the latter process. As a result, such seasonal effect can reduce the sensitivity of genosensing tools employing bacterial functional genes to sense oil. A better understanding of the use of natural organic matter by bacteria involved in oil-biodegradation is needed to develop an array of functional markers enabling the rapid and specific in situ detection of anthropogenic pollution.
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Affiliation(s)
| | | | | | - Thierry Baussant
- NORCE Environment, NORCE Norwegian Research Centre AS, 4070 Randaberg, Norway; (K.K.); (A.B.); (A.K.)
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14
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Peng C, Tang Y, Yang H, He Y, Liu Y, Liu D, Qian Y, Lu L. Time- and compound-dependent microbial community compositions and oil hydrocarbon degrading activities in seawater near the Chinese Zhoushan Archipelago. MARINE POLLUTION BULLETIN 2020; 152:110907. [PMID: 31957682 DOI: 10.1016/j.marpolbul.2020.110907] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/03/2020] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
Marine microorganisms play an irreplaceable role in removing spilled oil. Zhoushan archipelago has one of the busiest ports and oil stockpiles in China. However, little is known about which and how fast oil-degrading microorganisms could biodegrade spilled oil here. By combining 14C-/3H-based radiotracer assays and MiSeq sequencing, we report the successive pattern of microbial oil-degrading activities and community compositions. The biodegradation rates of alkanes and PAHs (Polycyclic Aromatic Hydrocarbons) were significantly stimulated by oil addition, and reached their maximum after incubation for 3 and 7 days, respectively. Meanwhile, the abundances of alkB and phnAc genes increased and the bacterial communities continuously shifted. Potential oil-degrading bacteria Alcanivorax, Erythrobacter were the dominant degraders by day 3, whereas the dominant degraders shifted to C1-B045, Alteromonas, Pseudohongiella in the later period. These results provide valuable insights into the cooperative system of the versatile oil-degrading bacteria in successively biodegrading complex oil hydrocarbons in oil spills.
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Affiliation(s)
- Chao Peng
- College of Life Sciences, China West Normal University, Nanchong 637002, China; Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Yun Tang
- College of Life Sciences, China West Normal University, Nanchong 637002, China.
| | - Hong Yang
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Yan He
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Yan Liu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Dan Liu
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Yongming Qian
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China..
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15
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Mitter EK, de Freitas JR, Germida JJ. Hydrocarbon-degrading genes in root endophytic communities on oil sands reclamation covers. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2020; 22:703-712. [PMID: 31905300 DOI: 10.1080/15226514.2019.1707480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In response to environmental regulations, the Canadian oil sands industry aims to reclaim all disturbed areas to equivalent land capability prior to mining operations. However, tailing sands used in reclamation contain residual hydrocarbons and plants growing in these areas may rely on hydrocarbon-degrading endophytic bacteria to survive. This study assessed the hydrocarbon-degrading potential (genes: CYP153, alkB and nah) of culturable and unculturable endophytic bacteria associated with annual barley (Hordeum vulgare) and sweet clover (Melilotus albus) plants in an oil sands reclamation area. Our results suggest higher CYP153 gene copy numbers in sweet clover when compared to barley. Yet, no significant differences were detected in 16S rRNA, alkB and nah genes. In addition, total hydrocarbons, pH, total soil carbon, organic carbon and total nitrogen play an important role in determining hydrocarbon-degrading potential in these communities. The assessment of culturable hydrocarbon-degrading bacteria revealed 42 isolates (total of 316) that were positive for at least one hydrocarbon-degrading gene. Most of these isolates were positive for alkB, and closely match the database for Pantoea, Pseudomonas and Enterobacter spp. Thus, to improve oil sands reclamation strategies, plant inoculation with select hydrocarbon-degrading endophytes could be used to increase plant tolerance and hydrocarbon degradation in these areas.
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Affiliation(s)
- Eduardo K Mitter
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Canada
| | | | - James J Germida
- Department of Soil Science, University of Saskatchewan, Saskatoon, Canada
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16
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van de Kamp J, Hook SE, Williams A, Tanner JE, Bodrossy L. Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep-sea sediments of the Great Australian Bight, Australia. Environ Microbiol 2019; 21:1782-1797. [PMID: 30761716 DOI: 10.1111/1462-2920.14559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/28/2019] [Accepted: 02/07/2019] [Indexed: 11/30/2022]
Abstract
Exploratory drilling for deep-sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes (alkB, c23o and pmoA) to detect and characterize the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m. Clustering at 97% demonstrated differences in community structure with depth, changing most markedly between 400 and 1000 m depth on the continental slope, and identified putative functional 'ecotypes' related to depth. Observed differences in community structure showed strong correlations with temperature, other physicochemical properties of the overlying water column and are further modulated by differences in sediment grain size. This study provides important baseline data on hydrocarbon degrading microbial communities prior to the start of petroleum resource extraction. Our data will inform future ecological monitoring of the GAB deep-sea ecosystem.
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Affiliation(s)
- Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Sharon E Hook
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Lucas Heights, New South Wales, 2234, Australia
| | - Alan Williams
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Jason E Tanner
- Aquatic Sciences, South Australian Research and Development Institute, West Beach, South Australia, 5024, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
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17
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Xu X, Liu W, Tian S, Wang W, Qi Q, Jiang P, Gao X, Li F, Li H, Yu H. Petroleum Hydrocarbon-Degrading Bacteria for the Remediation of Oil Pollution Under Aerobic Conditions: A Perspective Analysis. Front Microbiol 2018; 9:2885. [PMID: 30559725 PMCID: PMC6287552 DOI: 10.3389/fmicb.2018.02885] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/12/2018] [Indexed: 11/13/2022] Open
Abstract
With the sharp increase in population and modernization of society, environmental pollution resulting from petroleum hydrocarbons has increased, resulting in an urgent need for remediation. Petroleum hydrocarbon-degrading bacteria are ubiquitous in nature and can utilize these compounds as sources of carbon and energy. Bacteria displaying such capabilities are often exploited for the bioremediation of petroleum oil-contaminated environments. Recently, microbial remediation technology has developed rapidly and achieved major gains. However, this technology is not omnipotent. It is affected by many environmental factors that hinder its practical application, limiting the large-scale application of the technology. This paper provides an overview of the recent literature referring to the usage of bacteria as biodegraders, discusses barriers regarding the implementation of this microbial technology, and provides suggestions for further developments.
