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Fan L, Gong X, Lv Q, Bin D, Wang L. Construction of Shale Gas Oil-Based Drilling Cuttings Degrading Bacterial Consortium and Their Degradation Characteristics. Microorganisms 2024; 12:318. [PMID: 38399720 PMCID: PMC10891884 DOI: 10.3390/microorganisms12020318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/13/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024] Open
Abstract
Oil-based drilling cuttings (OBDCs) contain petroleum hydrocarbons with complex compositions and high concentrations, which have highly carcinogenic, teratogenic, and mutagenic properties. In this study, three highly efficient petroleum hydrocarbon-degrading bacteria were screened from OBDCs of different shale gas wells in Chongqing, China, and identified as Rhodococcus sp. and Dietzia sp. Because of their ability to degrade hydrocarbons of various chain lengths, a new method was proposed for degrading petroleum hydrocarbons in shale gas OBDCs by combining different bacterial species. Results showed that the bacterial consortium, consisting of the three strains, exhibited the highest degradation rate for petroleum hydrocarbons, capable of degrading 74.38% of long-chain alkanes and 93.57% of short-chain alkanes, respectively. Moreover, the petroleum hydrocarbon degradation performance of the bacterial consortium in actual OBDCs could reach 90.60% in the optimal conditions, and the degradation kinetic process followed a first-order kinetic model. This study provides a certain technical reserve for the bioremediation of shale gas OBDCs.
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Affiliation(s)
- Li Fan
- College of Resource and Safety Engineering, Chongqing University, Chongqing 400044, China
- Chongqing Academy of Ecology and Environmental Sciences, Chongqing 401336, China; (X.G.); (D.B.)
| | - Xianhe Gong
- Chongqing Academy of Ecology and Environmental Sciences, Chongqing 401336, China; (X.G.); (D.B.)
- The Southwest Branch of the Chinese Academy of Environmental Sciences, Chongqing 401336, China
| | - Quanwei Lv
- College of Resource and Safety Engineering, Chongqing University, Chongqing 400044, China
| | - Denghui Bin
- Chongqing Academy of Ecology and Environmental Sciences, Chongqing 401336, China; (X.G.); (D.B.)
- The Southwest Branch of the Chinese Academy of Environmental Sciences, Chongqing 401336, China
| | - Li’Ao Wang
- College of Resource and Safety Engineering, Chongqing University, Chongqing 400044, China
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Yessentayeva K, Reinhard A, Berzhanova R, Mukasheva T, Urich T, Mikolasch A. Bacterial crude oil and polyaromatic hydrocarbon degraders from Kazakh oil fields as barley growth support. Appl Microbiol Biotechnol 2024; 108:189. [PMID: 38305872 PMCID: PMC10837267 DOI: 10.1007/s00253-024-13010-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024]
Abstract
Bacterial strains of the genera Arthrobacter, Bacillus, Dietzia, Kocuria, and Micrococcus were isolated from oil-contaminated soils of the Balgimbaev, Dossor, and Zaburunye oil fields in Kazakhstan. They were selected from 1376 isolated strains based on their unique ability to use crude oil and polyaromatic hydrocarbons (PAHs) as sole source of carbon and energy in growth experiments. The isolated strains degraded a wide range of aliphatic and aromatic components from crude oil to generate a total of 170 acid metabolites. Eight metabolites were detected during the degradation of anthracene and of phenanthrene, two of which led to the description of a new degradation pathway. The selected bacterial strains Arthrobacter bussei/agilis SBUG 2290, Bacillus atrophaeus SBUG 2291, Bacillus subtilis SBUG 2285, Dietzia kunjamensis SBUG 2289, Kocuria rosea SBUG 2287, Kocuria polaris SBUG 2288, and Micrococcus luteus SBUG 2286 promoted the growth of barley shoots and roots in oil-contaminated soil, demonstrating the enormous potential of isolatable and cultivable soil bacteria in soil remediation. KEY POINTS: • Special powerful bacterial strains as potential crude oil and PAH degraders. • Growth on crude oil or PAHs as sole source of carbon and energy. • Bacterial support of barley growth as resource for soil remediation.
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Affiliation(s)
- Kuralay Yessentayeva
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave 71, 050040, Almaty, Kazakhstan
| | - Anne Reinhard
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Ramza Berzhanova
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave 71, 050040, Almaty, Kazakhstan
| | - Togzhan Mukasheva
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave 71, 050040, Almaty, Kazakhstan
| | - Tim Urich
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Annett Mikolasch
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany.
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Salam LB. Diverse hydrocarbon degradation genes, heavy metal resistome, and microbiome of a fluorene-enriched animal-charcoal polluted soil. Folia Microbiol (Praha) 2024; 69:59-80. [PMID: 37450270 DOI: 10.1007/s12223-023-01077-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
Environmental compartments polluted with animal charcoal from the skin and hide cottage industries are rich in toxic heavy metals and diverse hydrocarbon classes, some of which are carcinogenic, mutagenic, and genotoxic, and thus require a bio-based eco-benign decommission strategies. A shotgun metagenomic approach was used to decipher the microbiome, hydrocarbon degradation genes, and heavy metal resistome of a microbial consortium (FN8) from an animal-charcoal polluted site enriched with fluorene. Structurally, the FN8 microbial consortium consists of 26 phyla, 53 classes, 119 orders, 245 families, 620 genera, and 1021 species. The dominant phylum, class, order, family, genus, and species in the consortium are Proteobacteria (51.37%), Gammaproteobacteria (39.01%), Bacillales (18.09%), Microbulbiferaceae (11.65%), Microbulbifer (12.21%), and Microbulbifer sp. A4B17 (19.65%), respectively. The microbial consortium degraded 57.56% (28.78 mg/L) and 87.14% (43.57 mg/L) of the initial fluorene concentration in 14 and 21 days. Functional annotation of the protein sequences (ORFs) of the FN8 metagenome using the KEGG GhostKOALA, KofamKOALA, NCBI's conserved domain database, and BacMet revealed the detection of hydrocarbon degradation genes for benzoate, aminobenzoate, polycyclic aromatic hydrocarbons (PAHs), chlorocyclohexane/chlorobenzene, chloroalkane/chloroalkene, toluene, xylene, styrene, naphthalene, nitrotoluene, and several others. The annotation also revealed putative genes for the transport, uptake, efflux, and regulation of heavy metals such as arsenic, cadmium, chromium, mercury, nickel, copper, zinc, and several others. Findings from this study have established that members of the FN8 consortium are well-adapted and imbued with requisite gene sets and could be a potential bioresource for on-site depuration of animal charcoal polluted sites.
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Affiliation(s)
- Lateef Babatunde Salam
- Department of Biological Sciences, Microbiology unit, Elizade University, Ilara-Mokin, Ondo State, Nigeria.
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Park J, Yoon SG, Lee H, An J, Nam K. Effects of in situ Fe oxide precipitation on As stabilization and soil ecological resilience under salt stress. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132629. [PMID: 37832440 DOI: 10.1016/j.jhazmat.2023.132629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/04/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023]
Abstract
Iron (Fe) oxide precipitation is a promising method for stabilizing arsenic (As) in contaminated soils; however, the addition of salts during the process can negatively affect soil functions. This study investigated the effects of in situ Fe oxide precipitation on As stabilization and the impact of salt stress on soil functions and microbial communities. Fe oxide precipitation reduced the concentration of bioaccessible As by 84% in the stabilized soil, resulting in the formation of ferrihydrite and lepidocrocite, as confirmed by XANES. Nevertheless, an increase in salt stress reduced barley development, microbial enzyme activities, and microbial diversity compared to those in the original soil. Despite this, the stabilized soil exhibited natural resilience and potential for enhanced microbial adaptations, with increased retention of salt-tolerant bacteria. Washing the stabilized soil with water restored EC1:5 to the level of the original soil, resulting in increased barley growth rates and enzyme activities after 5-d and 20-week incubation periods, suggesting soil function recovery. 16 S rRNA sequencing revealed the retention of salt-tolerant bacteria in the stabilized soil, while salt-removed soil exhibited an increase in Proteobacteria, which could facilitate ecological functions. Overall, Fe oxide precipitation effectively stabilized soil As and exhibited potential for restoring the natural resilience and ecological functions of soils through microbial adaptations and salt removal.
