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Hanano A, Shaban M, Almousally I. Biochemical, Molecular, and Transcriptional Highlights of the Biosynthesis of an Effective Biosurfactant Produced by Bacillus safensis PHA3, a Petroleum-Dwelling Bacteria. Front Microbiol 2017; 8:77. [PMID: 28179901 PMCID: PMC5263155 DOI: 10.3389/fmicb.2017.00077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/11/2017] [Indexed: 11/13/2022] Open
Abstract
Petroleum crude oil (PCO)-dwelling microorganisms have exceptional biological capabilities to tolerate the toxicity of petroleum contaminants and are therefore promising emulsifier and/or degraders of PCO. This study describes a set of PCO-inhabiting bacterial species, one of which, identified as Bacillus safensis PHA3, produces an efficient biosurfactant which was characterized as a glycolipid. Fourier transform infrared spectrometer, nuclear magnetic resonance, Thin layer chromatography, HPLC, and GC-MS analysis of the purified biosurfactant revealed that the extracted molecule under investigation is likely a mannolipid molecule with a hydrophilic part as mannose and a hydrophobic part as hexadecanoic acid (C16:0). The data reveal that: (i) PHA3 is a potential producer of biosurfactant (9.8 ± 0.5 mg mL-1); (ii) pre-adding 0.15% of the purified glycolipid enhanced the degradation of PCO by approximately 2.5-fold; (iii) the highest emulsifying activity of biosurfactant was found against the PCO and the lowest was against the naphthalene; (iv) the optimal PCO-emulsifying activity was found at 30-60°C, pH 8 and a high salinity. An orthologous gene encodes a putative β-diglucosyldiacylglycerol synthase (β-DGS) was identified in PHA3 and its transcripts were significantly up-regulated by exogenous PAHs, i.e., pyrene and benzo(e)pyrene but much less by mid-chain n-alkanes (ALKs) and fatty acids. Subsequently, the accumulation of β-DGS transcripts coincided with an optimal growth of bacteria and a maximal accumulation of the biosurfactant. Of particular interest, we found that PHA3 actively catalyzed the degradation of PAHs notably the pyrene and benzo(e)pyrene but was much less effective in the mono-terminal oxidation of ALKs. Such characteristics make Bacillus safensis PHA3 a promising model for enhanced microbial oil recovery and environmental remediation.
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Affiliation(s)
- Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria Damascus, Syria
| | - Mouhnad Shaban
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria Damascus, Syria
| | - Ibrahem Almousally
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria Damascus, Syria
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Horel A, Schiewer S. Impact of VOC removal by activated carbon on biodegradation rates of diesel, Syntroleum and biodiesel in contaminated sand. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 573:106-114. [PMID: 27552734 DOI: 10.1016/j.scitotenv.2016.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/23/2016] [Accepted: 08/01/2016] [Indexed: 06/06/2023]
Abstract
The degradation of conventional diesel (D), synthetic diesel (Syntroleum), and pure fish biodiesel (B100) by indigenous microbes was investigated in laboratory microcosms containing contaminated sand. The fate of volatiles and the influence of volatilization on degradation rates were examined by placing activated carbon (AC) in microcosm headspaces to sorb volatiles. Three AC regimes were compared: no activated carbon (NAC), regular weekly AC change (RAC), and frequent AC change (FAC), where the frequency of activated carbon exchange declined from daily to weekly. Generally, the alternative fuels were biodegraded faster than diesel fuel. Hydrocarbon mineralization percentages for the different fuel types over 28days were between 23% (D) and 48% (B100) in the absence of activated carbon, decreased to 12% (D) - 37% (B100) with weekly AC exchange, and were further reduced to 9-22% for more frequent AC change. Sorption of volatiles to AC lowered their availability as a substrate for microbes, reducing respiration. Volatilization was negligible for the biodiesel. A mass balance for the carbon initially present as hydrocarbons in microcosms with activated carbon in the head space was on average 92% closed, with 45-70% remaining in the soil after 4weeks, 9-37% mineralized and up to 12% volatilized. Based on nutrient consumption, up to 29% of the contaminants were likely converted into biomass.
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Affiliation(s)
- Agota Horel
- Institute of Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of Sciences, Herman O. 15, Budapest 1022, Hungary; Civil and Environmental Engineering Department, Water and Environmental Research Center, University of Alaska Fairbanks, P.O. Box 755900, Fairbanks, AK 99775-5900, USA
| | - Silke Schiewer
- Civil and Environmental Engineering Department, Water and Environmental Research Center, University of Alaska Fairbanks, P.O. Box 755900, Fairbanks, AK 99775-5900, USA.
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Sydow M, Owsianiak M, Szczepaniak Z, Framski G, Smets BF, Ławniczak Ł, Lisiecki P, Szulc A, Cyplik P, Chrzanowski Ł. Evaluating robustness of a diesel-degrading bacterial consortium isolated from contaminated soil. N Biotechnol 2016; 33:852-859. [DOI: 10.1016/j.nbt.2016.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 08/23/2016] [Accepted: 08/23/2016] [Indexed: 10/21/2022]
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Chettri B, Mukherjee A, Langpoklakpam JS, Chattopadhyay D, Singh AK. Kinetics of nutrient enhanced crude oil degradation by Pseudomonas aeruginosa AKS1 and Bacillus sp. AKS2 isolated from Guwahati refinery, India. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 216:548-558. [PMID: 27317496 DOI: 10.1016/j.envpol.2016.06.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 03/26/2016] [Accepted: 06/03/2016] [Indexed: 06/06/2023]
Abstract
Bacterial degradation of crude oil in response to nutrient treatments has been vastly studied. But there is a paucity of information on kinetic parameters of crude oil degradation. Here we report the nutrient stimulated kinetic parameters of crude oil degradation assessed in terms of CO2 production and oil removal by Pseudomonas aeruginosa AKS1 and Bacillus sp. AKS2. The hydrocarbon degradation rate of P. aeruginosa AKS1 in oil only amended sediment was 10.75 ± 0.65 μg CO2-C g(-1) sediment day(-1) which was similar to degradation rate in sediments with no oil. In presence of both inorganic N & P, the degradation rate increased to 47.22 ± 1.32 μg CO2-C g(-1) sediment day(-1). The half-saturation constant (Ks) and maximum degradation rate (Vmax) for P. aeruginosa AKS1 under increasing N and saturating P concentration were 13.57 ± 0.53 μg N g(-1) sediment and 39.36 ± 1.42 μg CO2-C g(-1) sediment day(-1) respectively. The corresponding values at increasing P and a constant N concentration were 1.60 ± 0.13 μg P g(-1) sediment and 43.90 ± 1.03 μg CO2-C g(-1) sediment day(-1) respectively. Similarly the degradation rate of Bacillus sp. AKS2 in sediments amended with both inorganic nutrients N & P was seven fold higher than the rates in oil only or nutrient only treated sediments. The Ks and Vmax estimates of Bacillus sp. AKS2 under increasing N and saturating P concentration were 9.96 ± 1.25 μg N g(-1) sediment and 59.96 ± 7.56 μg CO2-C g(-1) sediment day(-1) respectively. The corresponding values for P at saturating N concentration were 0.46 ± 0.24 μg P g(-1) sediment and 63.63 ± 3.54 μg CO2-C g(-1) sediment day(-1) respectively. The rates of CO2 production by both isolates were further stimulated when oil concentration was increased above 12.5 mg g(-1) sediment. However, oil degradation activity declined at oil concentration above 40 mg g(-1) sediment when treated with constant nutrient: oil ratio. Both isolates exhibited alkane hydroxylase activity but aromatic degrading catechol 1, 2-dioxygenase and catechol 2, 3-dioxygenase activities were shown by P. aeruginosa AKS1 only.
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Affiliation(s)
- Bobby Chettri
- Department of Biochemistry, North Eastern Hill University, Shillong, 793022, India
| | - Arghya Mukherjee
- Department of Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | | | - Dhrubajyoti Chattopadhyay
- Department of Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Arvind K Singh
- Department of Biochemistry, North Eastern Hill University, Shillong, 793022, India.