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Affiliation(s)
- Xingjian Xu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.,Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Wenming Liu
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Shuhua Tian
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Wei Wang
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Qige Qi
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Pan Jiang
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Xinmei Gao
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Fengjiao Li
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, China
| | - Haiyan Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.,School of Life Science and Technology, Changchun University of Science and Technology, Changchun, China
| | - Hongwen Yu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.,School of Life Science and Technology, Changchun University of Science and Technology, Changchun, China
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18
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Catania V, Cappello S, Di Giorgi V, Santisi S, Di Maria R, Mazzola A, Vizzini S, Quatrini P. Microbial communities of polluted sub-surface marine sediments. MARINE POLLUTION BULLETIN 2018; 131:396-406. [PMID: 29886964 DOI: 10.1016/j.marpolbul.2018.04.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 03/08/2018] [Accepted: 04/09/2018] [Indexed: 06/08/2023]
Abstract
Microbial communities of coastal marine sediment play a key role in degradation of petroleum contaminants. Here the bacterial and archaeal communities of sub-surface sediments (5-10 cm) of the chronically polluted Priolo Bay (eastern coast of Sicily, Italy), contaminated mainly by n-alkanes and biodegraded/weathered oils, were characterized by cultural and molecular approaches. 16S-PCR-DGGE analysis at six stations, revealed that bacterial communities are highly divergent and display lower phylogenetic diversity than the surface sediment; sub-surface communities respond to oil supplementation in microcosms with a significant reduction in biodiversity and a shift in composition; they retain high biodegradation capacities and host hydrocarbon (HC) degraders that were isolated and identified. HC-degrading Alfa, Gamma and Epsilon proteobacteria together with Clostridia and Archaea are a common feature of sub-surface communities. These assemblages show similarities with that of subsurface petroleum reservoirs also characterized by the presence of biodegraded and weathered oils where anaerobic or microaerophilic syntrophic HC metabolism has been proposed.
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Affiliation(s)
- Valentina Catania
- Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Simone Cappello
- Institute for Coastal Marine Environment (IAMC)-CNR of Messina, Messina, Italy
| | - Vincenzo Di Giorgi
- Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Santina Santisi
- Institute for Coastal Marine Environment (IAMC)-CNR of Messina, Messina, Italy
| | - Roberta Di Maria
- Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Antonio Mazzola
- Dept. of Earth and Marine Sciences (DISTEM) University of Palermo, Palermo, Italy; Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma, Italy
| | - Salvatrice Vizzini
- Dept. of Earth and Marine Sciences (DISTEM) University of Palermo, Palermo, Italy; Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma, Italy
| | - Paola Quatrini
- Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy.
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19
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Omrani R, Spini G, Puglisi E, Saidane D. Modulation of microbial consortia enriched from different polluted environments during petroleum biodegradation. Biodegradation 2018; 29:187-209. [DOI: 10.1007/s10532-018-9823-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/23/2018] [Indexed: 02/06/2023]
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20
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Aerobic degradation of crude oil by microorganisms in soils from four geographic regions of China. Sci Rep 2017; 7:14856. [PMID: 29093536 PMCID: PMC5665864 DOI: 10.1038/s41598-017-14032-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 10/05/2017] [Indexed: 11/13/2022] Open
Abstract
A microcosm experiment was conducted for 112 d by spiking petroleum hydrocarbons into soils from four regions of China. Molecular analyses of soils from microcosms revealed changes in taxonomic diversity and oil catabolic genes of microbial communities. Degradation of total petroleum hydrocarbons (TPHs) in Sand from the Bohai Sea (SS) and Northeast China (NE) exhibited greater microbial mineralization than those of the Dagang Oilfield (DG) and Xiamen (XM). High-throughput sequencing and denaturing gradient gel electrophoresis (DGGE) profiles demonstrated an obvious reconstruction of the bacterial community in all soils. The dominant phylum of the XM with clay soil texture was Firmicutes instead of Proteobacteria in others (DG, SS, and NE) with silty or sandy soil texture. Abundances of alkane monooxygenase gene AlkB increased by 10- to 1000-fold, relative to initial values, and were positively correlated with rates of degradation of TPHs and n-alkanes C13-C30. Abundances of naphthalene dioxygenase gene Nah were positively correlated with degradation of naphthalene and total tricyclic PAHs. Redundancy analysis (RDA) showed that abiotic process derived from geographical heterogeneity was the primary effect on bioremediation of soils contaminated with oil. The optimization of abiotic and biotic factors should be the focus of future bioremediation of oil contaminated soil.
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21
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Liu Q, Tang J, Liu X, Song B, Zhen M, Ashbolt N. Response of microbial community and catabolic genes to simulated petroleum hydrocarbon spills in soils/sediments from different geographic locations. J Appl Microbiol 2017; 123:875-885. [DOI: 10.1111/jam.13549] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/30/2017] [Accepted: 07/12/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Q. Liu
- College of Environmental Science and Engineering; Nankai University; Tianjin China
| | - J. Tang
- College of Environmental Science and Engineering; Nankai University; Tianjin China
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education); Tianjin China
- Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation; Tianjin China
| | - X. Liu
- College of Environmental Science and Engineering; Nankai University; Tianjin China
| | - B. Song
- College of Environmental Science and Engineering; Nankai University; Tianjin China
| | - M. Zhen
- College of Environmental Science and Engineering; Nankai University; Tianjin China
| | - N.J. Ashbolt
- School of Public Health; University of Alberta; Edmonton AB Canada
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22
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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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23
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Koshlaf E, Ball AS. Soil bioremediation approaches for petroleum hydrocarbon polluted environments. AIMS Microbiol 2017; 3:25-49. [PMID: 31294147 PMCID: PMC6604977 DOI: 10.3934/microbiol.2017.1.25] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/22/2016] [Indexed: 12/31/2022] Open
Abstract
Increasing industrialisation, continued population growth and heavy demand and reliance on petrochemical products have led to unprecedented economic growth and development. However, inevitably this dependence on fossil fuels has resulted in serious environmental issues over recent decades. The eco-toxicity and the potential health implications that petroleum hydrocarbons pose for both environmental and human health have led to increased interest in developing environmental biotechnology-based methodologies to detoxify environments impacted by petrogenic compounds. Different approaches have been applied for remediating polluted sites with petroleum derivatives. Bioremediation represents an environmentally sustainable and economical emerging technology for maximizing the metabolism of organic pollutants and minimizing the ecological effects of oil spills. Bioremediation relies on microbial metabolic activities in the presence of optimal ecological factors and necessary nutrients to transform organic pollutants such as petrogenic hydrocarbons. Although, biodegradation often takes longer than traditional remediation methods, the complete degradation of the contaminant is often accomplished. Hydrocarbon biodegradation in soil is determined by a number of environmental and biological factors varying from site to site such as the pH of the soil, temperature, oxygen availability and nutrient content, the growth and survival of hydrocarbon-degrading microbes and bioavailability of pollutants to microbial attack. In this review we have attempted to broaden the perspectives of scientists working in bioremediation. We focus on the most common bioremediation technologies currently used for soil remediation and the mechanisms underlying the degradation of petrogenic hydrocarbons by microorganisms.