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Affiliation(s)
- Jinhee Park
- Department of Civil & Environmental Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Sang-Gyu Yoon
- Department of Smart City Engineering, Hanyang University, Ansan 15588, South Korea
| | - Hosub Lee
- Department of Civil & Environmental Engineering, Seoul National University, Seoul 08826, South Korea
| | - Jinsung An
- Department of Smart City Engineering, Hanyang University, Ansan 15588, South Korea; Department of Civil & Environmental Engineering, Hanyang University, Ansan 15588, South Korea.
| | - Kyoungphile Nam
- Department of Civil & Environmental Engineering, Seoul National University, Seoul 08826, South Korea
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Singh S, Thakur RS, Manickam N. Insights into molecular mechanism of plasticizer biodegradation in Dietzia kunjamensis IITR165 and Brucella intermedia IITR166 isolated from a solid waste dumpsite. J Appl Microbiol 2023; 134:lxad231. [PMID: 37838476 DOI: 10.1093/jambio/lxad231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/04/2023] [Accepted: 10/13/2023] [Indexed: 10/16/2023]
Abstract
AIMS Isolation of phthalate esters (PAEs) degrading bacteria from a solid waste dumpsite could degrade many plasticizers efficiently and to investigate their degrading kinetics, pathways, and genes. METHODS AND RESULTS Based on their 16S rRNA gene sequence the strains were identified as Dietzia kunjamensis IITR165 and Brucella intermedia IITR166, which showed a first-order degradation kinetic model under lab conditions. The quantification of phthalates and their intermediate metabolites identification were done by using ultra-high-performance liquid chromatography (UHPLC) and gas chromatography-tandem mass-spectrometry (GC-MS/MS), respectively. Both the bacteria utilized >99% dibutyl phthalate at a high concentration of 100-400 mg L-1 within 192 h as monitored by UHPLC. GC-MS/MS revealed the presence of metabolites dimethyl phthalate (DMP), phthalic acid (PA), and benzoic acid (BA) during DBP degradation by IITR165 while monobutyl phthalate (MBP) and PA were identified in IITR166. Phthalate esters degrading gene cluster in IITR165 comprised two novel genes coding for carboxylesterase (dkca1) and mono-alkyl phthalate hydrolase (maph), having only 37.47% and 47.74% homology, respectively, with reported phthalate degradation genes, along with the terephthalate dioxygenase system (tphA1, A2, A3, and B). However, IITR166 harbored different gene clusters comprising di-alkyl phthalate hydrolase (dph_bi), and phthalate dioxygenase (ophA, B, and C) genes. CONCLUSIONS Two novel bacterial strains, Dietzia kunjamensis IITR165 and Brucella intermedia IITR166, were isolated and found to efficiently degrade DBP at high concentrations. The degradation followed first-order kinetics, and both strains exhibited a removal efficiency of over 99%. Metabolite analysis revealed that both bacteria utilized de-methylation, de-esterification, and decarboxylation steps during degradation.
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Affiliation(s)
- Saurabh Singh
- FEST Division, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Ravindra Singh Thakur
- Analytical Sciences and Accredited Testing Services, CSIR-Indian Institute of Toxicology Research, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Natesan Manickam
- FEST Division, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
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Lyu L, Li J, Chen Y, Mai Z, Wang L, Li Q, Zhang S. Degradation potential of alkanes by diverse oil-degrading bacteria from deep-sea sediments of Haima cold seep areas, South China Sea. Front Microbiol 2022; 13:920067. [PMID: 36338091 PMCID: PMC9626528 DOI: 10.3389/fmicb.2022.920067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Marine oil spills are a significant concern worldwide, destroying the ecological environment and threatening the survival of marine life. Various oil-degrading bacteria have been widely reported in marine environments in response to marine oil pollution. However, little information is known about culturable oil-degrading bacteria in cold seep of the deep-sea environments, which are rich in hydrocarbons. This study enriched five oil-degrading consortia from sediments collected from the Haima cold seep areas of the South China Sea. Parvibaculum, Erythrobacter, Acinetobacter, Alcanivorax, Pseudomonas, Marinobacter, Halomonas, and Idiomarina were the dominant genera. Further results of bacterial growth and degradation ability tests indicated seven efficient alkane-degrading bacteria belonging to Acinetobacter, Alcanivorax, Kangiella, Limimaricola, Marinobacter, Flavobacterium, and Paracoccus, whose degradation rates were higher in crude oil (70.3–78.0%) than that in diesel oil (62.7–66.3%). From the view of carbon chain length, alkane degradation rates were medium chains > long chains > short chains. In addition, Kangiella aquimarina F7, Acinetobacter venetianus F1, Limimaricola variabilis F8, Marinobacter nauticus J5, Flavobacterium sediminis N3, and Paracoccus sediminilitoris N6 were first identified as oil-degrading bacteria from deep-sea environments. This study will provide insight into the bacterial community structures and oil-degrading bacterial diversity in the Haima cold seep areas, South China Sea, and offer bacterial resources to oil bioremediation applications.
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Affiliation(s)
- Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Lina Lyu,
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- *Correspondence: Si Zhang,
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Zhao Q, Hu Q, Qiu Z, Yu C. Biodegradation characteristics and mechanism of quinoline by Ochrobactrum sp. strain C2. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2022; 86:1284-1298. [PMID: 36358061 DOI: 10.2166/wst.2022.249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A quinoline-degrading strain, C2, which could completely degrade 250 mg/L of quinoline within 24 h, was isolated from coking wastewater. Strain C2 was identified as Ochrobactrum sp. on the basis of 16S rDNA sequence analysis According to 16S rDNA gene sequence analysis, Strain C2 was identified as Ochrobactrum sp. Strain C2 could utilize quinoline as the sole carbon sources and nitrogen sources to grow and degrade quinoline well under acidic conditions. The optimum inoculum concentration, temperature and shaking speed for quinoline degradation were 10%, 30 °C and 150 r/min, respectively. The degradation of quinoline at low concentration by the strain followed the first-order kinetic model. The growth process of strain C2 was more consistent with the Haldane model than the Monod model, and the kinetic parameters were: Vmax = 0.08 h-1, Ks = 131.5 mg/L, Ki = 183.1 mg/L. Compared with suspended strains, strain C2 immobilized by sodium alginate had better degradation efficiency of quinoline and COD. The metabolic pathway of quinoline by Strain C2 was tentatively proposed, quinoline was firstly converted into 2(1H) quinolone, then the benzene ring was opened with the action of catechol 1,2-dioxygenase and subsequently transformed into benzaldehyde, 2-pentanone, hydroxyphenyl propionic acid and others.
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Affiliation(s)
- Qiancheng Zhao
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China E-mail:
| | - Qiaoyu Hu
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China E-mail:
| | - Ziliang Qiu
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China E-mail:
| | - Caihong Yu
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China E-mail:
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Behera ID, Nayak M, Mishra A, Meikap BC, Sen R. Strategic implementation of integrated bioaugmentation and biostimulation for efficient mitigation of petroleum hydrocarbon pollutants from terrestrial and aquatic environment. MARINE POLLUTION BULLETIN 2022; 177:113492. [PMID: 35305374 DOI: 10.1016/j.marpolbul.2022.113492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Release of petroleum hydrocarbon pollutants poses a serious problem to the terrestrial as well as marine ecosystem. This study investigated and compared the potency of different biodegradation strategies for mitigating total petroleum hydrocarbon (TPH) of petroleum refinery sludge by an integrated action of bioaugmentation and biostimulation vis-à-vis separate bioaugmentation and biostimulation approaches. The implementation of a concomitant bioaugmentation-biostimulation strategy (BABSS) involving the indigenously developed bacterial consortium and poultry litter extract showed the best performance by mitigating the TPH up to 90.3 ± 3.7% in 21 days. The GC-FID analysis confirmed the efficacy of different TPH degradation strategies. The kinetic study of TPH degradation of BABSS resulted first-order with rate 0.11 day-1. Thus, the BABSS proved to be more efficient in degrading TPH in an eco-friendly manner and hence, may pave the way for better management of petroleum hydrocarbon pollutants, while providing a sustainable solution to the disposal of poultry wastes.