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Wang X, Zhao X, Li H, Jia J, Liu Y, Ejenavi O, Ding A, Sun Y, Zhang D. Separating and characterizing functional alkane degraders from crude-oil-contaminated sites via magnetic nanoparticle-mediated isolation. Res Microbiol 2016; 167:731-744. [PMID: 27475037 DOI: 10.1016/j.resmic.2016.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 07/06/2016] [Accepted: 07/08/2016] [Indexed: 11/18/2022]
Abstract
Uncultivable microorganisms account for over 99% of all species on the planet, but their functions are yet not well characterized. Though many cultivable degraders for n-alkanes have been intensively investigated, the roles of functional n-alkane degraders remain hidden in the natural environment. This study introduces the novel magnetic nanoparticle-mediated isolation (MMI) technology in Nigerian soils and successfully separates functional microbes belonging to the families Oxalobacteraceae and Moraxellaceae, which are dominant and responsible for alkane metabolism in situ. The alkR-type n-alkane monooxygenase genes, instead of alkA- or alkP-type, were the key functional genes involved in the n-alkane degradation process. Further physiological investigation via a BIOLOG PM plate revealed some carbon (Tween 20, Tween 40 and Tween 80) and nitrogen (tyramine, l-glutamine and d-aspartic acid) sources promoting microbial respiration and n-alkane degradation. With further addition of promoter carbon or nitrogen sources, the separated functional alkane degraders significantly improved n-alkane biodegradation rates. This suggests that MMI is a promising technology for separating functional microbes from complex microbiota, with deeper insight into their ecological functions and influencing factors. The technique also broadens the application of the BIOLOG PM plate for physiological research on functional yet uncultivable microorganisms.
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Affiliation(s)
- Xinzi Wang
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK
| | - Xiaohui Zhao
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK; College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Hanbing Li
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK
| | - Jianli Jia
- School of Chemical and Environmental Engineering, China University of Mining & Technology (Beijing), Beijing 100083, PR China
| | - Yueqiao Liu
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK; College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Odafe Ejenavi
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Yujiao Sun
- College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Dayi Zhang
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK.
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Nguyen TM, Kim J. Rhodococcus pedocola sp. nov. and Rhodococcus humicola sp. nov., two antibiotic-producing actinomycetes isolated from soil. Int J Syst Evol Microbiol 2016; 66:2362-2369. [DOI: 10.1099/ijsem.0.001039] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tuan Manh Nguyen
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 443-760, Republic of Korea
- Thai Nguyen University of Agriculture and Forestry, Quyet Thang commune, Thai Nguyen City, Vietnam
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 443-760, Republic of Korea
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Microbial diversity and community structure in an antimony-rich tailings dump. Appl Microbiol Biotechnol 2016; 100:7751-63. [PMID: 27188777 DOI: 10.1007/s00253-016-7598-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/25/2016] [Accepted: 04/28/2016] [Indexed: 10/21/2022]
Abstract
To assess the impact of antimony (Sb) on microbial community structure, 12 samples were taken from an Sb tailings pile in Guizhou Province, Southwest China. All 12 samples exhibited elevated Sb concentrations, but the mobile and bioaccessible fractions were small in comparison to total Sb concentrations. Besides the geochemical analyses, microbial communities inhabiting the tailing samples were characterized to investigate the interplay between the microorganisms and environmental factors in mine tailings. In all samples, Proteobacteria and Actinobacteria were the most dominant phyla. At the genus level, Thiobacillus, Limnobacter, Nocardioides, Lysobacter, Phormidium, and Kaistobacter demonstrated relatively high abundances. The two most abundant genera, Thiobacillus and Limnobacter, are characterized as sulfur-oxidizing bacteria and thiosulfate-oxidizing bacteria, respectively, while the genus Lysobacter contains arsenic (As)-resistant bacteria. Canonical correspondence analysis (CCA) indicates that TOC and the sulfate to sulfide ratio strongly shaped the microbial communities, suggesting the influence of the environmental factors in the indigenous microbial communities.
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58
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Patel V, Sharma A, Lal R, Al-Dhabi NA, Madamwar D. Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates. BMC Microbiol 2016; 16:50. [PMID: 27001503 PMCID: PMC4802719 DOI: 10.1186/s12866-016-0669-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 03/09/2016] [Indexed: 01/27/2023] Open
Abstract
Background Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation. Results Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum “Proteobacteria” and genus “Chromobacterium,” respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions. Conclusion To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0669-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vrutika Patel
- Post Graduate Department of Biosciences, Centre of Advanced Study in Bioresource Technology, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, 388 315, Gujarat, India
| | | | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, Addiriya Chair for Environmental Studies, College of Science, King Saud University, P.O. Box # 2455, Riyadh, 11451, Saudi Arabia
| | - Datta Madamwar
- Post Graduate Department of Biosciences, Centre of Advanced Study in Bioresource Technology, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, 388 315, Gujarat, India.
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59
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Morais D, Pylro V, Clark IM, Hirsch PR, Tótola MR. Responses of microbial community from tropical pristine coastal soil to crude oil contamination. PeerJ 2016; 4:e1733. [PMID: 26925341 PMCID: PMC4768689 DOI: 10.7717/peerj.1733] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 02/02/2016] [Indexed: 02/01/2023] Open
Abstract
Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi) from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg(-1)), in triplicate. Soils were incubated for 38 days, with CO2 measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2 emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required.
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Affiliation(s)
- Daniel Morais
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil; AgroEcology Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Victor Pylro
- Genomics and Computational Biology Group, René Rachou Research Center (CPqRR-FIOCRUZ) , Belo Horizonte, Minas Gerais , Brazil
| | - Ian M Clark
- AgroEcology Department, Rothamsted Research , Harpenden, Hertfordshire , United Kingdom
| | - Penny R Hirsch
- AgroEcology Department, Rothamsted Research , Harpenden, Hertfordshire , United Kingdom
| | - Marcos R Tótola
- Department of Microbiology, Universidade Federal de Viçosa , Viçosa, Minas Gerais , Brazil
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60
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Podgorskii VS, Nogina TN, Dumanskaya TM, Ostapchuk AN. Change of the composition parafinnaphthenic hydrocarbon fraction in biological purification of water of oil. J WATER CHEM TECHNO+ 2016. [DOI: 10.3103/s1063455x15060089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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61
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Hanafy AAELMEL, Anwar Y, Mohamed SA, Al-Garni SMS, Sabir JSM, AbuZinadah OA, Mehdar HA, Alfaidi AW, Ahmed MMM. Isolation and identification of bacterial consortia responsible for degrading oil spills from the coastal area of Yanbu, Saudi Arabia. BIOTECHNOL BIOTEC EQ 2015. [DOI: 10.1080/13102818.2015.1086282] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Hanano A, Shaban M, Almousally I, Al-Ktaifani M. Saccharomyces cerevisiae SHSY detoxifies petroleum n-alkanes by an induced CYP52A58 and an enhanced order in cell surface hydrophobicity. CHEMOSPHERE 2015; 135:418-426. [PMID: 25434275 DOI: 10.1016/j.chemosphere.2014.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/03/2014] [Accepted: 11/05/2014] [Indexed: 06/04/2023]
Abstract
Environmental hydrocarbon contamination has a serious hazard to human health. Alkanes, the major component of hydrocarbons, can be consumed by various species of yeast. We previously identified a new strain SHSY of Saccharomyces cerevisiae with a remarkable ability to utilize the petroleum crude-oil (PCO) in aqueous solution. The current study demonstrated that the n-alkanes-assimilation activity of S. cerevisiae SHSY was related to an induced microsomal protein of 59 kDa approximately. The identified ORF encoded a protein of 517 amino acids and shared 93% sequence identity with an alkane-inducible hydroxylase CYP52A53 isolated from Scheffersomyces stipitis CBS. It was therefore referred as CYP52A58. The catalytic activity of the recombinant CYP52A58 was confirmed by the hydroxylation of n-alkanes, it showed an optimal mono-terminal hydroxylation activity toward n-hexadecane. Moreover, the ability of the yeast to use n-alkanes was accompanied with an increasing level in cell wall mannoproteins. Two differential protein bands were detected in the mannoproteins extracted from PCO-grown yeast. In parallel, a significant increase in the fatty acids content with a high degree of unsaturation was subsequently detected in the PCO-grown yeast. This study characterizes a safe and potential microorganism to remove n-alkanes from the aquatic environment.