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Affiliation(s)
- Eman Koshlaf
- Department of Biology, Faculty of Science Algabal Algarbi University, Gharian, Libya
| | - Andrew S Ball
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, Victoria 3083, Australia
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Pasumarthi R, Mutnuri S. Horizontal gene transfer versus biostimulation: A strategy for bioremediation in Goa. MARINE POLLUTION BULLETIN 2016; 113:271-276. [PMID: 28029340 DOI: 10.1016/j.marpolbul.2016.09.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/15/2016] [Accepted: 09/19/2016] [Indexed: 06/06/2023]
Abstract
Bioaugmentation, Biostimulation and Horizontal gene transfer (HGT) of catabolic genes have been proven for their role in bioremediation of hydrocarbons. It also has been proved that selection of either biostimulation or bioremediation varies for every contaminated site. The reliability of HGT compared to biostimulation and bioremediation was not tested. The present study focuses on reliability of biostimulatiion, bioaugmentation and HGT during biodegradation of Diesel oil and Non aqueous phase liquids (NAPL). Pseudomonas aeruginosa (AEBBITS1) having alkB and NDO genes was used for bioaugmentation and the experiment was conducted using seawater as medium. Based on Gas chromatography results diesel was found to be degraded to 100% in both presence and absence of AEBBITS1. Denturing gradient gel electrophoresis result showed same pattern in presence and absence of AEBBITS1 indicating no HGT. NAPL degradation was found to be more by Biostimulated Bioaugmentation compared to biostimulation and bioaugmentation alone. This proves that biostimulated bioaugmentation is better strategy for oil contamination (tarabll) in Velsao beach, Goa.
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Affiliation(s)
- Rajesh Pasumarthi
- Applied and Environmental Biotechnology Laboratory, Department of Biological Sciences, BITS-Pilani, K K Birla Goa Campus, India.
| | - Srikanth Mutnuri
- Applied and Environmental Biotechnology Laboratory, Department of Biological Sciences, BITS-Pilani, K K Birla Goa Campus, India.
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Burns KA, Jones R. Assessment of sediment hydrocarbon contamination from the 2009 Montara oil blow out in the Timor Sea. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 211:214-225. [PMID: 26774768 DOI: 10.1016/j.envpol.2015.10.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
In August 2009, a blowout of the Montara H1 well 260 km off the northwest coast of Australia resulted in the uncontrolled release of about 4.7 M L of light crude oil and gaseous hydrocarbons into the Timor Sea. Over the 74 day period of the spill, the oil remained offshore and did not result in shoreline incidents on the Australia mainland. At various times slicks were sighted over a 90,000 km(2) area, forming a layer of oil which was tracked by airplanes and satellites but the slicks typically remained within 35 km of the well head platform and were treated with 183,000 L of dispersants. The shelf area where the spill occurred is shallow (100-200 m) and includes off shore emergent reefs and cays and submerged banks and shoals. This study describes the increased inputs of oil to the system and assesses the environmental impact. Concentrations of hydrocarbon in the sediment at the time of survey were very low (total aromatic hydrocarbons (PAHs) ranged from 0.04 to 31 ng g(-1)) and were orders of magnitude lower than concentrations at which biological effects would be expected.
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Affiliation(s)
- Kathryn A Burns
- James Cook University, TROPWATER Group, ATSIP Building, Douglas, Qld 4814 Australia.
| | - Ross Jones
- Australian Institute of Marine Sciences, University of WA, Perth, 8001 WA, Australia.
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26
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Kurtböke Dİ. Applied Microbiology and Biotechnology teaching tailored towards regional needs and graduate employment. MICROBIOLOGY AUSTRALIA 2016. [DOI: 10.1071/ma16023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The University of the Sunshine Coast (USC) opened in 1996 and since 1999 held the full university status as well as being the first ‘Greenfield’ university to open in Australia since 1971 (https://my.usc.edu.au/). This status was in line with its mission to become an institution with strong emphasis on sustainability and environmentally friendly regional development while transforming a former cane farm into today’s multi award-winning modern and distinctive sub-tropical architectural structure. Over the past 20 years the university has played a role as an ‘urban catalyst’ in one of the rapidly growing and transforming regions of Australia with a foundational mission statement: ‘To be the major catalyst for the academic cultural and economic advancement of the region: by leadership; by pursuit of international standards in teaching and research; and by responsiveness to the needs of students, staff, community and the environment’.
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Guibert LM, Loviso CL, Borglin S, Jansson JK, Dionisi HM, Lozada M. Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments. MICROBIAL ECOLOGY 2016; 71:100-112. [PMID: 26547568 DOI: 10.1007/s00248-015-0698-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
We aimed to gain insight into the alkane degradation potential of microbial communities from chronically polluted sediments of a subantarctic coastal environment using a combination of metagenomic approaches. A total of 6178 sequences annotated as alkane-1-monooxygenases (EC 1.14.15.3) were retrieved from a shotgun metagenomic dataset that included two sites analyzed in triplicate. The majority of the sequences binned with AlkB described in Bacteroidetes (32 ± 13 %) or Proteobacteria (29 ± 7 %), although a large proportion remained unclassified at the phylum level. Operational taxonomic unit (OTU)-based analyses showed small differences in AlkB distribution among samples that could be correlated with alkane concentrations, as well as with site-specific variations in pH and salinity. A number of low-abundance OTUs, mostly affiliated with Actinobacterial sequences, were found to be only present in the most contaminated samples. On the other hand, the molecular screening of a large-insert metagenomic library of intertidal sediments from one of the sampling sites identified two genomic fragments containing novel alkB gene sequences, as well as various contiguous genes related to lipid metabolism. Both genomic fragments were affiliated with the phylum Planctomycetes, and one could be further assigned to the genus Rhodopirellula due to the presence of a partial sequence of the 23S ribosomal RNA (rRNA) gene. This work highlights the diversity of bacterial groups contributing to the alkane degradation potential and reveals patterns of functional diversity in relation with environmental stressors in a chronically polluted, high-latitude coastal environment. In addition, alkane biodegradation genes are described for the first time in members of Planctomycetes.
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Affiliation(s)
- Lilian M Guibert
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CENPAT-CONICET), Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut Province, Argentina
| | - Claudia L Loviso
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CENPAT-CONICET), Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut Province, Argentina
| | - Sharon Borglin
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CENPAT-CONICET), Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut Province, Argentina
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CENPAT-CONICET), Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut Province, Argentina.