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Affiliation(s)
- Ipsita Dipamitra Behera
- Department of Chemical Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Manoranjan Nayak
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India; Biorefinery and Bioenergy Research Laboratory, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida 201313, India
| | - Asmita Mishra
- Department of Chemical Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Bhim Charan Meikap
- Department of Chemical Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India; Department of Chemical Engineering, School of Engineering, Howard College, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Ramkrishna Sen
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India; Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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Characterization of Dietzia maris AURCCBT01 from oil-contaminated soil for biodegradation of crude oil. 3 Biotech 2021; 11:291. [PMID: 34109094 DOI: 10.1007/s13205-021-02807-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 04/22/2021] [Indexed: 10/21/2022] Open
Abstract
A bacterial strain was isolated from an oil-contaminated site and on its' further characterization, exhibited the potential of synthesising metabolites and the ability to degrade crude oil. Its' morphological, biochemical and 16S rRNA analysis suggested that the bacterium belongs to Dietzia maris AURCCBT01. This strain rapidly grew in the medium supplemented with n-alkanes C14, C18, C20, C28 and C32 utilizing them as a sole carbon source and produced a maximum canthaxanthin pigment of 971.37 µg/L in the n-C14 supplemented medium and produced the lowest pigment yield of 389.48 µg/L in the n-C-32 supplemented medium. Moreover, the strain effectively degraded 91.87% of crude oil in 7 days. The emulsification activity of the strain was 25% with the highest cell surface hydrophobicity (70.26%) and it showed a decrease in surface tension, indicating that the biosurfactant production lowers the surface tension. This is the first report on the characterization of the strain, Dietzia maris AURCCBT01 and its' novelty of alkane degradation and simultaneous production of canthaxanthin pigment. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02807-7.
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Li YP, Pan JC, Ma YL. Elucidation of multiple alkane hydroxylase systems in biodegradation of crude oil
n
‐alkane pollution by
Pseudomonas aeruginosa
DN1. J Appl Microbiol 2019; 128:151-160. [DOI: 10.1111/jam.14470] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 09/17/2019] [Accepted: 09/22/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Y. P. Li
- Shaanxi Provincial Key Laboratory of Biotechnology Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Science Northwest University Xi’an, Shaanxi China
| | - J. C. Pan
- Shaanxi Provincial Key Laboratory of Biotechnology Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Science Northwest University Xi’an, Shaanxi China
| | - Y. L. Ma
- Shaanxi Provincial Key Laboratory of Biotechnology Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Science Northwest University Xi’an, Shaanxi China
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Kim HS, Dong K, Kim J, Lee SS. Characteristics of crude oil-degrading bacteria Gordonia iterans isolated from marine coastal in Taean sediment. Microbiologyopen 2018; 8:e00754. [PMID: 30338941 PMCID: PMC6562140 DOI: 10.1002/mbo3.754] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/18/2018] [Accepted: 09/20/2018] [Indexed: 01/01/2023] Open
Abstract
Crude oil is a major pollutant of marine and coastal ecosystems, and it causes environmental problems more seriously. It is believed ultimate and complete degradation is accomplished mainly by microorganisms. In this study, we aim to search out for bacterial strains with high ability in degrading crude oil. From sediments contaminated by the petroleum spilled in 2007, an accident in Taean, South Korea, we isolated thirty‐one bacterial strains in total with potential application in crude oil contamination remediation. In terms of removal percentage after 7 days, one of the strains, Co17, showed the highest removal efficiency with 84.2% of crude oil in Bushnell‐Haas media. The Co17 strain even exhibited outstanding ability removing crude oil at a high salt concentration. Through the whole genome sequencing annotation results, many genes related with n‐alkane degradation in the genome of Gordonia sp. Co17, revealed alkane‐1‐monooxygenase, alcohol dehydrogenase, and Baeyer–Villiger monooxygenase. Specially, for confirmation of gene‐level, alkB gene encoding alkane hydroxylase (alkane‐1‐monooxygenase) was found in the strain Co17. The expression of alkB upregulated 125‐fold after 18 hr accompany with the removal of n‐alkanes of 48.9%. We therefore propose the strain Gordonia iterans Co17, isolated from crude oil‐contaminated marine sediment, could be used to offer a new strategy for bioremediation with high efficiency.
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Affiliation(s)
- Hyun-Sook Kim
- Department of Biological Engineering, Kyonggi University, Suwon-si, Korea
| | - Ke Dong
- Department of Life Science, Kyonggi University, Suwon-si, Korea
| | - Jinsoo Kim
- Department of Life Science, Kyonggi University, Suwon-si, Korea
| | - Sang-Seob Lee
- Department of Biological Engineering, Kyonggi University, Suwon-si, Korea.,Department of Life Science, Kyonggi University, Suwon-si, Korea
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Brzeszcz J, Kaszycki P. Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility. Biodegradation 2018; 29:359-407. [PMID: 29948519 DOI: 10.1007/s10532-018-9837-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
Environmental pollution with petroleum toxic products has afflicted various ecosystems, causing devastating damage to natural habitats with serious economic implications. Some crude oil components may serve as growth substrates for microorganisms. A number of bacterial strains reveal metabolic capacities to biotransform various organic compounds. Some of the hydrocarbon degraders are highly biochemically specialized, while the others display a versatile metabolism and can utilize both saturated aliphatic and aromatic hydrocarbons. The extended catabolic profiles of the latter group have been subjected to systematic and complex studies relatively rarely thus far. Growing evidence shows that numerous bacteria produce broad biochemical activities towards different hydrocarbon types and such an enhanced metabolic potential can be found in many more species than the already well-known oil-degraders. These strains may play an important role in the removal of heterogeneous contamination. They are thus considered to be a promising solution in bioremediation applications. The main purpose of this article is to provide an overview of the current knowledge on aerobic bacteria involved in the mineralization or transformation of both n-alkanes and aromatic hydrocarbons. Variant scientific approaches enabling to evaluate these features on biochemical as well as genetic levels are presented. The distribution of multidegradative capabilities between bacterial taxa is systematically shown and the possibility of simultaneous transformation of complex hydrocarbon mixtures is discussed. Bioinformatic analysis of the currently available genetic data is employed to enable generation of phylogenetic relationships between environmental strain isolates belonging to the phyla Actinobacteria, Proteobacteria, and Firmicutes. The study proves that the co-occurrence of genes responsible for concomitant metabolic bioconversion reactions of structurally-diverse hydrocarbons is not unique among various systematic groups.
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Affiliation(s)
- Joanna Brzeszcz
- Department of Microbiology, Oil and Gas Institute-National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland.
| | - Paweł Kaszycki
- Unit of Biochemistry, Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Kraków, al. 29 Listopada 54, 31-425, Kraków, Poland
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Hvidsten I, Mjøs SA, Holmelid B, Bødtker G, Barth T. Lipids of Dietzia sp. A14101. Part I: A study of the production dynamics of surface-active compounds. Chem Phys Lipids 2017; 208:19-30. [DOI: 10.1016/j.chemphyslip.2017.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 08/06/2017] [Accepted: 08/14/2017] [Indexed: 11/25/2022]
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14
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Balseiro-Romero M, Gkorezis P, Kidd PS, Van Hamme J, Weyens N, Monterroso C, Vangronsveld J. Characterization and degradation potential of diesel-degrading bacterial strains for application in bioremediation. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2017; 19:955-963. [PMID: 28598213 DOI: 10.1080/15226514.2017.1337065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bioremediation of polluted soils is a promising technique with low environmental impact, which uses soil organisms to degrade soil contaminants. In this study, 19 bacterial strains isolated from a diesel-contaminated soil were screened for their diesel-degrading potential, biosurfactant (BS) production, and biofilm formation abilities, all desirable characteristics when selecting strains for re-inoculation into hydrocarbon-contaminated soils. Diesel-degradation rates were determined in vitro in minimal medium with diesel as the sole carbon source. The capacity to degrade diesel range organics (DROs) of strains SPG23 (Arthobacter sp.) and PF1 (Acinetobacter oleivorans) reached 17-26% of total DROs after 10 days, and 90% for strain GK2 (Acinetobacter calcoaceticus). The amount and rate of alkane degradation decreased significantly with increasing carbon number for strains SPG23 and PF1. Strain GK2, which produced BSs and biofilms, exhibited a greater extent, and faster rate of alkane degradation compared to SPG23 and PF1. Based on the outcomes of degradation experiments, in addition to BS production, biofilm formation capacities, and previous genome characterizations, strain GK2 is a promising candidate for microbial-assisted phytoremediation of diesel-contaminated soils. These results are of particular interest to select suitable strains for bioremediation, not only presenting high diesel-degradation rates, but also other characteristics which could improve rhizosphere colonization.