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Affiliation(s)
- Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), B.P. Box 6091, Damascus, Syria.
| | - Mouhnad Shaban
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), B.P. Box 6091, Damascus, Syria
| | - Ibrahem Almousally
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), B.P. Box 6091, Damascus, Syria
| | - Mahmoud Al-Ktaifani
- Department of Chemistry, Atomic Energy Commission of Syria (AECS), B.P. Box 6091, Damascus, Syria
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63
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Jiang L, Song M, Luo C, Zhang D, Zhang G. Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing. PLoS One 2015; 10:e0130846. [PMID: 26098417 PMCID: PMC4476716 DOI: 10.1371/journal.pone.0130846] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 05/13/2015] [Indexed: 01/20/2023] Open
Abstract
Microorganisms responsible for the degradation of phenanthrene in a clean forest soil sample were identified by DNA-based stable isotope probing (SIP). The soil was artificially amended with either 12C- or 13C-labeled phenanthrene, and soil DNA was extracted on days 3, 6 and 9. Terminal restriction fragment length polymorphism (TRFLP) results revealed that the fragments of 219- and 241-bp in HaeIII digests were distributed throughout the gradient profile at three different sampling time points, and both fragments were more dominant in the heavy fractions of the samples exposed to the 13C-labeled contaminant. 16S rRNA sequencing of the 13C-enriched fraction suggested that Acidobacterium spp. within the class Acidobacteria, and Collimonas spp. within the class Betaproteobacteria, were directly involved in the uptake and degradation of phenanthrene at different times. To our knowledge, this is the first report that the genus Collimonas has the ability to degrade PAHs. Two PAH-RHDα genes were identified in 13C-labeled DNA. However, isolation of pure cultures indicated that strains of Staphylococcus sp. PHE-3, Pseudomonas sp. PHE-1, and Pseudomonas sp. PHE-2 in the soil had high phenanthrene-degrading ability. This emphasizes the role of a culture-independent method in the functional understanding of microbial communities in situ.
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Affiliation(s)
- Longfei Jiang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Mengke Song
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
- * E-mail:
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, United Kingdom
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
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Abed RMM, Al-Kindi S, Al-Kharusi S. Diversity of bacterial communities along a petroleum contamination gradient in desert soils. MICROBIAL ECOLOGY 2015; 69:95-105. [PMID: 25103912 DOI: 10.1007/s00248-014-0475-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/25/2014] [Indexed: 06/03/2023]
Abstract
Microbial communities in oil-polluted desert soils have been rarely studied compared to their counterparts from freshwater and marine environments. We investigated bacterial diversity and changes therein in five desert soils exposed to different levels of oil pollution. Automated rRNA intergenic spacer (ARISA) analysis profiles showed that the bacterial communities of the five soils were profoundly different (analysis of similarities (ANOSIM), R = 0.45, P < 0.0001) and shared less than 20 % of their operational taxonomic units (OTUs). OTU richness was relatively higher in the soils with the higher oil pollution levels. Multivariate analyses of ARISA profiles revealed that the microbial communities in the S soil, which contains the highest level of contamination, were different from the other soils and formed a completely separate cluster. A total of 16,657 ribosomal sequences were obtained, with 42-89 % of these sequences belonging to the phylum Proteobacteria. While sequences belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, and Actinobacteria were encountered in all soils, sequences belonging to anaerobic bacteria from the classes Deltaproteobacteria, Clostridia, and Anaerolineae were only detected in the S soil. Sequences belonging to the genus Terriglobus of the class Acidobacteria were only detected in the B3 soil with the lowest level of contamination. Redundancy analysis (RDA) showed that oil contamination level was the most determinant factor that explained variations in the microbial communities. We conclude that the exposure to different levels of oil contamination exerts a strong selective pressure on bacterial communities and that desert soils are rich in aerobic and anaerobic bacteria that could potentially contribute to the degradation of hydrocarbons.
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Affiliation(s)
- Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, P.O. Box: 36, 123 Al Khoud, Muscat, Sultanate of Oman,
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65
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Das D, Baruah R, Sarma Roy A, Singh AK, Deka Boruah HP, Kalita J, Bora TC. Complete genome sequence analysis of Pseudomonas aeruginosa N002 reveals its genetic adaptation for crude oil degradation. Genomics 2014; 105:182-90. [PMID: 25546474 DOI: 10.1016/j.ygeno.2014.12.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 10/24/2022]
Abstract
The present research work reports the whole genome sequence analysis of Pseudomonas aeruginosa strain N002 isolated from crude oil contaminated soil of Assam, India having high crude oil degradation ability. The whole genome of the strain N002 was sequenced by shotgun sequencing using Ion Torrent method and complete genome sequence analysis was done. It was found that the strain N002 revealed versatility for degradation, emulsification and metabolizing of crude oil. Analysis of cluster of orthologous group (COG) revealed that N002 has significantly higher gene abundance for cell motility, lipid transport and metabolism, intracellular trafficking, secretion and vesicular transport, secondary metabolite biosynthesis, transport and catabolism, signal transduction mechanism and transcription than average levels found in other genome sequences of the same bacterial species. However, lower gene abundance for carbohydrate transport and metabolism, replication, recombination and repair, translation, ribosomal structure, biogenesis was observed in N002 than average levels of other bacterial species.
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Affiliation(s)
- Dhrubajyoti Das
- Department of Biotechnology, CSIR-North East Institute of Science & Technology, Jorhat 785006, Assam, India
| | - Reshita Baruah
- Department of Biotechnology, CSIR-North East Institute of Science & Technology, Jorhat 785006, Assam, India
| | - Abhijit Sarma Roy
- Department of Biotechnology, CSIR-North East Institute of Science & Technology, Jorhat 785006, Assam, India
| | - Anil Kumar Singh
- Department of Biotechnology, CSIR-North East Institute of Science & Technology, Jorhat 785006, Assam, India.
| | - Hari Prasanna Deka Boruah
- Department of Biotechnology, CSIR-North East Institute of Science & Technology, Jorhat 785006, Assam, India.
| | - Jatin Kalita
- Department of Biotechnology, CSIR-North East Institute of Science & Technology, Jorhat 785006, Assam, India
| | - Tarun Chandra Bora
- Department of Biotechnology, CSIR-North East Institute of Science & Technology, Jorhat 785006, Assam, India
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66
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Włóka D, Kacprzak M, Grobelak A, Grosser A, Napora A. The Impact of PAHs Contamination on the Physicochemical Properties and Microbiological Activity of Industrial Soils. Polycycl Aromat Compd 2014. [DOI: 10.1080/10406638.2014.918887] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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67
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Auffret MD, Yergeau E, Labbé D, Fayolle-Guichard F, Greer CW. Importance of Rhodococcus strains in a bacterial consortium degrading a mixture of hydrocarbons, gasoline, and diesel oil additives revealed by metatranscriptomic analysis. Appl Microbiol Biotechnol 2014; 99:2419-30. [PMID: 25343979 DOI: 10.1007/s00253-014-6159-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/12/2014] [Indexed: 11/29/2022]
Abstract
A bacterial consortium (Mix3) composed of microorganisms originating from different environments (soils and wastewater) was obtained after enrichment in the presence of a mixture of 16 hydrocarbons, gasoline, and diesel oil additives. After addition of the mixture, the development of the microbial composition of Mix3 was monitored at three different times (35, 113, and 222 days) using fingerprinting method and dominant bacterial species were identified. In parallel, 14 bacteria were isolated after 113 days and identified. Degradation capacities for Mix3 and the isolated bacterial strains were characterized and compared. At day 113, we induced the expression of catabolic genes in Mix3 by adding the substrate mixture to resting cells and the metatranscriptome was analyzed. After addition of the substrate mixture, the relative abundance of Actinobacteria increased at day 222 while a shift between Rhodococcus and Mycobacterium was observed after 113 days. Mix3 was able to degrade 13 compounds completely, with partial degradation of isooctane and 2-ethylhexyl nitrate, but tert-butyl alcohol was not degraded. Rhodococcus wratislaviensis strain IFP 2016 isolated from Mix3 showed almost the same degradation capacities as Mix3: these results were not observed with the other isolated strains. Transcriptomic results revealed that Actinobacteria and in particular, Rhodococcus species, were major contributors in terms of total and catabolic gene transcripts while other species were involved in cyclohexane degradation. Not all the microorganisms identified at day 113 were active except R. wratislaviensis IFP 2016 that appeared to be a major player in the degradation activity observed in Mix3.
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Affiliation(s)
- Marc D Auffret
- Institut Français du Pétrole (IFP), 1-4 Avenue de Bois-Préau, 92852, Rueil-Malmaison, France,
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68
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Ganesh Kumar A, Vijayakumar L, Joshi G, Magesh Peter D, Dharani G, Kirubagaran R. Biodegradation of complex hydrocarbons in spent engine oil by novel bacterial consortium isolated from deep sea sediment. BIORESOURCE TECHNOLOGY 2014; 170:556-564. [PMID: 25171211 DOI: 10.1016/j.biortech.2014.08.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 08/01/2014] [Accepted: 08/03/2014] [Indexed: 05/20/2023]
Abstract
Complex hydrocarbon and aromatic compounds degrading marine bacterial strains were isolated from deep sea sediment after enrichment on spent engine (SE) oil. Phenotypic characterization and phylogenetic analysis of 16S rRNA gene sequences showed the isolates were related to members of the Pseudoalteromonas sp., Ruegeria sp., Exiguobacterium sp. and Acinetobacter sp. Biodegradation using 1% (v/v) SE oil with individual and mixed strains showed the efficacy of SE oil utilization within a short retention time. The addition of non-ionic surfactant 0.05% (v/v) Tween 80 as emulsifying agent enhanced the solubility of hydrocarbons and renders them more accessible for biodegradation. The degradation of several compounds and the metabolites formed during the microbial oxidation process were confirmed by Fourier transform infrared spectroscopy and Gas chromatography-mass spectrometry analyses. The potential of this consortium to biodegrade SE oil with and without emulsifying agent provides possible application in bioremediation of oil contaminated marine environment.