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28
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Viggor S, Jõesaar M, Vedler E, Kiiker R, Pärnpuu L, Heinaru A. Occurrence of diverse alkane hydroxylase alkB genes in indigenous oil-degrading bacteria of Baltic Sea surface water. MARINE POLLUTION BULLETIN 2015; 101:507-516. [PMID: 26541986 DOI: 10.1016/j.marpolbul.2015.10.064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/21/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
Formation of specific oil degrading bacterial communities in diesel fuel, crude oil, heptane and hexadecane supplemented microcosms of the Baltic Sea surface water samples was revealed. The 475 sequences from constructed alkane hydroxylase alkB gene clone libraries were grouped into 30 OPFs. The two largest groups were most similar to Pedobacter sp. (245 from 475) and Limnobacter sp. (112 from 475) alkB gene sequences. From 56 alkane-degrading bacterial strains 41 belonged to the Pseudomonas spp. and 8 to the Rhodococcus spp. having redundant alkB genes. Together 68 alkB gene sequences were identified. These genes grouped into 20 OPFs, half of them being specific only to the isolated strains. Altogether 543 diverse alkB genes were characterized in the brackish Baltic Sea water; some of them representing novel lineages having very low sequence identities with corresponding genes of the reference strains.
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Affiliation(s)
- Signe Viggor
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia.
| | - Merike Jõesaar
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Eve Vedler
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Riinu Kiiker
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Liis Pärnpuu
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Ain Heinaru
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
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29
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Wang Z, Dai Y, Zhao Q, Li N, Zhou Q, Xie S. Nonylphenol biodegradation, functional gene abundance and bacterial community in bioaugmented sediment: effect of external carbon source. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:12083-12091. [PMID: 25874439 DOI: 10.1007/s11356-015-4509-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
Nonylphenol (NP) biodegradation in river sediment using Stenotrophomonas strain Y1 and Sphingobium strain Y2 were proved to be an effective strategy to remediate NP pollution in our earlier study. The purpose of this study is to investigate the influence of glucose addition on their ability to degrade NP in both liquid cultures and sediment microcosms. The shift in bacterial community structure and relative abundance of NP degraders in sediment microcosms were characterized using terminal restriction fragment length polymorphism analysis. The proportion of NP-degrading alkB and sMO genes was assessed using quantitative polymerase chain reaction (PCR) assay. The growth of Stenotrophomonas strain Y1 and its NP biodegradation efficiency were inhibited by glucose supplementation, while the relative abundance of alkB gene increased. However, NP degradation, as well as the growth of added degraders and proportion of sMO gene, was enhanced in the glucose-amended sediment microcosms inoculated with Sphingobium strain Y2. Moreover, external glucose addition altered bacterial community structures in bioaugmented sediment microcosms, depending on the level of glucose dosage.
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Affiliation(s)
- Zhao Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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Liu Q, Tang J, Bai Z, Hecker M, Giesy JP. Distribution of petroleum degrading genes and factor analysis of petroleum contaminated soil from the Dagang Oilfield, China. Sci Rep 2015; 5:11068. [PMID: 26086670 PMCID: PMC4478889 DOI: 10.1038/srep11068] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 05/14/2015] [Indexed: 11/09/2022] Open
Abstract
Genes that encode for enzymes that can degrade petroleum hydrocarbons (PHs) are critical for the ability of microorganisms to bioremediate soils contaminated with PHs. Distributions of two petroleum-degrading genes AlkB and Nah in soils collected from three zones of the Dagang Oilfield, Tianjin, China were investigated. Numbers of copies of AlkB ranged between 9.1 × 10(5) and 1.9 × 10(7) copies/g dry mass (dm) soil, and were positively correlated with total concentrations of PHs (TPH) (R(2) = 0.573, p = 0.032) and alkanes (C33 ~ C40) (R(2) = 0.914, p < 0.01). The Nah gene was distributed relatively evenly among sampling zones, ranging between 1.9 × 10(7) and 1.1 × 10(8) copies/g dm soil, and was negatively correlated with concentrations of total aromatic hydrocarbons (TAH) (R(2) = -0.567, p = 0.035) and ∑16 PAHs (R(2) = -0.599, p = 0.023). Results of a factor analysis showed that individual samples of soils were not ordinated as a function of the zones.
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Affiliation(s)
- Qinglong Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Center of Pollution Diagnosis and Environmental Restoration, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Jingchun Tang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Center of Pollution Diagnosis and Environmental Restoration, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Zhihui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Markus Hecker
- 1] School of Environment and sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada [2] Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - John P Giesy
- 1] Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada [2] Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada [3] School of Biological Sciences, University of Hong Kong, Hong Kong, SAR, China [4] State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, People's Republic of China [5] Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China
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31
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Rodrigues EM, Kalks KHM, Tótola MR. Prospect, isolation, and characterization of microorganisms for potential use in cases of oil bioremediation along the coast of Trindade Island, Brazil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2015; 156:15-22. [PMID: 25791233 DOI: 10.1016/j.jenvman.2015.03.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 06/04/2023]
Abstract
In the present study, acrylic coupons with a thin layer of oil on the surface were incubated in the coastal water of Trindade Island, Brazil, for 60 days. The microorganisms adhered to the coupons were isolated using enrichment medium with hexadecane and naphthalene as the sole carbon and energy source. A total of 15 bacterial isolates were obtained, and the ability of these isolates to use different hydrocarbons as the source of carbon and energy was investigated. None of the isolates produced biosurfactants under our experimental conditions. Subsequently, identification methods such as partial sequencing of the 16S rRNA gene and analysis of fatty acids (MIDI) profile were employed. Among the 15 isolates, representatives of Actinobacteria, Firmicutes, and Alphaproteobacteria were detected. The isolates Rhodococcus rhodochrous TRN7 and Nocardia farcinica TRH1 were able to use all the hydrocarbons added to the culture medium (toluene, octane, xylene, naphthalene, phenanthrene, pyrene, hexadecane, anthracene, eicosane, tetracosane, triacontane, and pentacontane). Polymerase chain reaction amplification of the DNA isolated by employing primers for catechol 2,3-dioxygenase, alkane dehydrogenase and the alpha subunit of hydroxylating dioxygenases polycyclic aromatic hydrocarbon rings genes demonstrated that various isolates capable of utilizing hydrocarbons do not exhibit genes of known routes of catabolism, suggesting the existence of unknown catabolic pathways in these microorganisms. Our findings suggest that the microbiota associated to the coast of tropical oceanic islands has the ability to assist in environmental regeneration in cases of accidents involving oil spills in its shore. Thus, it motivates studies to map bioremediation strategies using the autochthonous microbiota from these environments.