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Affiliation(s)
- María Balseiro-Romero
- a Department of Chemical Engineering , University of Santiago de Compostela , Campus Vida, Santiago de Compostela , Spain
| | - Panagiotis Gkorezis
- b Centre for Environmental Sciences, University of Hasselt , Diepenbeek , Belgium
| | - Petra S Kidd
- c Instituto de Investigacións Agrobiolóxicas de Galicia (IIAG), Consejo Superior de Investigaciones Científicas (CSIC) , Santiago de Compostela , Spain
| | - Jonathan Van Hamme
- d Department of Biological Sciences , Thompson Rivers University , Kamloops , Canada
| | - Nele Weyens
- b Centre for Environmental Sciences, University of Hasselt , Diepenbeek , Belgium
| | - Carmen Monterroso
- a Department of Chemical Engineering , University of Santiago de Compostela , Campus Vida, Santiago de Compostela , Spain
| | - Jaco Vangronsveld
- b Centre for Environmental Sciences, University of Hasselt , Diepenbeek , Belgium
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15
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Yang S, Yu M, Chen J. Draft genome analysis of Dietzia sp. 111N12-1, isolated from the South China Sea with bioremediation activity. Braz J Microbiol 2017; 48:393-394. [PMID: 28347590 PMCID: PMC5498438 DOI: 10.1016/j.bjm.2016.10.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/28/2016] [Accepted: 10/05/2016] [Indexed: 12/03/2022] Open
Abstract
Dietzia sp. 111N12-1, isolated from the seawater of South China Sea, shows strong petroleum hydrocarbons degradation activity. Here, we report the draft sequence of approximately 3.7-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Dietzia strain isolated from the sea. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of hydrocarbons degradation in this strain.
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Affiliation(s)
- Shanjun Yang
- State Oceanic Administration, Third Institute of Oceanography, Engineering Research Center of Marine Biological Resource Comprehensive Utilization, Xiamen, Fujian Province, People's Republic of China
| | - Mingjia Yu
- State Oceanic Administration, Third Institute of Oceanography, Engineering Research Center of Marine Biological Resource Comprehensive Utilization, Xiamen, Fujian Province, People's Republic of China.
| | - Jianming Chen
- State Oceanic Administration, Third Institute of Oceanography, Engineering Research Center of Marine Biological Resource Comprehensive Utilization, Xiamen, Fujian Province, People's Republic of China
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16
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Isolation and Characterization of a Novel Electrogenic Bacterium, Dietzia sp. RNV-4. PLoS One 2017; 12:e0169955. [PMID: 28192491 PMCID: PMC5305051 DOI: 10.1371/journal.pone.0169955] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/27/2016] [Indexed: 11/30/2022] Open
Abstract
Electrogenic bacteria are organisms that can transfer electrons to extracellular electron acceptors and have the potential to be used in devices such as bioelectrochemical systems (BES). In this study, Dietzia sp. RNV-4 bacterium has been isolated and identified based on its biochemical, physiological and morphological characteristics, as well as by its 16S rRNA sequence analysis. Furthermore, the current density production and electron transfer mechanisms were investigated using bioelectrochemical methods. The chronoamperometric data showed that the biofilm of Dietzia sp. RNV-4 grew as the current increased with time, reaching a maximum of 176.6 ± 66.1 mA/m2 at the end of the experiment (7 d); this highly suggests that the current was generated by the biofilm. The main electron transfer mechanism, indicated by the cyclic voltammograms, was due to secreted redox mediators. By high performance liquid chromatography, canthaxanthin was identified as the main compound involved in charge transfer between the bacteria and the solid electrodes. Dietzia sp. RNV-4 was used as biological material in a microbial fuel cell (MFC) and the current density production was 299.4 ± 40.2 mA/m2. This is the first time that Dietzia sp. RNV-4 has been electrochemically characterized and identified as a new electrogenic strain.
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17
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18
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Dai X, Yan G, Guo S. Characterization of Dietzia cercidiphylli C-1 isolated from extra-heavy oil contaminated soil. RSC Adv 2017. [DOI: 10.1039/c7ra00786h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Dietzia cercidiphylliC-1 isolated from extra-heavy oil contaminated soil can efficiently degrade extra-heavy oil.
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Affiliation(s)
- Xiaoli Dai
- State Key Laboratory of Heavy Oil Processing
- Beijing Key Laboratory of Oil & Gas Pollution Control
- China University of Petroleum-Beijing
- Beijing 102249
- PR China
| | - Guangxu Yan
- State Key Laboratory of Heavy Oil Processing
- Beijing Key Laboratory of Oil & Gas Pollution Control
- China University of Petroleum-Beijing
- Beijing 102249
- PR China
| | - Shaohui Guo
- State Key Laboratory of Heavy Oil Processing
- Beijing Key Laboratory of Oil & Gas Pollution Control
- China University of Petroleum-Beijing
- Beijing 102249
- PR China
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19
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Feknous N, Branes Z, Rouabhia K, Batisson I, Amblard C. Isolation characterization and growth of locally isolated hydrocarbonoclastic marine bacteria (eastern Algerian coast). ENVIRONMENTAL MONITORING AND ASSESSMENT 2017; 189:49. [PMID: 28058612 DOI: 10.1007/s10661-016-5758-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/19/2016] [Indexed: 06/06/2023]
Abstract
The Algerian coastline is being exposed to several types of pollution, including that of hydrocarbons. This environment rich in oil could be the source of proliferation of hydrocarbonoclastic bacteria. The objective of the study is to isolate and identify indigenous bacterial strains from marine waters of two ports in the eastern Algerian coast and to test their growth in the presence of hydrocarbons with and without biostimulation throughout the intake of nitrogen and phosphate. Results recorded the highest level of both total hydrocarbons and phosphates in the port of Annaba, followed by El-Kala station and then the control station, while that of total nitrogen was vice versa. Fifty-three bacterial strains were identified from which four were selected to perform the growth tests. Results showed that the growth and the biodegradation differ from one species to another. Thus, the strains tested (Halomonas venusta NY-8, Exiguobacterium aurantiacum NB11-3A, Vibrio alginolyticus Pb-WC11099, and Dietzia sp. CNJ898 PL04) seem very active, in which better growth was obtained with the last two strains during nitrogen and phosphate supplementation. Such strains are suggested to participate a lot in the biodegradation of oil at polluted sites.
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Affiliation(s)
- N Feknous
- Laboratory of Microbiology, Department of Biochemistry, Faculty of Science, Badji Mokhtar University, BP 12, 23000, Annaba, Algeria
| | - Z Branes
- Laboratory of Microbiology, Department of Biochemistry, Faculty of Science, Badji Mokhtar University, BP 12, 23000, Annaba, Algeria.
| | - K Rouabhia
- Laboratory of Microbiology, Department of Biochemistry, Faculty of Science, Badji Mokhtar University, BP 12, 23000, Annaba, Algeria
| | - I Batisson
- Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France
- CNRS, UMR 6023, Laboratoire Microorganismes: Génome et Environnement, TSA 60026, CS 60026, 63178, Aubière Cedex, France
| | - C Amblard
- Clermont Université, Université Blaise Pascal, F-63000, Clermont-Ferrand, France
- CNRS, UMR 6023, Laboratoire Microorganismes: Génome et Environnement, TSA 60026, CS 60026, 63178, Aubière Cedex, France
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20
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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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21
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Nkem BM, Halimoon N, Yusoff FM, Johari WLW, Zakaria MP, Medipally SR, Kannan N. Isolation, identification and diesel-oil biodegradation capacities of indigenous hydrocarbon-degrading strains of Cellulosimicrobium cellulans and Acinetobacter baumannii from tarball at Terengganu beach, Malaysia. MARINE POLLUTION BULLETIN 2016; 107:261-268. [PMID: 27085593 DOI: 10.1016/j.marpolbul.2016.03.060] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/25/2016] [Accepted: 03/29/2016] [Indexed: 06/05/2023]
Abstract
In this study, we isolated two indigenous hydrocarbon-degrading bacteria from tarball found in Rhu Sepuluh beach, Terengganu, Malaysia. These bacteria were identified based on their physiological characteristic and 16S rRNA gene sequence analysis, and they showed 99% similarity with Cellulosimicrobium cellulans DSM 43879 and Acinetobacter baumannii ATCC 19606 respectively. Their hydrocarbon-degrading capabilities were tested using diesel-oil as sole carbon source. Results analysed using GC-MS, showed diesel-oil alkanes were degraded an average 64.4% by C. cellulans and 58.1% by A. baumannii with medium optical density reaching 0.967 (C. cellulans) and 1.515 (A. baumannii) in minimal salt media at 32°C for 10days. Individual diesel-oil alkanes were degraded between 10%-95.4% by C. cellulans and 0.2%-95.9% by A. baumannii. Both strains utilized diesel-oil for growth. The study suggests both strains are part of indigenous hydrocarbon-degrading bacteria in tarball with potential for bioremediation of oil-polluted marine environment.