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Affiliation(s)
- A Ganesh Kumar
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, ESSO - National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai 600100, India
| | - Lakshmi Vijayakumar
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, ESSO - National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai 600100, India
| | - Gajendra Joshi
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, ESSO - National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai 600100, India
| | - D Magesh Peter
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, ESSO - National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai 600100, India
| | - G Dharani
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, ESSO - National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai 600100, India
| | - R Kirubagaran
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, ESSO - National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai 600100, India.
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69
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Yang Y, Wang J, Liao J, Xie S, Huang Y. Abundance and diversity of soil petroleum hydrocarbon-degrading microbial communities in oil exploring areas. Appl Microbiol Biotechnol 2014; 99:1935-46. [PMID: 25236802 DOI: 10.1007/s00253-014-6074-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 01/23/2023]
Abstract
Alkanes and polycyclic aromatic hydrocarbons (PAHs) are the commonly detected petroleum hydrocarbon contaminants in soils in oil exploring areas. Hydrocarbon-degrading genes are useful biomarks for estimation of the bioremediation potential of contaminated sites. However, the links between environmental factors and the distribution of alkane and PAH metabolic genes still remain largely unclear. The present study investigated the abundances and diversities of soil n-alkane and PAH-degrading bacterial communities targeting both alkB and nah genes in two oil exploring areas at different geographic regions. A large variation in the abundances and diversities of alkB and nah genes occurred in the studied soil samples. Various environmental variables regulated the spatial distribution of soil alkane and PAH metabolic genes, dependent on geographic location. The soil alkane-degrading bacterial communities in oil exploring areas mainly consisted of Pedobacter, Mycobacterium, and unknown alkB-harboring microorganisms. Moreover, the novel PAH-degraders predominated in nah gene clone libraries from soils of the two oil exploring areas. This work could provide some new insights towards the distribution of hydrocarbon-degrading microorganisms and their biodegradation potential in soil ecosystems.
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Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control (Peking University), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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70
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Zyakun AM, Brodskii ES, Baskunov BP, Zakharchenko VN, Peshenko VP, Filonov AE, Vetrova AA, Ivanova AA, Boronin AM. Bioremediation of oil-polluted soils: Using the [13C]/[12C] ratio to characterize microbial products of oil hydrocarbon biodegradation. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814040152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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71
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Liang Y, Zhao H, Zhang X, Zhou J, Li G. Contrasting microbial functional genes in two distinct saline-alkali and slightly acidic oil-contaminated sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 487:272-278. [PMID: 24784752 DOI: 10.1016/j.scitotenv.2014.04.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 04/08/2014] [Accepted: 04/08/2014] [Indexed: 06/03/2023]
Abstract
To compare the functional gene structure and diversity of microbial communities in saline-alkali and slightly acidic oil-contaminated sites, 40 soil samples were collected from two typical oil exploration sites in North and South China and analyzed with a comprehensive functional gene array (GeoChip 3.0). The overall microbial pattern was significantly different between the two sites, and a more divergent pattern was observed in slightly acidic soils. Response ratio was calculated to compare the microbial functional genes involved in organic contaminant degradation and carbon, nitrogen, phosphorus, and sulfur cycling. The results indicated a significantly low abundance of most genes involved in organic contaminant degradation and in the cycling of nitrogen and phosphorus in saline-alkali soils. By contrast, most carbon degradation genes and all carbon fixation genes had similar abundance at both sites. Based on the relationship between the environmental variables and microbial functional structure, pH was the major factor influencing the microbial distribution pattern in the two sites. This study demonstrated that microbial functional diversity and heterogeneity in oil-contaminated environments can vary significantly in relation to local environmental conditions. The limitation of nitrogen and phosphorus and the low degradation capacity of organic contaminant should be carefully considered, particularly in most oil-exploration sites with saline-alkali soils.
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Affiliation(s)
- Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Nanjing 210008, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Huihui Zhao
- School of Environmental & Safety Engineering, Changzhou University, Jiangsu 213164, China
| | - Xu Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Guanghe Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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72
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Chioma BC, Chioma BE. Culture-dependent characterization of hydrocarbon utilizing bacteria in selected crude oil-impacted sites in Bodo, Ogoniland, Nigeria. ACTA ACUST UNITED AC 2014. [DOI: 10.5897/ajest2014.1707] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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73
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Bacterial targets as potential indicators of diesel fuel toxicity in subantarctic soils. Appl Environ Microbiol 2014; 80:4021-33. [PMID: 24771028 DOI: 10.1128/aem.03939-13] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Appropriate remediation targets or universal guidelines for polar regions do not currently exist, and a comprehensive understanding of the effects of diesel fuel on the natural microbial populations in polar and subpolar soils is lacking. Our aim was to investigate the response of the bacterial community to diesel fuel and to evaluate if these responses have the potential to be used as indicators of soil toxicity thresholds. We set up short- and long-exposure tests across a soil organic carbon gradient. Utilizing broad and targeted community indices, as well as functional genes involved in the nitrogen cycle, we investigated the bacterial community structure and its potential functioning in response to special Antarctic blend (SAB) diesel fuel. We found the primary effect of diesel fuel toxicity was a reduction in species richness, evenness, and phylogenetic diversity, with the resulting community heavily dominated by a few species, principally Pseudomonas. The decline in richness and phylogenetic diversity was linked to disruption of the nitrogen cycle, with species and functional genes involved in nitrification significantly reduced. Of the 11 targets we evaluated, we found the bacterial amoA gene indicative of potential ammonium oxidation, the most suitable indicator of toxicity. Dose-response modeling for this target generated an average effective concentration responsible for 20% change (EC20) of 155 mg kg(-1), which is consistent with previous Macquarie Island ecotoxicology assays. Unlike traditional single-species tolerance testing, bacterial targets allowed us to simultaneously evaluate more than 1,700 species from 39 phyla, inclusive of rare, sensitive, and functionally relevant portions of the community.
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74
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Martin BC, George SJ, Price CA, Ryan MH, Tibbett M. The role of root exuded low molecular weight organic anions in facilitating petroleum hydrocarbon degradation: current knowledge and future directions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 472:642-653. [PMID: 24317170 DOI: 10.1016/j.scitotenv.2013.11.050] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/10/2013] [Accepted: 11/10/2013] [Indexed: 05/28/2023]
Abstract
Rhizoremediation is a bioremediation technique whereby enhanced microbial degradation of organic contaminants occurs within the plant root zone (rhizosphere). It is considered an effective and affordable 'green technology' for remediating soils contaminated with petroleum hydrocarbons (PHCs). This paper critically reviews the potential role of root exuded compounds in rhizoremediation, with emphasis on commonly exuded low molecular weight aliphatic organic acid anions (carboxylates). The extent to which remediation is achieved shows wide disparity among plant species. Therefore, plant selection is crucial for the advancement and widespread adoption of this technology. Root exudation is speculated to be one of the predominant factors leading to microbial changes in the rhizosphere and thus the potential driver behind enhanced petroleum biodegradation. Carboxylates can form a significant component of the root exudate mixture and are hypothesised to enhance petroleum biodegradation by: i) providing an easily degradable energy source; ii) increasing phosphorus supply; and/or iii) enhancing the contaminant bioavailability. These differing hypotheses, which are not mutually exclusive, require further investigation to progress our understanding of plant-microbe interactions with the aim to improve plant species selection and the efficacy of rhizoremediation.
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Affiliation(s)
- Belinda C Martin
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Suman J George
- School of Earth and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Charles A Price
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Megan H Ryan
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Mark Tibbett
- School of Earth and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; Department of Environmental Science and Technology, Cranfield University, College Road, Bedfordshire, MK43 0AL England, United Kingdom.