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Affiliation(s)
- Edmo M Rodrigues
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| | - Karlos H M Kalks
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marcos R Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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Smith CB, Tolar BB, Hollibaugh JT, King GM. Alkane hydroxylase gene (alkB) phylotype composition and diversity in northern Gulf of Mexico bacterioplankton. Front Microbiol 2013; 4:370. [PMID: 24376439 PMCID: PMC3860262 DOI: 10.3389/fmicb.2013.00370] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 11/20/2013] [Indexed: 11/13/2022] Open
Abstract
Natural and anthropogenic activities introduce alkanes into marine systems where they are degraded by alkane hydroxylases expressed by phylogenetically diverse bacteria. Partial sequences for alkB, one of the structural genes of alkane hydroxylase, have been used to assess the composition of alkane-degrading communities, and to determine their responses to hydrocarbon inputs. We present here the first spatially extensive analysis of alkB in bacterioplankton of the northern Gulf of Mexico (nGoM), a region that experiences numerous hydrocarbon inputs. We have analyzed 401 partial alkB gene sequences amplified from genomic extracts collected during March 2010 from 17 water column samples that included surface waters and bathypelagic depths. Previous analyses of 16S rRNA gene sequences for these and related samples have shown that nGoM bacterial community composition and structure stratify strongly with depth, with distinctly different communities above and below 100 m. Although we hypothesized that alkB gene sequences would exhibit a similar pattern, PCA analyses of operational protein units (OPU) indicated that community composition did not vary consistently with depth or other major physical-chemical variables. We observed 22 distinct OPUs, one of which was ubiquitous and accounted for 57% of all sequences. This OPU clustered with AlkB sequences from known hydrocarbon oxidizers (e.g., Alcanivorax and Marinobacter). Some OPUs could not be associated with known alkane degraders, however, and perhaps represent novel hydrocarbon-oxidizing populations or genes. These results indicate that the capacity for alkane hydrolysis occurs widely in the nGoM, but that alkane degrader diversity varies substantially among sites and responds differently than bulk communities to physical-chemical variables.
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Affiliation(s)
- Conor B. Smith
- Department of Biological Sciences, Louisiana State UniversityBaton Rouge, LA, USA
| | - Bradley B. Tolar
- Department of Marine Studies, University of GeorgiaAthens, GA, USA
| | | | - Gary M. King
- Department of Biological Sciences, Louisiana State UniversityBaton Rouge, LA, USA
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Adetutu E, Weber J, Aleer S, Dandie CE, Aburto-Medina A, Ball AS, Juhasz AL. Assessing impediments to hydrocarbon biodegradation in weathered contaminated soils. JOURNAL OF HAZARDOUS MATERIALS 2013; 261:847-853. [PMID: 23454918 DOI: 10.1016/j.jhazmat.2013.01.052] [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: 05/08/2012] [Revised: 12/03/2012] [Accepted: 01/23/2013] [Indexed: 06/01/2023]
Abstract
In this study, impediments to hydrocarbon biodegradation in contaminated soils were assessed using chemical and molecular methodologies. Two long-term hydrocarbon contaminated soils were utilised which were similar in physico-chemical properties but differed in the extent of hydrocarbon (C10-C40) contamination (S1: 16.5 g kg(-1); S2: 68.9 g kg(-1)). Under enhanced natural attenuation (ENA) conditions, hydrocarbon biodegradation was observed in S1 microcosms (26.4% reduction in C10-C40 hydrocarbons), however, ENA was unable to stimulate degradation in S2. Although eubacterial communities (PCR-DGGE analysis) were similar for both soils, the alkB bacterial community was less diverse in S2 presumably due to impacts associated with elevated hydrocarbons. When hydrocarbon bioaccessibility was assessed using HP-β-CD extraction, large residual concentrations remained in the soil following the extraction procedure. However, when linear regression models were used to predict the endpoints of hydrocarbon degradation, there was no significant difference (P>0.05) between HP-β-CD predicted and microcosm measured biodegradation endpoints. This data suggested that the lack of hydrocarbon degradation in S2 resulted primarily from limited hydrocarbon bioavailability.
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Affiliation(s)
- Eric Adetutu
- School of Biological Sciences, Flinders University, Adelaide, South Australia, 5001, Australia
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Bertrand EM, Keddis R, Groves JT, Vetriani C, Austin RN. Identity and mechanisms of alkane-oxidizing metalloenzymes from deep-sea hydrothermal vents. Front Microbiol 2013; 4:109. [PMID: 23825470 PMCID: PMC3695450 DOI: 10.3389/fmicb.2013.00109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/16/2013] [Indexed: 12/21/2022] Open
Abstract
Six aerobic alkanotrophs (organism that can metabolize alkanes as their sole carbon source) isolated from deep-sea hydrothermal vents were characterized using the radical clock substrate norcarane to determine the metalloenzyme and reaction mechanism used to oxidize alkanes. The organisms studied were Alcanivorax sp. strains EPR7 and MAR14, Marinobacter sp. strain EPR21, Nocardioides sp. strains EPR26w, EPR28w, and Parvibaculum hydrocarbonoclasticum strain EPR92. Each organism was able to grow on n-alkanes as the sole carbon source and therefore must express genes encoding an alkane-oxidizing enzyme. Results from the oxidation of the radical-clock diagnostic substrate norcarane demonstrated that five of the six organisms (EPR7, MAR14, EPR21, EPR26w, and EPR28w) used an alkane hydroxylase functionally similar to AlkB to catalyze the oxidation of medium-chain alkanes, while the sixth organism (EPR92) used an alkane-oxidizing cytochrome P450 (CYP)-like protein to catalyze the oxidation. DNA sequencing indicated that EPR7 and EPR21 possess genes encoding AlkB proteins, while sequencing results from EPR92 confirmed the presence of a gene encoding CYP-like alkane hydroxylase, consistent with the results from the norcarane experiments.