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Affiliation(s)
- Bruno Martins Nkem
- Faculty of Environmental Studies, Department of Environmental Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Normala Halimoon
- Faculty of Environmental Studies, Department of Environmental Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia.
| | - Fatimah Md Yusoff
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Wan Lufti Wan Johari
- Faculty of Environmental Studies, Department of Environmental Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Mohamad Pauzi Zakaria
- Faculty of Environmental Studies, Department of Environmental Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Srikanth Reddy Medipally
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Narayanan Kannan
- Faculty of Environmental Studies, Department of Environmental Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
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22
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Alvarez VM, Jurelevicius D, Marques JM, de Souza PM, de Araújo LV, Barros TG, de Souza ROMA, Freire DMG, Seldin L. Bacillus amyloliquefaciens TSBSO 3.8, a biosurfactant-producing strain with biotechnological potential for microbial enhanced oil recovery. Colloids Surf B Biointerfaces 2015; 136:14-21. [DOI: 10.1016/j.colsurfb.2015.08.046] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/11/2015] [Accepted: 08/25/2015] [Indexed: 12/21/2022]
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23
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Kavynifard A, Ebrahimipour G, Ghasempour A. Optimization of crude oil degradation by Dietzia cinnamea KA1, capable of biosurfactant production. J Basic Microbiol 2015; 56:566-75. [PMID: 26615815 DOI: 10.1002/jobm.201500386] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 11/11/2015] [Indexed: 11/07/2022]
Abstract
The aim of this study was isolation and characterization of a crude oil degrader and biosurfactant-producing bacterium, along with optimization of conditions for crude oil degradation. Among 11 isolates, 5 were able to emulsify crude oil in Minimal Salt Medium (MSM) among which one isolate, named KA1, showed the highest potency for growth rate and biodegradation. The isolate was identified as Dietzia cinnamea KA1 using morphological and biochemical characteristics and 16S rRNA gene sequencing. The optimal conditions were 510 mM NaCl, pH 9.0, 35 °C, and minimal requirement of 46.5 mM NH4 Cl and 2.10 mM NaH2 PO4 . Gravimetric test and Gas chromatography-Mass spectroscopy technique (GC-MS) showed that Dietzia cinnamea KA1 was able to utilize and degrade 95.7% of the crude oil after 5 days, under the optimal conditions. The isolate was able to grow and produce biosurfactant when cultured in MSM supplemented with crude oil, glycerol or whey as the sole carbon sources, but bacterial growth was occurred using molasses with no biosurfactant production. This is the first report of biosurfactant production by D. cinnamea using crude oil, glycerol and whey and the first study to report a species of Dietzia degrading a wide range of hydrocarbons in a short time.
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Affiliation(s)
- Amirarsalan Kavynifard
- Department of Microbiology, Faculty of Biological Sciences, Shahid Beheshti University, Tehran, Iran
| | | | - Alireza Ghasempour
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
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24
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Shivlata L, Satyanarayana T. Thermophilic and alkaliphilic Actinobacteria: biology and potential applications. Front Microbiol 2015; 6:1014. [PMID: 26441937 PMCID: PMC4585250 DOI: 10.3389/fmicb.2015.01014] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.
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25
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Hvidsten I, Mjøs SA, Bødtker G, Barth T. Fatty acids in bacterium Dietzia sp. grown on simple and complex hydrocarbons determined as FAME by GC-MS. Chem Phys Lipids 2015; 190:15-26. [PMID: 26120076 DOI: 10.1016/j.chemphyslip.2015.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 05/07/2015] [Accepted: 06/18/2015] [Indexed: 11/29/2022]
Abstract
The influence of growth substrates on the fatty acids produced by Dietzia sp. A14101 has been studied to investigate how qualitative and semi-quantitative information on fatty acids correlates with the ability of this strain to access and utilize a wide range of water-immiscible HC-substrates by modifying the FA content and thus also the properties of the cellular membrane. After incubation on different substrates and media, the profiles of fatty acids (FA) were analyzed by gas chromatography and mass spectrometry (GC-MS). The equivalent chain length (ECL) index calibration system was employed to identify FA. The effect of each substrate on the cell surface charge and on the hydrophobicity of the cellular membrane was also investigated. The results indicate that the variation of the content of saturated fatty acids (SAT-FA) versus mono-unsaturated fatty acids (MUFA) was found to be the most pronounced while branched FA exhibited much less variation in spite of different substrate regimes. The regulation of the ratio of SAT-FA and MUFA seems to be coupled with the regulation of the charge and hydrophobicity of the outer cellular surface. The exposure to a water immiscible substrate led to the development of the negative cellular surface charge, production of carotenoid-type pigments and increased hydrophobicity of the cellular surface. The specific aspects of the adaptation mechanism could have implications for bioremediation and/or (M)EOR applications.
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Affiliation(s)
- Ina Hvidsten
- Department of Chemistry, University of Bergen, Allégaten 41, 5007 Bergen, Norway.
| | - Svein Are Mjøs
- Department of Chemistry, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Gunhild Bødtker
- Uni Research CIPR, Uni Research, P.O. Box 7810, 5020 Bergen, Norway
| | - Tanja Barth
- Department of Chemistry, University of Bergen, Allégaten 41, 5007 Bergen, Norway
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Nazina TN, Shumkova ES, Sokolova DS, Babich TL, Zhurina MV, Xue YF, Osipov GA, Poltaraus AB, Tourova TP. Identification of hydrocarbon-oxidizing Dietzia bacteria from petroleum reservoirs based on phenotypic properties and analysis of the 16S rRNA and gyrB genes. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715030145] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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27
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Wang W, Cai B, Shao Z. Oil degradation and biosurfactant production by the deep sea bacterium Dietzia maris As-13-3. Front Microbiol 2014; 5:711. [PMID: 25566224 PMCID: PMC4267283 DOI: 10.3389/fmicb.2014.00711] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/29/2014] [Indexed: 11/29/2022] Open
Abstract
Recent investigations of extreme environments have revealed numerous bioactive natural products. However, biosurfactant-producing strains from deep sea extreme environment are largely unknown. Here, we show that Dietzia maris As-13-3 isolated from deep sea hydrothermal field could produce di-rhamnolipid as biosurfactant. The critical micelle concentration (CMC) of the purified di-rhamnolipid was determined to be 120 mgL−1, and it lowered the surface tension of water from 74 ± 0.2 to 38 ± 0.2 mN m−1. Further, the alkane metabolic pathway-related genes and di-rhamnolipid biosynthesis-related genes were also analyzed by the sequencing genome of D. maris As-13-3 and quantitative real-time PCR (Q-PCR), respectively. Q-PCR analysis showed that all these genes were induced by n-Tetradecane, n-Hexadecane, and pristane. To the best of our knowledge, this is first report about the complete pathway of the di-rhamnolipid synthesis process in the genus Dietzia. Thus, our study provided the insights into Dietzia in respects of oil degradation and biosurfactant production, and will help to evaluate the potential of Dietzia in marine oil removal.