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75
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Determining the metabolic footprints of hydrocarbon degradation using multivariate analysis. PLoS One 2013; 8:e81910. [PMID: 24282619 PMCID: PMC3839897 DOI: 10.1371/journal.pone.0081910] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/28/2013] [Indexed: 11/22/2022] Open
Abstract
The functional dynamics of microbial communities are largely responsible for the clean-up of hydrocarbons in the environment. However, knowledge of the distinguishing functional genes, known as the metabolic footprint, present in hydrocarbon-impacted sites is still scarcely understood. Here, we conducted several multivariate analyses to characterise the metabolic footprints present in a variety of hydrocarbon-impacted and non-impacted sediments. Non-metric multi-dimensional scaling (NMDS) and canonical analysis of principal coordinates (CAP) showed a clear distinction between the two groups. A high relative abundance of genes associated with cofactors, virulence, phages and fatty acids were present in the non-impacted sediments, accounting for 45.7 % of the overall dissimilarity. In the hydrocarbon-impacted sites, a high relative abundance of genes associated with iron acquisition and metabolism, dormancy and sporulation, motility, metabolism of aromatic compounds and cell signalling were observed, accounting for 22.3 % of the overall dissimilarity. These results suggest a major shift in functionality has occurred with pathways essential to the degradation of hydrocarbons becoming overrepresented at the expense of other, less essential metabolisms.
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76
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Reunamo A, Riemann L, Leskinen P, Jørgensen KS. Dominant petroleum hydrocarbon-degrading bacteria in the Archipelago Sea in South-West Finland (Baltic Sea) belong to different taxonomic groups than hydrocarbon degraders in the oceans. MARINE POLLUTION BULLETIN 2013; 72:174-180. [PMID: 23711839 DOI: 10.1016/j.marpolbul.2013.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 04/05/2013] [Accepted: 04/08/2013] [Indexed: 06/02/2023]
Abstract
The natural petroleum hydrocarbon degrading capacity of the Archipelago Sea water in S-W Finland was studied in a microcosm experiment. Pristine and previously oil exposed sites were examined. Bacterial community fingerprinting was performed using terminal restriction fragment length polymorphism (T-RFLP) and samples from selected microcosms were sequenced. The abundance of PAH degradation genes was measured by quantitative PCR. Bacterial communities in diesel exposed microcosms diverged from control microcosms during the experiment. Gram positive PAH degradation genes dominated at both sites in situ, whereas gram negative PAH degrading genes became enriched in diesel microcosms. The dominant bacterial groups after a 14 days of diesel exposure were different depending on the sampling site, belonging to the class Actinobacteria (32%) at a pristine site and Betaproteobacteria (52%) at a previously oil exposed site. The hydrocarbon degrading bacteria in the Baltic Sea differ from those in the oceans, where most hydrocarbon degraders belong to Gammaproteobacteria.
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Affiliation(s)
- Anna Reunamo
- Division of Genetics and Physiology, Department of Biology, University of Turku, FI-20014 Turku, Finland.
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77
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Hanano A, Al-Arfi M, Shaban M, Daher A, Shamma M. Removal of petroleum-crude oil from aqueous solution bySaccharomyces cerevisiaeSHSY strain necessitates at least an inducible CYP450ALK homolog gene. J Basic Microbiol 2013; 54:358-68. [DOI: 10.1002/jobm.201200525] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 11/23/2012] [Indexed: 11/12/2022]
Affiliation(s)
- Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology; Atomic Energy Commission of Syria (AECS); Damascus Syria
| | - Malek Al-Arfi
- Department of Molecular Biology and Biotechnology; Atomic Energy Commission of Syria (AECS); Damascus Syria
| | - Mouhnad Shaban
- Department of Molecular Biology and Biotechnology; Atomic Energy Commission of Syria (AECS); Damascus Syria
| | - Amal Daher
- Department of Molecular Biology and Biotechnology; Atomic Energy Commission of Syria (AECS); Damascus Syria
| | - Motassim Shamma
- Department of Molecular Biology and Biotechnology; Atomic Energy Commission of Syria (AECS); Damascus Syria
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78
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Hamamura N, Ward DM, Inskeep WP. Effects of petroleum mixture types on soil bacterial population dynamics associated with the biodegradation of hydrocarbons in soil environments. FEMS Microbiol Ecol 2013; 85:168-78. [DOI: 10.1111/1574-6941.12108] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 02/19/2013] [Accepted: 03/04/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
| | - David M. Ward
- Department of Land Resources and Environmental Sciences; Montana State University; Bozeman; MT; USA
| | - William P. Inskeep
- Department of Land Resources and Environmental Sciences; Montana State University; Bozeman; MT; USA
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79
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Khan S, Afzal M, Iqbal S, Khan QM. Plant-bacteria partnerships for the remediation of hydrocarbon contaminated soils. CHEMOSPHERE 2013; 90:1317-32. [PMID: 23058201 DOI: 10.1016/j.chemosphere.2012.09.045] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 09/08/2012] [Accepted: 09/10/2012] [Indexed: 05/06/2023]
Abstract
Plant-bacteria partnerships have been extensively studied and applied to improve crop yield. In addition to their application in agriculture, a promising field to exploit plant-bacteria partnerships is the remediation of soil and water polluted with hydrocarbons. Application of effective plant-bacteria partnerships for the remediation of hydrocarbons depend mainly on the presence and metabolic activities of plant associated rhizo- and endophytic bacteria possessing specific genes required for the degradation of hydrocarbon pollutants. Plants and their associated bacteria interact with each other whereby plant supplies the bacteria with a special carbon source that stimulates the bacteria to degrade organic contaminants in the soil. In return, plant associated-bacteria can support their host plant to overcome contaminated-induced stress responses, and improve plant growth and development. In addition, plants further get benefits from their associated-bacteria possessing hydrocarbon-degradation potential, leading to enhanced hydrocarbon mineralization and lowering of both phytotoxicity and evapotranspiration of volatile hydrocarbons. A better understanding of plant-bacteria partnerships could be exploited to enhance the remediation of hydrocarbon contaminated soils in conjunction with sustainable production of non-food crops for biomass and biofuel production.
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Affiliation(s)
- Sumia Khan
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
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80
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Steliga T, Jakubowicz P, Kapusta P. Changes in toxicity during in situ bioremediation of weathered drill wastes contaminated with petroleum hydrocarbons. BIORESOURCE TECHNOLOGY 2012; 125:1-10. [PMID: 23018157 DOI: 10.1016/j.biortech.2012.08.092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 07/17/2012] [Accepted: 08/22/2012] [Indexed: 06/01/2023]
Abstract
Bioremediation of weathered drill wastes severely contaminated with total petroleum hydrocarbons (TPH) (90,000-170,000 mg kg(-1)) and BTEX (51.2-95.5 mg kg(-1)) to soil standards was achieved over a 3-year period in three phases: initial remediation, basic bioremediation and inoculation with a biopreparation. Fourteen non-pathogenic indigenous bacteria species belonging mainly to the Actinomycetales were identified and shown to be able to degrade 63-75% of nC(9)-nC(20), 36-51% of nC(21)-nC(36), 36% of BTEX and 20% of PAHs (polycyclic aromatic hydrocarbons). Addition of five non-pathogenic fungi species to the bacterial consortium allowed degradation of 69-89% of nC(9)-nC(20), 47-80% of nC(21)-nC(36), 76% of BTEX, and 68% of PAHs. Microtox, Ostacodtoxkit, Phytotoxkit and Ames tests indicated that changes in toxicity were not connected with the decrease in TPH contents, possibly due to the formation of toxic indirect metabolites during bioremediation. No toxicity was found in the soil after bioremediation.
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Affiliation(s)
- Teresa Steliga
- Department of Production Technology of Reservoir Fluids, Oil and Gas Institute, 31-503 Krakow, ul. Lubicz 25A, Poland.
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81
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Liang Y, Zhang X, Wang J, Li G. Spatial variations of hydrocarbon contamination and soil properties in oil exploring fields across China. JOURNAL OF HAZARDOUS MATERIALS 2012; 241-242:371-378. [PMID: 23069331 DOI: 10.1016/j.jhazmat.2012.09.055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 09/17/2012] [Accepted: 09/22/2012] [Indexed: 06/01/2023]
Abstract
Successful site remediation is critically based on a comprehensive understanding of distribution of contaminants, soil physico-chemical and microbial properties in oil contaminated sites. One hundred and ten topsoils were sampled from seven typical oil fields in different geoclimate regions across north to south China to investigate the spatial variances of oil contaminations and soil parameters. Oil concentrations and compositions, soil geochemical properties and microbial populations were analyzed and statistic analysis methods were used to analyze the spatial pattern of soil variables. The results indicated that oil contaminations were serious in most oil exploring areas in China, especially with high levels of polycyclic aromatic hydrocarbons (PAHs) from petrogenic origin. Ordination analyses indicated a relatively distinct spatial pattern that all soil samples grouped mainly by geographic locations, instead of distributing along contamination or other geochemical variable gradient. Microbial populations were found to be statistically positively correlated with soil nitrogen, phosphorus and water content, and negatively correlated with salt pH and soluble salts (P<0.05). This study provided insights into the spatial variability of soil variables in hydrocarbon-contaminated fields across large spatial scales, which is important for the environmental protection and further remediation in oil contaminated sites according to local conditions.