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Affiliation(s)
- Erin M Bertrand
- Department of Chemistry, Bates College Lewiston, ME, USA ; Microbial and Environmental Genomics, J. Craig Venter Institute San Diego, CA, USA
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Jurelevicius D, Alvarez VM, Peixoto R, Rosado AS, Seldin L. The Use of a Combination of alkB Primers to Better Characterize the Distribution of Alkane-Degrading Bacteria. PLoS One 2013; 8:e66565. [PMID: 23825163 PMCID: PMC3688950 DOI: 10.1371/journal.pone.0066565] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/08/2013] [Indexed: 11/22/2022] Open
Abstract
The alkane monooxygenase AlkB, which is encoded by the alkB gene, is a key enzyme involved in bacterial alkane degradation. To study the alkB gene within bacterial communities, researchers need to be aware of the variations in alkB nucleotide sequences; a failure to consider the sequence variations results in the low representation of the diversity and richness of alkane-degrading bacteria. To minimize this shortcoming, the use of a combination of three alkB-targeting primers to enhance the detection of the alkB gene in previously isolated alkane-degrading bacteria was proposed. Using this approach, alkB-related PCR products were detected in 79% of the strains tested. Furthermore, the chosen set of primers was used to study alkB richness and diversity in different soils sampled in Carmópolis, Brazil and King George Island, Antarctica. The DNA extracted from the different soils was PCR amplified with each set of alkB-targeting primers, and clone libraries were constructed, sequenced and analyzed. A total of 255 alkB phylotypes were detected. Venn diagram analyses revealed that only low numbers of alkB phylotypes were shared among the different libraries derived from each primer pair. Therefore, the combination of three alkB-targeting primers enhanced the richness of alkB phylotypes detected in the different soils by 45% to 139%, when compared to the use of a single alkB-targeting primer. In addition, a dendrogram analysis and beta diversity comparison of the alkB composition showed that each of the sampling sites studied had a particular set of alkane-degrading bacteria. The use of a combination of alkB primers was an efficient strategy for enhancing the detection of the alkB gene in cultivable bacteria and for better characterizing the distribution of alkane-degrading bacteria in different soil environments.
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Affiliation(s)
- Diogo Jurelevicius
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vanessa Marques Alvarez
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Peixoto
- Laboratório de Ecologia Molecular Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre S. Rosado
- Laboratório de Ecologia Molecular Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucy Seldin
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Viggor S, Juhanson J, Jõesaar M, Mitt M, Truu J, Vedler E, Heinaru A. Dynamic changes in the structure of microbial communities in Baltic Sea coastal seawater microcosms modified by crude oil, shale oil or diesel fuel. Microbiol Res 2013; 168:415-27. [PMID: 23510642 DOI: 10.1016/j.micres.2013.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 01/29/2013] [Accepted: 02/09/2013] [Indexed: 11/29/2022]
Abstract
The coastal waters of the Baltic Sea are constantly threatened by oil spills, due to the extensive transportation of oil products across the sea. To characterise the hydrocarbon-degrading bacterial community of this marine area, microcosm experiments on diesel fuel, crude oil and shale oil were performed. Analysis of these microcosms, using alkane monooxygenase (alkB) and 16S rRNA marker genes in PCR-DGGE experiments, demonstrated that substrate type and concentration strongly influence species composition and the occurrence of alkB genes in respective oil degrading bacterial communities. Gammaproteobacteria (particularly the genus Pseudomonas) and Alphaproteobacteria were dominant in all microcosms treated with oils. All alkB genes carried by bacterial isolates (40 strains), and 8 of the 11 major DGGE bands from the microcosms, had more than 95% sequence identity with the alkB genes of Pseudomonas fluorescens. However, the closest relatives of the majority of sequences (54 sequences from 79) of the alkB gene library from initially collected seawater DNA were Actinobacteria. alkB gene expression, induced by hexadecane, was recorded in isolated bacterial strains. Thus, complementary culture dependent and independent methods provided a more accurate picture about the complex seawater microbial communities of the Baltic Sea.
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Affiliation(s)
- Signe Viggor
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia.
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Guibert LM, Loviso CL, Marcos MS, Commendatore MG, Dionisi HM, Lozada M. Alkane biodegradation genes from chronically polluted subantarctic coastal sediments and their shifts in response to oil exposure. MICROBIAL ECOLOGY 2012; 64:605-616. [PMID: 22580956 DOI: 10.1007/s00248-012-0051-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 03/27/2012] [Indexed: 05/31/2023]
Abstract
Although sediments are the natural hydrocarbon sink in the marine environment, the ecology of hydrocarbon-degrading bacteria in sediments is poorly understood, especially in cold regions. We studied the diversity of alkane-degrading bacterial populations and their response to oil exposure in sediments of a chronically polluted Subantarctic coastal environment, by analyzing alkane monooxygenase (alkB) gene libraries. Sequences from the sediment clone libraries were affiliated with genes described in Proteobacteria and Actinobacteria, with 67 % amino acid identity in average to sequences from isolated microorganisms. The majority of the sequences were most closely related to uncultured microorganisms from cold marine sediments or soils from high latitude regions, highlighting the role of temperature in the structuring of this bacterial guild. The distribution of alkB sequences among samples of different sites and years, and selection after experimental oil exposure allowed us to identify ecologically relevant alkB genes in Subantarctic sediments, which could be used as biomarkers for alkane biodegradation in this environment. 16 S rRNA amplicon pyrosequencing indicated the abundance of several genera for which no alkB genes have yet been described (Oleispira, Thalassospira) or that have not been previously associated with oil biodegradation (Spongiibacter-formerly Melitea-, Maribius, Robiginitomaculum, Bizionia and Gillisia). These genera constitute candidates for future work involving identification of hydrocarbon biodegradation pathway genes.
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Affiliation(s)
- Lilian M Guibert
- Centro Nacional Patagónico (CENPAT - CONICET), Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
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Håvelsrud OE, Haverkamp THA, Kristensen T, Jakobsen KS, Rike AG. Metagenomic and geochemical characterization of pockmarked sediments overlaying the Troll petroleum reservoir in the North Sea. BMC Microbiol 2012; 12:203. [PMID: 22966776 PMCID: PMC3478177 DOI: 10.1186/1471-2180-12-203] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 06/28/2012] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Pockmarks (depressions in the seabed) have been discovered throughout the world's oceans and are often related to hydrocarbon seepage. Although high concentrations of pockmarks are present in the seabed overlaying the Troll oil and gas reservoir in the northern North Sea, geological surveys have not detected hydrocarbon seepage in this area at the present time. In this study we have used metagenomics to characterize the prokaryotic communities inhabiting the surface sediments in the Troll area in relation to geochemical parameters, particularly related to hydrocarbon presence. We also investigated the possibility of increased potential for methane oxidation related to the pockmarks. Five metagenomes from pockmarks and plain seabed sediments were sequenced by pyrosequencing (Roche/454) technology. In addition, two metagenomes from seabed sediments geologically unlikely to be influenced by hydrocarbon seepage (the Oslofjord) were included. The taxonomic distribution and metabolic potential of the metagenomes were analyzed by multivariate analysis and statistical comparisons to reveal variation within and between the two sampling areas. RESULTS The main difference identified between the two sampling areas was an overabundance of predominantly autotrophic nitrifiers, especially Nitrosopumilus, and oligotrophic marine Gammaproteobacteria in the Troll metagenomes compared to the Oslofjord. Increased potential for degradation of hydrocarbons, especially aromatic hydrocarbons, was detected in two of the Troll samples: one pockmark sample and one from the plain seabed. Although presence of methanotrophic organisms was indicated in all samples, no overabundance in pockmark samples compared to the Oslofjord samples supports no, or only low level, methane seepage in the Troll pockmarks at the present time. CONCLUSIONS Given the relatively low content of total organic carbon and great depths of hydrocarbon containing sediments in the Troll area, it is possible that at least part of the carbon source available for the predominantly autotrophic nitrifiers thriving in this area originates from sequential prokaryotic degradation and oxidation of hydrocarbons to CO2. By turning CO2 back into organic carbon this subcommunity could play an important environmental role in these dark oligotrophic sediments. The oxidation of ammonia to nitrite and nitrate in this process could further increase the supply of terminal electron acceptors for hydrocarbon degradation.