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Affiliation(s)
- Wanpeng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration Xiamen, China ; State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration Xiamen, China ; Collaborative Innovation Center of Deep Sea Biology, Third Institute of Oceanography, State Oceanic Administration Xiamen, China ; Key Laboratory of Marine Genetic Resources of Fujian Province Xiamen, China ; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources Xiamen, China
| | - Bobo Cai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration Xiamen, China ; State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration Xiamen, China ; Collaborative Innovation Center of Deep Sea Biology, Third Institute of Oceanography, State Oceanic Administration Xiamen, China ; Key Laboratory of Marine Genetic Resources of Fujian Province Xiamen, China ; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources Xiamen, China ; Life Science College, Xiamen University Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration Xiamen, China ; State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration Xiamen, China ; Collaborative Innovation Center of Deep Sea Biology, Third Institute of Oceanography, State Oceanic Administration Xiamen, China ; Key Laboratory of Marine Genetic Resources of Fujian Province Xiamen, China ; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources Xiamen, China
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28
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Wang W, Cai B, Shao Z. Oil degradation and biosurfactant production by the deep sea bacterium Dietzia maris As-13-3. Front Microbiol 2014. [DOI: 10.3389/fmicb.2014.00711 pmid: 25566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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29
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Dellagnezze BM, de Sousa GV, Martins LL, Domingos DF, Limache EEG, de Vasconcellos SP, da Cruz GF, de Oliveira VM. Bioremediation potential of microorganisms derived from petroleum reservoirs. MARINE POLLUTION BULLETIN 2014; 89:191-200. [PMID: 25457810 DOI: 10.1016/j.marpolbul.2014.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 10/03/2014] [Accepted: 10/04/2014] [Indexed: 06/04/2023]
Abstract
Bacterial strains and metagenomic clones, both obtained from petroleum reservoirs, were evaluated for petroleum degradation abilities either individually or in pools using seawater microcosms for 21 days. Gas Chromatography-Flame Ionization Detector (GC-FID) and Gas Chromatography-Mass Spectrometry (GC-MS) analyses were carried out to evaluate crude oil degradation. The results showed that metagenomic clones 1A and 2B were able to biodegrade n-alkanes (C14 to C33) and isoprenoids (phytane and pristane), with rates ranging from 31% to 47%, respectively. The bacteria Dietzia maris CBMAI 705 and Micrococcus sp. CBMAI 636 showed higher rates reaching 99% after 21 days. The metagenomic clone pool biodegraded these compounds at rates ranging from 11% to 45%. Regarding aromatic compound biodegradation, metagenomic clones 2B and 10A were able to biodegrade up to 94% of phenanthrene and methylphenanthrenes (3-MP, 2-MP, 9-MP and 1-MP) with rates ranging from 55% to 70% after 21 days, while the bacteria Dietzia maris CBMAI 705 and Micrococcus sp. CBMAI 636 were able to biodegrade 63% and up to 99% of phenanthrene, respectively, and methylphenanthrenes (3-MP, 2-MP, 9-MP and 1-MP) with rates ranging from 23% to 99% after 21 days. In this work, isolated strains as well as metagenomic clones were capable of degrading several petroleum compounds, revealing an innovative strategy and a great potential for further biotechnological and bioremediation applications.
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Affiliation(s)
- Bruna Martins Dellagnezze
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, CEP 13148-218, Paulinia, Brazil
| | - Gabriel Vasconcelos de Sousa
- Laboratory of Engineering and Petroleum Exploration, Darcy Ribeiro North Fluminense State University - LENEP/UENF, POB 119562, 27910-970 Macaé, RJ, Brazil
| | - Laercio Lopes Martins
- Laboratory of Engineering and Petroleum Exploration, Darcy Ribeiro North Fluminense State University - LENEP/UENF, POB 119562, 27910-970 Macaé, RJ, Brazil
| | - Daniela Ferreira Domingos
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, CEP 13148-218, Paulinia, Brazil
| | - Elmer E G Limache
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, CEP 13148-218, Paulinia, Brazil
| | | | - Georgiana Feitosa da Cruz
- Laboratory of Engineering and Petroleum Exploration, Darcy Ribeiro North Fluminense State University - LENEP/UENF, POB 119562, 27910-970 Macaé, RJ, Brazil
| | - Valéria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, CEP 13148-218, Paulinia, Brazil.
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Lu S, Nie Y, Tang YQ, Xiong G, Wu XL. A critical combination of operating parameters can significantly increase the electrotransformation efficiency of a gram-positive Dietzia strain. J Microbiol Methods 2014; 103:144-51. [DOI: 10.1016/j.mimet.2014.05.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 12/21/2022]
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Procópio L, de Cassia Pereira e Silva M, van Elsas JD, Seldin L. Transcriptional profiling of genes involved in n-hexadecane compounds assimilation in the hydrocarbon degrading Dietzia cinnamea P4 strain. Braz J Microbiol 2013; 44:633-41. [PMID: 24294263 PMCID: PMC3833169 DOI: 10.1590/s1517-83822013000200044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 07/23/2012] [Indexed: 11/24/2022] Open
Abstract
The petroleum-derived degrading Dietzia cinnamea strain P4 recently had its genome sequenced and annotated. This allowed employing the data on genes that are involved in the degradation of n-alkanes. To examine the physiological behavior of strain P4 in the presence of n-alkanes, the strain was grown under varying conditions of pH and temperature. D. cinnamea P4 was able to grow at pH 7.0–9.0 and at temperatures ranging from 35 ºC to 45 ºC. Experiments of gene expression by real-time quantitative RT-PCR throughout the complete growth cycle clearly indicated the induction of the regulatory gene alkU (TetR family) during early growth. During the logarithmic phase, a large increase in transcriptional levels of a lipid transporter gene was noted. Also, the expression of a gene that encodes the protein fused rubredoxin-alkane monooxygenase was enhanced. Both genes are probably under the influence of the AlkU regulator.
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Affiliation(s)
- Luciano Procópio
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Ilha do Fundão, Rio de Janeiro, RJ, Brazil. ; Department of Microbial Ecology, University of Groningen, Kerklaan, Haren, The Netherlands
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Jurelevicius D, Alvarez VM, Peixoto R, Rosado AS, Seldin L. The Use of a Combination of alkB Primers to Better Characterize the Distribution of Alkane-Degrading Bacteria. PLoS One 2013; 8:e66565. [PMID: 23825163 PMCID: PMC3688950 DOI: 10.1371/journal.pone.0066565] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/08/2013] [Indexed: 11/22/2022] Open
Abstract
The alkane monooxygenase AlkB, which is encoded by the alkB gene, is a key enzyme involved in bacterial alkane degradation. To study the alkB gene within bacterial communities, researchers need to be aware of the variations in alkB nucleotide sequences; a failure to consider the sequence variations results in the low representation of the diversity and richness of alkane-degrading bacteria. To minimize this shortcoming, the use of a combination of three alkB-targeting primers to enhance the detection of the alkB gene in previously isolated alkane-degrading bacteria was proposed. Using this approach, alkB-related PCR products were detected in 79% of the strains tested. Furthermore, the chosen set of primers was used to study alkB richness and diversity in different soils sampled in Carmópolis, Brazil and King George Island, Antarctica. The DNA extracted from the different soils was PCR amplified with each set of alkB-targeting primers, and clone libraries were constructed, sequenced and analyzed. A total of 255 alkB phylotypes were detected. Venn diagram analyses revealed that only low numbers of alkB phylotypes were shared among the different libraries derived from each primer pair. Therefore, the combination of three alkB-targeting primers enhanced the richness of alkB phylotypes detected in the different soils by 45% to 139%, when compared to the use of a single alkB-targeting primer. In addition, a dendrogram analysis and beta diversity comparison of the alkB composition showed that each of the sampling sites studied had a particular set of alkane-degrading bacteria. The use of a combination of alkB primers was an efficient strategy for enhancing the detection of the alkB gene in cultivable bacteria and for better characterizing the distribution of alkane-degrading bacteria in different soil environments.