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82
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Schulz S, Giebler J, Chatzinotas A, Wick LY, Fetzer I, Welzl G, Harms H, Schloter M. Plant litter and soil type drive abundance, activity and community structure of alkB harbouring microbes in different soil compartments. THE ISME JOURNAL 2012; 6:1763-74. [PMID: 22402403 PMCID: PMC3498921 DOI: 10.1038/ismej.2012.17] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 02/10/2012] [Accepted: 02/10/2012] [Indexed: 11/09/2022]
Abstract
Alkanes are major constituents of plant-derived waxy materials. In this study, we investigated the abundance, community structure and activity of bacteria harbouring the alkane monooxygenase gene alkB, which catalyses a major step in the pathway of aerobic alkane degradation in the litter layer, the litter-soil interface and in bulk soil at three time points during the degradation of maize and pea plant litter (2, 8 and 30 weeks) to improve our understanding about drivers for microbial performance in different soil compartments. Soil cores of different soil textures (sandy and silty) were taken from an agricultural field and incubated at constant laboratory conditions. The abundance of alkB genes and transcripts (by qPCR) as well as the community structure (by terminal restriction fragment polymorphism fingerprinting) were measured in combination with the concentrations and composition of alkanes. The results obtained indicate a clear response pattern of all investigated biotic and abiotic parameters depending on the applied litter material, the type of soil used, the time point of sampling and the soil compartment studied. As expected the distribution of alkanes of different chain length formed a steep gradient from the litter layer to the bulk soil. Mainly in the two upper soil compartments community structure and abundance patterns of alkB were driven by the applied litter type and its degradation. Surprisingly, the differences between the compartments in one soil were more pronounced than the differences between similar compartments in the two soils studied. This indicates the necessity for analysing processes in different soil compartments to improve our mechanistic understanding of the dynamics of distinct functional groups of microbes.
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Affiliation(s)
- Stephan Schulz
- Chair of Soil Ecology, Technische Universität München, Neuherberg, Germany
- Research Unit for Environmental Genomics, HelmholtzZentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Julia Giebler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Ingo Fetzer
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Gerhard Welzl
- Institute of Developmental Genetics, HelmholtzZentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Michael Schloter
- Research Unit for Environmental Genomics, HelmholtzZentrum München, German Research Center for Environmental Health, Neuherberg, Germany
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83
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Chikere CB, Surridge K, Okpokwasili GC, Cloete TE. Dynamics of indigenous bacterial communities associated with crude oil degradation in soil microcosms during nutrient-enhanced bioremediation. WASTE MANAGEMENT & RESEARCH : THE JOURNAL OF THE INTERNATIONAL SOLID WASTES AND PUBLIC CLEANSING ASSOCIATION, ISWA 2012; 30:225-36. [PMID: 21824988 DOI: 10.1177/0734242x11410114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Bacterial population dynamics were examined during bioremediation of an African soil contaminated with Arabian light crude oil and nutrient enrichment (biostimulation). Polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) were used to generate bacterial community fingerprints of the different treatments employing the 16S ribosomal ribonucleic acid (rRNA) gene as molecular marker. The DGGE patterns of the nutrient-amended soils indicated the presence of distinguishable bands corresponding to the oil-contaminated-nutrient-enriched soils, which were not present in the oil-contaminated and pristine control soils. Further characterization of the dominant DGGE bands after excision, reamplification and sequencing revealed that Corynebacterium spp., Dietzia spp., Rhodococcus erythropolis sp., Nocardioides sp., Low G+C (guanine plus cytosine) Gram positive bacterial clones and several uncultured bacterial clones were the dominant bacterial groups after biostimulation. Prominent Corynebacterium sp. IC10 sequence was detected across all nutrient-amended soils but not in oil-contaminated control soil. Total heterotrophic and hydrocarbon utilizing bacterial counts increased significantly in the nutrient-amended soils 2 weeks post contamination whereas oil-contaminated and pristine control soils remained fairly stable throughout the experimental period. Gas chromatographic analysis of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second to the sixth week after contamination whereas no significant reduction in hydrocarbon peaks were seen in the oil-contaminated control soil throughout the 6-week experimental period. Results obtained indicated that nutrient amendment of oil-contaminated soil selected and enriched the bacterial communities mainly of the Actinobacteria phylogenetic group capable of surviving in toxic contamination with concomitant biodegradation of the hydrocarbons. The present study therefore demonstrated that the soil investigated harbours hydrocarbon-degrading bacterial populations which can be biostimulated to achieve effective bioremediation of oil-contaminated soil.
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Affiliation(s)
- Chioma B Chikere
- Department of Microbiology, University of Port-Harcourt, P.M.B. 5323, Port Harcourt, Rivers State, Nigeria.
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84
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Zyakun AM, Boronin AM, Kochetkov VV, Baskunov BP, Laurinavichus KS, Zakharchenko VN, Peshenko VP, Anokhina TO, Siunova TV. Ratio [13C]/[12C] as an index for express estimation of hydrocarbon-oxidizing potential of microbiota in soil polluted with crude oil. APPL BIOCHEM MICRO+ 2012. [DOI: 10.1134/s0003683812020159] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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85
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Granzotto G, Marcelino PRF, Barbosa ADM, Rodrigues EP, Rezende MI, Oliveira ALMD. Culturable bacterial pool from aged petroleum-contaminated soil: identification of oil-eating Bacillus strains. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0425-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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86
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Chikere CB, Okpokwasili GC, Chikere BO. Monitoring of microbial hydrocarbon remediation in the soil. 3 Biotech 2011; 1:117-138. [PMID: 22611524 PMCID: PMC3339601 DOI: 10.1007/s13205-011-0014-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 06/06/2011] [Indexed: 11/09/2022] Open
Abstract
Bioremediation of hydrocarbon pollutants is advantageous owing to the cost-effectiveness of the technology and the ubiquity of hydrocarbon-degrading microorganisms in the soil. Soil microbial diversity is affected by hydrocarbon perturbation, thus selective enrichment of hydrocarbon utilizers occurs. Hydrocarbons interact with the soil matrix and soil microorganisms determining the fate of the contaminants relative to their chemical nature and microbial degradative capabilities, respectively. Provided the polluted soil has requisite values for environmental factors that influence microbial activities and there are no inhibitors of microbial metabolism, there is a good chance that there will be a viable and active population of hydrocarbon-utilizing microorganisms in the soil. Microbial methods for monitoring bioremediation of hydrocarbons include chemical, biochemical and microbiological molecular indices that measure rates of microbial activities to show that in the end the target goal of pollutant reduction to a safe and permissible level has been achieved. Enumeration and characterization of hydrocarbon degraders, use of micro titer plate-based most probable number technique, community level physiological profiling, phospholipid fatty acid analysis, 16S rRNA- and other nucleic acid-based molecular fingerprinting techniques, metagenomics, microarray analysis, respirometry and gas chromatography are some of the methods employed in bio-monitoring of hydrocarbon remediation as presented in this review.
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Affiliation(s)
- Chioma Blaise Chikere
- Department of Microbiology, University of Port-Harcourt, P.M.B. 5323, Port Harcourt, Rivers State Nigeria
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87
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Stancu MM, Grifoll M. Multidrug resistance in hydrocarbon-tolerant Gram-positive and Gram-negative bacteria. J GEN APPL MICROBIOL 2011; 57:1-18. [PMID: 21478643 DOI: 10.2323/jgam.57.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
New Gram-positive and Gram-negative bacteria were isolated from Poeni oily sludge, using enrichment procedures. The six Gram-positive strains belong to Bacillus, Lysinibacillus and Rhodococcus genera. The eight Gram-negative strains belong to Shewanella, Aeromonas, Pseudomonas and Klebsiella genera. Isolated bacterial strains were tolerant to saturated (i.e., n-hexane, n-heptane, n-decane, n-pentadecane, n-hexadecane, cyclohexane), monoaromatic (i.e., benzene, toluene, styrene, xylene isomers, ethylbenzene, propylbenzene) and polyaromatic (i.e., naphthalene, 2-methylnaphthalene, fluorene) hydrocarbons, and also resistant to different antimicrobial agents (i.e., ampicillin, kanamycin, rhodamine 6G, crystal violet, malachite green, sodium dodecyl sulfate). The presence of hydrophilic antibiotics like ampicillin or kanamycin in liquid LB-Mg medium has no effects on Gram-positive and Gram-negative bacteria resistance to toxic compounds. The results indicated that Gram-negative bacteria are less sensitive to toxic compounds than Gram-positive bacteria, except one bacteria belonging to Lysinibacillus genus. There were observed cellular and molecular modifications induced by ampicillin or kanamycin to isolated bacterial strains. Gram-negative bacteria possessed between two and four catabolic genes (alkB, alkM, alkB/alkB1, todC1, xylM, PAH dioxygenase, catechol 2,3-dioxygenase), compared with Gram-positive bacteria (except one bacteria belonging to Bacillus genus) which possessed one catabolic gene (alkB/alkB1). Transporter genes (HAE1, acrAB) were detected only in Gram-negative bacteria.