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Affiliation(s)
- Othilde Elise Håvelsrud
- Norwegian Geotechnical Institute, Sognsveien 72, P.O. Box 3930, Ullevål Stadion N-0806, Oslo, Norway
- Department of Molecular Biosciences, University of Oslo, Blindernveien 31, P.O. Box 1041, Blindern N-0316, Oslo, Norway
- Microbial Evolution Research Group, MERG, Department of Biology, University of Oslo, Blindernveien 31, P.O. Box 1066, Blindern N-0316, Oslo, Norway
| | - Thomas HA Haverkamp
- Microbial Evolution Research Group, MERG, Department of Biology, University of Oslo, Blindernveien 31, P.O. Box 1066, Blindern N-0316, Oslo, Norway
- Centre for Evolutionary and Ecological Synthesis (CEES), Department of Biology, University of Oslo, Blindernveien 31, P.O. Box 1066, Blindern N-0316, Oslo, Norway
| | - Tom Kristensen
- Department of Molecular Biosciences, University of Oslo, Blindernveien 31, P.O. Box 1041, Blindern N-0316, Oslo, Norway
- Microbial Evolution Research Group, MERG, Department of Biology, University of Oslo, Blindernveien 31, P.O. Box 1066, Blindern N-0316, Oslo, Norway
| | - Kjetill S Jakobsen
- Microbial Evolution Research Group, MERG, Department of Biology, University of Oslo, Blindernveien 31, P.O. Box 1066, Blindern N-0316, Oslo, Norway
- Centre for Evolutionary and Ecological Synthesis (CEES), Department of Biology, University of Oslo, Blindernveien 31, P.O. Box 1066, Blindern N-0316, Oslo, Norway
| | - Anne Gunn Rike
- Norwegian Geotechnical Institute, Sognsveien 72, P.O. Box 3930, Ullevål Stadion N-0806, Oslo, Norway
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McGenity TJ, Folwell BD, McKew BA, Sanni GO. Marine crude-oil biodegradation: a central role for interspecies interactions. AQUATIC BIOSYSTEMS 2012; 8:10. [PMID: 22591596 PMCID: PMC3465203 DOI: 10.1186/2046-9063-8-10] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 04/25/2012] [Indexed: 05/11/2023]
Abstract
The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such "microbial modules" interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons.
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Affiliation(s)
- Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Benjamin D Folwell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Gbemisola O Sanni
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
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Adetutu EM, Ball AS, Weber J, Aleer S, Dandie CE, Juhasz AL. Impact of bacterial and fungal processes on 14C-hexadecane mineralisation in weathered hydrocarbon contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2012; 414:585-91. [PMID: 22154183 DOI: 10.1016/j.scitotenv.2011.11.044] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 10/11/2011] [Accepted: 11/03/2011] [Indexed: 05/10/2023]
Abstract
In this study, the impact of bacterial and fungal processes on (14)C-hexadecane mineralisation was investigated in weathered hydrocarbon contaminated soil. The extent of (14)C-hexadecane mineralisation varied depending on the bioremediation strategy employed. Under enhanced natural attenuation conditions, (14)C-hexadecane mineralisation after 98 days was 8.5 ± 3.7% compared to <1.2% without nitrogen and phosphorus additions. (14)C-hexadecane mineralisation was further enhanced through Tween 80 amendments (28.9 ± 2.4%) which also promoted the growth of a Phanerochaete chyrsosporium fungal mat. Although fungal growth in weathered hydrocarbon contaminated soil could be promoted through supplementing additional carbon sources (Tween 80, sawdust, compost, pea straw), fungal (14)C-hexadecane mineralisation was negligible when sodium azide was added to soil microcosms to inhibit bacterial activity. In contrast, when fungal activity was inhibited through nystatin additions, (14)C-hexadecane mineralisation ranged from 6.5 ± 0.2 to 35.8 ± 3.8% after 98 days depending on the supplied amendment. Bacteria inhibition with sodium azide resulted in a reduction in bacterial diversity (33-37%) compared to microcosms supplemented with nystatin or microcosms without inhibitory supplements. However, alkB bacterial groups were undetected in sodium azide supplemented microcosms, highlighting the important role of this bacterial group in (14)C-hexadecane mineralisation.
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Affiliation(s)
- Eric M Adetutu
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia
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Marine biocatalysts: enzymatic features and applications. Mar Drugs 2011; 9:478-499. [PMID: 21731544 PMCID: PMC3124967 DOI: 10.3390/md9040478] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 02/28/2011] [Accepted: 03/23/2011] [Indexed: 11/21/2022] Open
Abstract
In several recent reports related to biocatalysis the enormous pool of biodiversity found in marine ecosystems is considered a profitable natural reservoir for acquiring an inventory of useful biocatalysts. These enzymes are characterized by well-known habitat-related features such as salt tolerance, hyperthermostability, barophilicity and cold adaptivity. In addition, their novel chemical and stereochemical characteristics increase the interest of biocatalysis practitioners both in academia and research industry. In this review, starting from the analysis of these featuring habitat-related properties, important examples of marine enzymes in biocatalysis will be reported. Completion of this report is devoted to the analysis of novel chemical and stereochemical biodiversity offered by marine biocatalysts with particular emphasis on current or potential applications of these enzymes in chemical and pharmaceutical fields. The analysis of literature cited here and the many published patent applications concerning the use of marine enzymes supports the view that these biocatalysts are just waiting to be discovered, reflecting the importance of the marine environment. The potential of this habitat should be thoroughly explored and possibly the way to access useful biocatalysts should avoid destructive large-scale collections of marine biomass for enzyme production. These two aspects are day by day increasing in interest and a future increase in the use of marine enzymes in biocatalysis should be expected.