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Affiliation(s)
- Diogo Jurelevicius
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vanessa Marques Alvarez
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Peixoto
- Laboratório de Ecologia Molecular Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre S. Rosado
- Laboratório de Ecologia Molecular Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucy Seldin
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Zhou X, Xin ZJ, Lu XH, Yang XP, Zhao MR, Wang L, Liang JP. High efficiency degradation crude oil by a novel mutant irradiated from Dietzia strain by 12C6+ heavy ion using response surface methodology. BIORESOURCE TECHNOLOGY 2013; 137:386-393. [PMID: 23603188 DOI: 10.1016/j.biortech.2013.03.097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/03/2013] [Accepted: 03/06/2013] [Indexed: 06/02/2023]
Abstract
Crude oil is an extremely complex mixture of hydrocarbons; also contaminate environmental, leading to carcinogenic, teratogenic and mutagenic. Petroleum hydrocarbons degradation Dietzia strain DMYR9 was isolated from oilfield. Response surface methodology was applied for statistical designing of process parameters for dry weight of biomass production in the process of degradation. The optimization process parameters were successfully employed for degradation crude oil and confirmed through confirmatory experiments. On 28th day, analysis was done by GC-MS, These data show that the crude oil samples of n-Hexadecane, Octadecane, n-Nonadecanec, n-Pentacosane, n-Hexacosane, n-Heneicosane, n-Docosane, n-Tetracosane, n-Octacosane and Tetraethyl removal efficiency could reach up to 0%. RSM optimization and use of effective (12)C(6+)-ion irradiation methods can considerably enhance ability to degradation of microbial. Hence, bioresource Dietzia strain DMYR9, high ability to degradation, can be further used for subsequent repair hydrocarbons polluted of environment.
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Affiliation(s)
- Xiang Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China
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Characterization of a CYP153 alkane hydroxylase gene in a Gram-positive Dietzia sp. DQ12-45-1b and its "team role" with alkW1 in alkane degradation. Appl Microbiol Biotechnol 2013; 98:163-73. [PMID: 23504079 DOI: 10.1007/s00253-013-4821-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 02/26/2013] [Indexed: 01/07/2023]
Abstract
CYP153 and AlkB-like hydroxylases were recently discovered in Gram-positive alkane-degrading bacteria. However, it is unclear whether they cooperate with each other in alkane degradation as they do in Gram-negative bacteria. In this paper, we cloned the CYP153 gene from a representative Gram-positive alkane-degrading bacterium, Dietzia sp. DQ12-45-1b. The CYP153 gene transcription in Dietzia sp. DQ12-45-1b and heterologous expression in alkB gene knockout mutant strain Pseudomonas fluorescens KOB2∆1 both confirmed the functions of CYP153 on C6-C10 n-alkanes degradation, but not on longer chain-length n-alkanes. In addition, substrate-binding analysis of the purified CYP153 protein revealed different substrate affinities to C6-C16 n-alkanes, confirming n-alkanes binding to CYP153 protein. Along with AlkW1, an AlkB-like alkane hydroxylase in Dietzia sp. DQ12-45-1b, a teamwork pattern was found in n-alkane degradation, i.e. CYP153 was responsible for hydroxylating n-alkanes shorter than C10 while AlkW1 was responsible for those longer than C14. Further sequence analysis suggested that the high horizontal gene transfer (HGT) potential of CYP153 genes may be universal in Gram-positive alkane-degrading actinomycetes that contain both alkB and CYP153 genes.
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Jin Q, Hu Z, Jin Z, Qiu L, Zhong W, Pan Z. Biodegradation of aniline in an alkaline environment by a novel strain of the halophilic bacterium, Dietzia natronolimnaea JQ-AN. BIORESOURCE TECHNOLOGY 2012; 117:148-154. [PMID: 22613890 DOI: 10.1016/j.biortech.2012.04.068] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 06/01/2023]
Abstract
Dietzia natronolimnaea JQ-AN was isolated from industrial wastewater containing aniline. Under aerobic conditions, the JQ-AN strain degraded 87% of the aniline in a 300 mg L(-1) aniline solution after 120 h of shake flask incubation in a medium containing sodium acetate. This strain had an unusually high salinity tolerance in minimal medium (0-6% NaCl, w/v). The optimal pH for microbial growth and aniline biodegradation was pH 8.0. Two liters of simulated aniline wastewater was created in a reactor at pH 8.0 and 3% NaCl (w/v), and biodegradation of aniline was tested over 7 days at 30 °C. For the initial concentrations of 100, 300, and 500 mg L(-1), 100%, 80.5% and 72% of the aniline was degraded, respectively. Strain JQ-AN may use an ortho-cleavage pathway for dissimilation of the catechol intermediate.
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Affiliation(s)
- Qiong Jin
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, PR China
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Tuo BH, Yan JB, Fan BA, Yang ZH, Liu JZ. Biodegradation characteristics and bioaugmentation potential of a novel quinoline-degrading strain of Bacillus sp. isolated from petroleum-contaminated soil. BIORESOURCE TECHNOLOGY 2012; 107:55-60. [PMID: 22243925 DOI: 10.1016/j.biortech.2011.12.114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/06/2011] [Accepted: 12/06/2011] [Indexed: 05/11/2023]
Abstract
Quinoline and its derivatives are widely considered to be environmental pollutants. In this study, the biodegradation characteristics and bioaugmentation potential for a novel strain were described. The strain, named Q2, which could utilize quinoline as the sole carbon, nitrogen and energy source, was isolated and identified as a Bacillus sp. The optimum temperature, initial pH and shaker rotary speed for quinoline degradation were 30°C, pH 8-10 and 100-200 rpm, respectively. During the biodegradation process, the quinoline-N was released as ammonium and the culture broth became yellow, pink and brown in turn, which indicated that several intermediates were generated. GC/MS analysis showed that 2(1H)-quinolinone and 8-hydroxycoumarin were produced. Furthermore, the bioaugmentation of Q2 into the sludge consortium, which was taken from refinery wastewater treatment plant, to degrade quinoline was investigated. The results showed that it could coexist with the other microbes and the remarkably enhanced quinoline biodegradation ability was achieved.
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Affiliation(s)
- Bao-hua Tuo
- College of Chemical Engineering and Technology, Wuhan University of Science and Technology, Wuhan 430081, People's Republic of China
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Nie Y, Liang J, Fang H, Tang YQ, Wu XL. Two novel alkane hydroxylase-rubredoxin fusion genes isolated from a Dietzia bacterium and the functions of fused rubredoxin domains in long-chain n-alkane degradation. Appl Environ Microbiol 2011; 77:7279-88. [PMID: 21873474 PMCID: PMC3194844 DOI: 10.1128/aem.00203-11] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 08/19/2011] [Indexed: 11/20/2022] Open
Abstract
Two alkane hydroxylase-rubredoxin fusion gene homologs (alkW1 and alkW2) were cloned from a Dietzia strain, designated DQ12-45-1b, which can grow on crude oil and n-alkanes ranging in length from 6 to 40 carbon atoms as sole carbon sources. Both AlkW1 and AlkW2 have an integral-membrane alkane monooxygenase (AlkB) conserved domain and a rubredoxin (Rd) conserved domain which are fused together. Phylogenetic analysis showed that these two AlkB-fused Rd domains formed a novel third cluster with all the Rds from the alkane hydroxylase-rubredoxin fusion gene clusters in Gram-positive bacteria and that this third cluster was distant from the known AlkG1- and AlkG2-type Rds. Expression of the alkW1 gene in DQ12-45-1b was induced when cells were grown on C(8) to C(32) n-alkanes as sole carbon sources, but expression of the alkW2 gene was not detected. Functional heterologous expression in an alkB deletion mutant of Pseudomonas fluorescens KOB2Δ1 suggested the alkW1 could restore the growth of KOB2Δ1 on C(14) and C(16) n-alkanes and induce faster growth on C(18) to C(32) n-alkanes than alkW1ΔRd, the Rd domain deletion mutant gene of alkW1, which also caused faster growth than KOB2Δ1 itself. In addition, the artificial fusion of AlkB from the Gram-negative P. fluorescens CHA0 and the Rds from both Gram-negative P. fluorescens CHA0 and Gram-positive Dietzia sp. DQ12-45-1b significantly increased the degradation of C(32) alkane compared to that seen with AlkB itself. In conclusion, the alkW1 gene cloned from Dietzia species encoded an alkane hydroxylase which increased growth on and degradation of n-alkanes up to C(32) in length, with its fused rubredoxin domain being necessary to maintain the functions. In addition, the fusion of alkane hydroxylase and rubredoxin genes from both Gram-positive and -negative bacteria can increase the degradation of long-chain n-alkanes (such as C(32)) in the Gram-negative bacterium.