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Affiliation(s)
- Mihaela Marilena Stancu
- Institute of Biology, Center of Microbiology, 296 Spl. Independentei St, Bucharest, Romania.
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88
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Pathak A, Shanker R, Garg SK, Manickam N. Profiling of biodegradation and bacterial 16S rRNA genes in diverse contaminated ecosystems using 60-mer oligonucleotide microarray. Appl Microbiol Biotechnol 2011; 90:1739-54. [DOI: 10.1007/s00253-011-3268-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 03/16/2011] [Accepted: 03/16/2011] [Indexed: 12/01/2022]
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89
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Steliga T, Jakubowicz P, Kapusta P. Optimisation research of petroleum hydrocarbon biodegradation in weathered drilling wastes from waste pits. WASTE MANAGEMENT & RESEARCH : THE JOURNAL OF THE INTERNATIONAL SOLID WASTES AND PUBLIC CLEANSING ASSOCIATION, ISWA 2010; 28:1065-1075. [PMID: 20022901 DOI: 10.1177/0734242x09351906] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The aim of this article is to discuss the problem of drilling waste remediation. Analyses and research showed that material stored in waste pits could be classified as soil with a high level of petroleum impurities (total petroleum hydrocarbons [TPH] = 102,417-132,472 mg kg(-1) dry mass). While preparing the complex technology of soil decontamination (which included primary reclamation, basic bioremediation and inoculation with biopreparations based on indigenous bacteria and fungi), laboratory tests indicated the use of an ex-situ method was fundamental. Remediation was controlled with a chromatographic method of qualitative and quantitative determination of petroleum hydrocarbons. Based on analytical data, there was the possibility to determine the effectiveness of consecutive purifying phases. Laboratory tests, following 135 days of basic bioremediation stimulated by optimum conditions to activate the growth of indigenous micro-organisms, resulted in a decrease in the TPH content, which was in the range of 52.3-72.5%. The next phase of soil decontamination lasted 135 days and involved the use of inoculation with biopreparations based on indigenous micro-organisms and fungi. This process enabled a TPH decrease of 93.8- 94.3%. Laboratory biodegradation research was done with the use of the biomarker C30-17α(H)21β(H)-hopane to normalize analyte (TPH, Σn-C8-n-C22 and Σn-C23-n-C36) concentrations. The calculated first-order biodegradation constants enable estimation of the purification stage dynamics and the effectiveness of the applied biopreparations. Furthermore, they represent the biodegradation degree of individual n-alkanes in subsequent stages of the soil purification process.
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90
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Genomic and functional analyses of Rhodococcus equi phages ReqiPepy6, ReqiPoco6, ReqiPine5, and ReqiDocB7. Appl Environ Microbiol 2010; 77:669-83. [PMID: 21097585 DOI: 10.1128/aem.01952-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The isolation and results of genomic and functional analyses of Rhodococcus equi phages ReqiPepy6, ReqiDocB7, ReqiPine5, and ReqiPoco6 (hereafter referred to as Pepy6, DocB7, Pine5, and Poco6, respectively) are reported. Two phages, Pepy6 and Poco6, more than 75% identical, exhibited genome organization and protein sequence likeness to Lactococcus lactis phage 1706 and clostridial prophage elements. An unusually high fraction, 27%, of Pepy6 and Poco6 proteins were predicted to possess at least one transmembrane domain, a value much higher than the average of 8.5% transmembrane domain-containing proteins determined from a data set of 36,324 phage protein entries. Genome organization and protein sequence comparisons place phage Pine5 as the first nonmycobacteriophage member of the large Rosebush cluster. DocB7, which had the broadest host range among the four isolates, was not closely related to any phage or prophage in the database, and only 23 of 105 predicted encoded proteins could be assigned a functional annotation. Because of the relationship of Rhodococcus to Mycobacterium, it was anticipated that these phages should exhibit some of the features characteristic of mycobacteriophages. Traits that were identified as shared by the Rhodococcus phages and mycobacteriophages include the prevalent long-tailed morphology and the presence of genes encoding LysB-like mycolate-hydrolyzing lysis proteins. Application of DocB7 lysates to soils amended with a host strain of R. equi reduced recoverable bacterial CFU, suggesting that phage may be useful in limiting R. equi load in the environment while foals are susceptible to infection.
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91
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Militon C, Boucher D, Vachelard C, Perchet G, Barra V, Troquet J, Peyretaillade E, Peyret P. Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil. FEMS Microbiol Ecol 2010; 74:669-81. [PMID: 21044099 DOI: 10.1111/j.1574-6941.2010.00982.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The microbial community response during the oxygen biostimulation process of aged oil-polluted soils is poorly documented and there is no reference for the long-term monitoring of the unsaturated zone. To assess the potential effect of air supply on hydrocarbon fate and microbial community structure, two treatments (0 and 0.056 mol h⁻¹ molar flow rate of oxygen) were performed in fixed bed reactors containing oil-polluted soil. Microbial activity was monitored continuously over 2 years throughout the oxygen biostimulation process. Microbial community structure before and after treatment for 12 and 24 months was determined using a dual rRNA/rRNA gene approach, allowing us to characterize bacteria that were presumably metabolically active and therefore responsible for the functionality of the community in this polluted soil. Clone library analysis revealed that the microbial community contained many rare phylotypes. These have never been observed in other studied ecosystems. The bacterial community shifted from Gammaproteobacteria to Actinobacteria during the treatment. Without aeration, the samples were dominated by a phylotype linked to the Streptomyces. Members belonging to eight dominant phylotypes were well adapted to the aeration process. Aeration stimulated an Actinobacteria phylotype that might be involved in restoring the ecosystem studied. Phylogenetic analyses suggested that this phylotype is a novel, deep-branching member of the Actinobacteria related to the well-studied genus Acidimicrobium.
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Affiliation(s)
- Cécile Militon
- Clermont Université, Université d'Auvergne, Laboratoire: Microorganismes Génome et Environnement, Clermont-Ferrand, France
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92
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Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. ISME JOURNAL 2010; 5:403-13. [PMID: 20861922 DOI: 10.1038/ismej.2010.142] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.
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93
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Marilena Lăzăroaie M. Multiple responses of gram-positive and gram-negative bacteria to mixture of hydrocarbons. Braz J Microbiol 2010; 41:649-67. [PMID: 24031541 PMCID: PMC3768651 DOI: 10.1590/s1517-83822010000300016] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2009] [Accepted: 03/29/2010] [Indexed: 11/22/2022] Open
Abstract
Most of our knowledge about pollutants and the way they are biodegraded in the environment has previously been shaped by laboratory studies using hydrocarbon-degrading bacterial strains isolated from polluted sites. In present study Gram-positive (Mycobacterium sp. IBBPo1, Oerskovia sp. IBBPo2, Corynebacterium sp. IBBPo3) and Gram-negative (Chryseomonas sp. IBBPo7, Pseudomonas sp. IBBPo10, Burkholderia sp. IBBPo12) bacteria, isolated from oily sludge, were found to be able to tolerate pure and mixture of saturated hydrocarbons, as well as pure and mixture of monoaromatic and polyaromatic hydrocarbons. Isolated Gram-negative bacteria were more tolerant to mixture of saturated (n-hexane, n-hexadecane, cyclohexane), monoaromatic (benzene, toluene, ethylbenzene) and polyaromatic (naphthalene, 2-methylnaphthalene, fluorene) hydrocarbons than Gram-positive bacteria. There were observed cellular and molecular modifications induced by mixture of saturated, monoaromatic and polyaromatic hydrocarbons to Gram-positive and Gram-negative bacteria. These modifications differ from one strain to another and even for the same bacterial strain, according to the nature of hydrophobic substrate.