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Jones DR. Case study: Using microbe molecular biology for Gulf oil spill clean up. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2011; 39:157-164. [PMID: 21445909 DOI: 10.1002/bmb.20471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This case has the student actively investigate the regulation of expression of a novel bacterial gene in the context of attempts to solve a real world problem, clean up of the April 2010 Deep Water Horizon oil spill in the Gulf of Mexico. Although the case is fictitious, it is based on factual gene regulatory characteristics of oil-degrading microbes. The case is written for a sophomore Cell Biology lecture course at Indiana Wesleyan University that is taught to Biology/Pre-Med majors. This study is also appropriate for use in undergraduate microbiology, biochemistry, molecular biology, and molecular genetics courses. The case is intended to enhance coverage of transcription, translation, control of gene expression, and selected molecular biology techniques. Opportunities to practice critical thinking skills and to a lesser extent an introduction to the paradigm of life science research at the industry level are provided.
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Affiliation(s)
- Daniel R Jones
- Division of Natural Sciences, Indiana Wesleyan University, Marion, Indiana 46953, USA.
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Vilchez-Vargas R, Junca H, Pieper DH. Metabolic networks, microbial ecology and ‘omics’ technologies: towards understanding in situ biodegradation processes. Environ Microbiol 2010; 12:3089-104. [DOI: 10.1111/j.1462-2920.2010.02340.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Wang W, Wang L, Shao Z. Diversity and abundance of oil-degrading bacteria and alkane hydroxylase (alkB) genes in the subtropical seawater of Xiamen Island. MICROBIAL ECOLOGY 2010; 60:429-39. [PMID: 20683589 DOI: 10.1007/s00248-010-9724-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 07/09/2010] [Indexed: 05/13/2023]
Abstract
In this report, the diversity of oil-degrading bacteria and alkB gene was surveyed in the seawater around Xiamen Island. Forty-four isolates unique in 16S rRNA sequence were obtained after enrichment with crude oil. Most of the obtained isolates exhibited growth with diesel oil and crude oil. alkB genes were positively detected in 16 isolates by degenerate polymerase chain reaction (PCR). And for the first time, alkB genes were found in bacteria of Gallaecimonas, Castellaniella, Paracoccus, and Leucobacter. Additional 29 alkB sequences were retrieved from genomic DNA of the oil-degrading communities. Phylogenetic analysis showed that the obtained alkB genes formed five groups, most of which exhibited 60-80% similarity at the amino acid level with sequences retrieved from the GenBank database. Furthermore, the abundance of alkB genes in seawater was examined by real-time PCR. The results showed that alkB genes of each group in situ ranged from about 3 × 10(3) to 3 × 10(5) copies L(-1), with the homologs of Alcanivorax and Pseudomonas being the most predominant. Bacteria of Alcanivorax, Acinetobacter, and Pseudomonas are important oil degraders in this area; while those frequently reported in other area, like Oleiphilus spp., Oleispira spp., and Thalassolituus spp. were not found in our report. These results indicate that bacteria and genes involved in oil degradation are quite diverse, and may have restriction in geographic distribution in some species.
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Affiliation(s)
- Wanpeng Wang
- School of Life Sciences, Xiamen University, Xiamen 361005, China
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Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism. Mar Drugs 2010; 8:608-28. [PMID: 20411118 PMCID: PMC2857354 DOI: 10.3390/md8030608] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 02/04/2010] [Accepted: 03/12/2010] [Indexed: 12/21/2022] Open
Abstract
The marine environment is extremely diverse, with huge variations in pressure and temperature. Nevertheless, life, especially microbial life, thrives throughout the marine biosphere and microbes have adapted to all the divergent environments present. Large scale DNA sequence based approaches have recently been used to investigate the marine environment and these studies have revealed that the oceans harbor unprecedented microbial diversity. Novel gene families with representatives only within such metagenomic datasets represent a large proportion of the ocean metagenome. The presence of so many new gene families from these uncultured and highly diverse microbial populations represents a challenge for the understanding of and exploitation of the biology and biochemistry of the ocean environment. The application of new metagenomic and single cell genomics tools offers new ways to explore the complete metabolic diversity of the marine biome.
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Panicker G, Mojib N, Aislabie J, Bej AK. Detection, expression and quantitation of the biodegradative genes in Antarctic microorganisms using PCR. Antonie van Leeuwenhoek 2009; 97:275-87. [PMID: 20043207 DOI: 10.1007/s10482-009-9408-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 12/16/2009] [Indexed: 11/29/2022]
Abstract
In this study, 28 hydrocarbon-degrading bacterial isolates from oil-contaminated Antarctic soils were screened for the presence of biodegradative genes such as alkane hydroxylase (alks), the ISPalpha subunit of naphthalene dioxygenase (ndoB), catechol 2,3-dioxygenase (C23DO) and toluene/biphenyl dioxygenase (todC1/bphA1) by using polymerase chain reaction (PCR) methods. All naphthalene degrading bacterial isolates exhibited the presence of a 648 bp amplicon that shared 97% identity to a known ndoB sequence from Pseudomonas putida. Twenty-two out of the twenty-eight isolates screened were positive for one, two or all three different regions of the C23DO gene. For alkane hydroxylase, all 6 Rhodococcus isolates were PCR-positive for a 194 bp and a 552 bp segment of the alkB gene, but exhibited variable results with primers located at different segments of this gene. Three Pseudomonas spp. 4/101, 19/1, 30/3 amplified 552 bp segment of alkB. Only two Pseudomonas sp. 7/156 and 4/101 amplified a segment of alkB exhibiting 89-94% nucleotide sequence identity with the existing sequence of alkB in the GenBank sequence database. Transcripts of three genes, alkB2, C23DO and ndoB, that were amplified by DNA-PCR in three different bacterial isolates also exhibited positive amplification by reverse transcriptase PCR (RT-PCR) method confirming that these genes are functional. A competitive PCR (cPCR) method was developed for a quantitative estimation of ndoB from pure cultures of the naphthalene-degrading Pseudomonas sp. 30/2. A minimum of 1 x 10(7) copies of the ndoB gene was detected based on the comparison of the intensities of the competitor and target DNA bands. It is expected that the identification and characterization of the biodegradative genes will provide a better understanding of the catabolic pathways in Antarctic psychrotolerant bacteria, and thereby help support bioremediation strategies for oil-contaminated Antarctic soils.
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Affiliation(s)
- Gitika Panicker
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294-1170, USA
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