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Affiliation(s)
- Mihaela Marilena Lăzăroaie
- Center of Microbiology, Institute of Biology , Romanian Academy, 296 Spl. Independentei St, 060031, PO 56-53, Bucharest , Romania
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94
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Tiwari JN, Reddy MMK, Patel DK, Jain SK, Murthy RC, Manickam N. Isolation of pyrene degrading Achromobacter xylooxidans and characterization of metabolic product. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0350-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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95
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Xiao Y, Roberts DJ, Zuo G, Badruzzaman M, Lehman GS. Characterization of microbial populations in pilot-scale fluidized-bed reactors treating perchlorate- and nitrate-laden brine. WATER RESEARCH 2010; 44:4029-4036. [PMID: 20605187 DOI: 10.1016/j.watres.2010.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2009] [Revised: 05/01/2010] [Accepted: 05/10/2010] [Indexed: 05/29/2023]
Abstract
A salt-tolerant, perchlorate- and nitrate-reducing bacterial culture developed previously was used to inoculate two acetate-fed fluidized bed reactors (FBRs) which treated a 6% ion-exchange regenerant brine containing 500 +/- 84 mg-N/L nitrate and 4.6 +/- 0.6 mg/L perchlorate. The reactors were operated in series in continuous flow mode for 107 days after an acclimation period of 65 days. Pilot operation data suggest that complete denitrification was achieved after 70 days of operation, but significant perchlorate removal was not observed. Molecular analysis of the inoculum culture and biomass from the pilot plant samples using denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH) revealed that the composition of the biomass in the pilot-plant was evolving with time in each FBR. The total number of Azoarcus/Denitromonas decreased in the first reactor with time and position in the bioreactor during acclimation and operation. FISH analysis clearly revealed that the number of Halomonas which was the dominant nitrate-reducing organism increased in the first reactor. This indicates a shift towards nitrate reduction which corresponds to the operation data. Both DGGE and FISH demonstrated that the Azoarcus/Denitromonas was still present in the second bioreactor, which indicated that the removal of nitrate in the first reactor was allowing the perchlorate-reducing organisms to establish themselves in the second reactor. The study also suggests that FISH was more effective for analysis of the composition of these cultures and it would be a better tool for the routine monitoring of cultures.
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Affiliation(s)
- Yeyuan Xiao
- School of Engineering, University of British Columbia Okanagan, 3333 University Way, Kelowna, B.C. Canada
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96
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Triky-Dotan S, Ofek M, Austerweil M, Steiner B, Minz D, Katan J, Gamliel A. Microbial aspects of accelerated degradation of metam sodium in soil. PHYTOPATHOLOGY 2010; 100:367-375. [PMID: 20205540 DOI: 10.1094/phyto-100-4-0367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Preplant soil fumigation with metam sodium is used worldwide to control soilborne diseases. The development of accelerated degradation of pesticides in soil, including metam sodium, results in reduced pesticide efficacy. Therefore, we studied microbial involvement in accelerated degradation of methyl isothiocyanate (MITC) following repeated soil applications of the parent compound, metam sodium. MITC degradation was reduced in soil with a history of metam sodium applications following sterilization, indicating the key role of microorganisms in accelerated degradation. Accelerated degradation of MITC was induced by inoculation of soil with no previous application of metam sodium with soil with a history of metam sodium applications. We developed a method to extract the active microbial fraction responsible for MITC degradation from soil with a history of metam sodium applications. This concentrated soil extract induced accelerated degradation of MITC when added to two different soils with no previous application of metam sodium. An extensive shift in total bacterial community composition in concentrated soil extracts occurred after a single metam sodium application. Two Oxalobacteraceae strains, MDB3 and MDB10, isolated from Rehovot soil following triple application of metam sodium rapidly degraded MITC in soil with no previous application of metam sodium. Polymerase chain reaction-denaturing gradient gel electrophoresis analysis of bacterial community composition showed relative enrichment of MDB3 following metam sodium application, suggesting its potential in situ involvement in accelerated degradation development in Rehovot soil. Responses of resident Oxalobacteraceae community members to metam sodium applications differed between Rehovot and En Tamar soils. Isolate MDB10 did not induce accelerated degradation of MITC in En Tamar soil and, with the slow dissipation of MITC, soil suppressiveness of accelerated degradation is suggested. The isolation and identification of MITC-degrading bacteria might be helpful in developing tools for managing accelerated degradation.
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Affiliation(s)
- Shachaf Triky-Dotan
- Institute of Agriclutural Engineering, The Volcani Center, Bet Dagan, Israel
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97
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Taketani RG, Franco NO, Rosado AS, van Elsas JD. Microbial community response to a simulated hydrocarbon spill in mangrove sediments. J Microbiol 2010; 48:7-15. [PMID: 20221723 DOI: 10.1007/s12275-009-0147-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 08/09/2009] [Indexed: 02/01/2023]
Abstract
In this study, we examined the hypothesis that the microbial communities in mangrove sediments with different chemical and historical characteristics respond differently to the disturbance of a hydrocarbon spill. Two different mangrove sediments were sampled, one close to an oil refinery that had suffered a recent oil spill and another that had not been in contact with oil. Based on the sampled sediment, two sets of mesocosms were built, and oil was added to one of them. They were subjected to mimicked mangrove conditions and monitored for 75 days. Archaeal and bacterial communities were evaluated through PCR-DGGE. Both communities showed the emergence of small numbers of novel bands in response to oil pollution. 16S rRNA gene clone libraries were constructed from both mesocosms before the addition of oil and at day 75 after oil addition. LIBSHUFF analysis showed that both mangrove-based mesocosms contained similar communities at the start of the experiment and that they were different from the initial one, as well as from each other, after 75 days. These results hint at a role of environmental history that is not obvious from community diversity indicators, but is apparent from the response to the applied stress.
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Affiliation(s)
- Rodrigo Gouvêa Taketani
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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98
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Liu R, Zhang Y, Ding R, Li D, Gao Y, Yang M. Comparison of archaeal and bacterial community structures in heavily oil-contaminated and pristine soils. J Biosci Bioeng 2010; 108:400-7. [PMID: 19804864 DOI: 10.1016/j.jbiosc.2009.05.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 04/27/2009] [Accepted: 05/16/2009] [Indexed: 11/16/2022]
Abstract
Archaeal and bacterial community structures in heavily oil-contaminated and pristine soils were compared using denaturing gradient gel electrophoresis and 16S rRNA gene libraries. The results showed that archaeal diversity was more complex in the contaminated soil than in the uncontaminated control soil. Archaeal populations in the contaminated soil consisted mainly of Euryarchaeota, with abundant methanogen-like operational taxonomic units (OTUs) and OTUs related to the phylogenetically diverse group, candidate division I, corresponding to rice cluster V. In contrast, only halophilic archaea were found in the pristine soil. Bacterial community structures also differed significantly between the contaminated and pristine soils. More clones from the contaminated soil were related to known hydrocarbon-degrading bacteria, implying that microorganisms with the potential to degrade petroleum were well-established. These results provide further insights into the composition of microbial communities in oil-contaminated soils.
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Affiliation(s)
- Ruyin Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
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99
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Application of Rhodococcus in Bioremediation of Contaminated Environments. BIOLOGY OF RHODOCOCCUS 2010. [DOI: 10.1007/978-3-642-12937-7_9] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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100
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Matias F, Bonatto D, Padilla G, Rodrigues MFDA, Henriques JAP. Polyhydroxyalkanoates production by actinobacteria isolated from soil. Can J Microbiol 2009; 55:790-800. [PMID: 19767851 DOI: 10.1139/w09-029] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are biodegradable and renewable polymers produced by a wide range of bacterial groups. New microbial bioprospection approaches have become an important way to find new PHA producers and new synthesized polymers. Over the past years, bacteria belonging to actinomycetes group have become known as PHA producers, such as Nocardia and Rhodococcus species, Kineosphaera limosa Liu et al. 2002, and, more recently, Streptomyces species. In this paper, we disclose that there are more actinobacteria PHA producers in addition to the genera cited. Some unusual genera, such as Streptoalloteichus, and some genera frequently present in soil, such as Streptacidiphilus, have been found. Thirty-four isolates were able to accumulate poly(3-hydroxybutyrate) and a number of these have traces of poly(3-hydroxyvalerate) when cultivated on glucose or glucose and casein as carbon source. Furthermore, some strains showed traces of medium chain length PHA. Transmission electron microscopy demonstrated that the PHA accumulation occurs in hyphae and spores.
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Affiliation(s)
- Fernanda Matias
- Universidade de São Paulo, Instituto de Ciências Biomédicas II, Av. Professor Lineu Prestes, 1374 São Paulo, São Paulo 05508-900, Brazil
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