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Affiliation(s)
- Yong Nie
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Jieliang Liang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Hui Fang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Yue-Qin Tang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
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Procópio L, Alvarez VM, Jurelevicius DA, Hansen L, Sørensen SJ, Cardoso JS, Pádula M, Leitão ÁC, Seldin L, van Elsas JD. Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential. Antonie van Leeuwenhoek 2011; 101:289-302. [PMID: 21901521 PMCID: PMC3261415 DOI: 10.1007/s10482-011-9633-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 08/20/2011] [Indexed: 01/17/2023]
Abstract
The draft genome of Dietzia cinnamea strain P4 was determined using pyrosequencing. In total, 428 supercontigs were obtained and analyzed. We here describe and interpret the main features of the draft genome. The genome contained a total of 3,555,295 bp, arranged in a single replicon with an average G+C percentage of 70.9%. It revealed the presence of complete pathways for basically all central metabolic routes. Also present were complete sets of genes for the glyoxalate and reductive carboxylate cycles. Autotrophic growth was suggested to occur by the presence of genes for aerobic CO oxidation, formate/formaldehyde oxidation, the reverse tricarboxylic acid cycle and the 3-hydropropionate cycle for CO2 fixation. Secondary metabolism was evidenced by the presence of genes for the biosynthesis of terpene compounds, frenolicin, nanaomycin and avilamycin A antibiotics. Furthermore, a probable role in azinomycin B synthesis, an important product with antitumor activity, was indicated. The complete alk operon for the degradation of n-alkanes was found to be present, as were clusters of genes for biphenyl ring dihydroxylation. This study brings new insights in the genetics and physiology of D. cinnamea P4, which is useful in biotechnology and bioremediation.
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Affiliation(s)
- Luciano Procópio
- Microbial Ecology Laboratory, Department of Microbial Ecology, CEES, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
- Laboratório de Genética Microbiana, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde (CCS), Ilha do Fundão, Rio de Janeiro, RJ 21941-901 Brazil
| | - Vanessa M. Alvarez
- Laboratório de Genética Microbiana, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde (CCS), Ilha do Fundão, Rio de Janeiro, RJ 21941-901 Brazil
| | - Diogo A. Jurelevicius
- Laboratório de Genética Microbiana, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde (CCS), Ilha do Fundão, Rio de Janeiro, RJ 21941-901 Brazil
| | - Lars Hansen
- Department of Microbiology, Institute of Biology, University of Copenhagen, Sølvgade 83H, 1307 Copenhagen, Denmark
| | - Søren J. Sørensen
- Department of Microbiology, Institute of Biology, University of Copenhagen, Sølvgade 83H, 1307 Copenhagen, Denmark
| | - Janine S. Cardoso
- Laboratório de Diagnóstico Molecular e Hematologia, Faculdade de Farmácia, UFRJ, CCS, Ilha do Fundão, Rio de Janeiro, RJ 21941-540 Brazil
| | - Marcelo Pádula
- Laboratório de Diagnóstico Molecular e Hematologia, Faculdade de Farmácia, UFRJ, CCS, Ilha do Fundão, Rio de Janeiro, RJ 21941-540 Brazil
| | - Álvaro C. Leitão
- Laboratório de Radiobiologia Molecular, Instituto de Biofísica Carlos Chagas Filho, UFRJ, CCS, Ilha do Fundão, Rio de Janeiro, RJ 21941-540 Brazil
| | - Lucy Seldin
- Laboratório de Genética Microbiana, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde (CCS), Ilha do Fundão, Rio de Janeiro, RJ 21941-901 Brazil
| | - Jan Dirk van Elsas
- Microbial Ecology Laboratory, Department of Microbial Ecology, CEES, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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Wang XB, Chi CQ, Nie Y, Tang YQ, Tan Y, Wu G, Wu XL. Degradation of petroleum hydrocarbons (C6-C40) and crude oil by a novel Dietzia strain. BIORESOURCE TECHNOLOGY 2011; 102:7755-7761. [PMID: 21715162 DOI: 10.1016/j.biortech.2011.06.009] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 06/03/2011] [Accepted: 06/04/2011] [Indexed: 05/31/2023]
Abstract
A novel bacterial strain, DQ12-45-1b, was isolated from the production water of a deep subterranean oil-reservoir. Morphological, physiological and phylogenetic analyses indicated that the strain belonged to the genus Dietzia with both alkB (coding for alkane monooxygenase) and CYP153 (coding for P450 alkane hydroxylase of the cytochrome CYP153 family) genes and their induction detected. It was capable of utilizing a wide range of n-alkanes (C6-C40), aromatic compounds and crude oil as the sole carbon sources for growth. In addition, it preferentially degraded short-chain hydrocarbons (≤C25) in the early cultivation phase and accumulated hydrocarbons with chain-lengths from C23 to C27 during later cultivation stage with crude oil as the sole carbon source. This is the first study to report the different behaviors of a bacterial species toward crude oil degradation as well as a species of Dietzia degrading a wide range of hydrocarbons.
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Affiliation(s)
- Xing-Biao Wang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China
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Alonso-Gutiérrez J, Teramoto M, Yamazoe A, Harayama S, Figueras A, Novoa B. Alkane-degrading properties of Dietzia sp. H0B, a key player in the Prestige oil spill biodegradation (NW Spain). J Appl Microbiol 2011; 111:800-10. [PMID: 21767337 DOI: 10.1111/j.1365-2672.2011.05104.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS Investigation of the alkane-degrading properties of Dietzia sp. H0B, one of the isolated Corynebacterineae strains that became dominant after the Prestige oil spill. METHODS AND RESULTS Using molecular and chemical analyses, the alkane-degrading properties of strain Dietzia sp. H0B were analysed. This Grampositive isolate was able to grow on n-alkanes ranging from C₁₂ to C₃₈ and branched alkanes (pristane and phytane). 8-Hexadecene was detected as an intermediate of hexadecane degradation by Dietzia H0B, suggesting a novel alkane-degrading pathway in this strain. Three putative alkane hydroxylase genes (one alkB homologue and two CYP153 gene homologues of cytochrome P450 family) were PCR-amplified from Dietzia H0B and differed from previously known hydroxylase genes, which might be related to the novel degrading activity observed on Dietzia H0B. The alkane degradation activity and the alkB and CYP153 gene expression were observed constitutively regardless of the presence of the substrate, suggesting additional, novel pathways for alkane degradation. CONCLUSIONS The results from this study suggest novel alkane-degrading pathways in Dietzia H0B and a genetic background coding for two different putative oil-degrading enzymes, which is mostly unexplored and worth to be subject of further functional analysis. SIGNIFICANCE AND IMPACT OF THE STUDY This study increases the scarce information available about the genetic background of alkane degradation in genus Dietzia and suggests new pathways and novel expression mechanisms of alkane degradation.
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Nakano M, Kihara M, Iehata S, Tanaka R, Maeda H, Yoshikawa T. Wax ester-like compounds as biosurfactants produced by Dietzia maris from n -alkane as a sole carbon source. J Basic Microbiol 2011; 51:490-8. [DOI: 10.1002/jobm.201000420] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 12/23/2010] [Indexed: 11/07/2022]
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Bihari Z, Szvetnik A, Szabó Z, Blastyák A, Zombori Z, Balázs M, Kiss I. Functional analysis of long-chain n-alkane degradation by Dietzia spp. FEMS Microbiol Lett 2011; 316:100-7. [DOI: 10.1111/j.1574-6968.2010.02198.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Szvetnik A, Bihari Z, Szabó Z, Kelemen O, Kiss I. Genetic manipulation tools for Dietzia spp. J Appl Microbiol 2010; 109:1845-52. [PMID: 20666867 DOI: 10.1111/j.1365-2672.2010.04818.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM To develop an applicable vector system and a transformation method for the manipulation of Dietzia spp. METHODS AND RESULTS The pNV18 Nocardia-E. coli shuttle vector was tested and found to be a replicating plasmid in Dietzia sp. E1. With the use of pNV18, an electroporation method was optimized for the transformation of Dietzia sp. E1, and a transformation efficiency suitable for genetic manipulations was achieved (2·18×10(4) transformants μg(-1) DNA). The method was also applied for the transformation of Dietzia cinnamea, D. maris, D. natronolimnaea and D. psychralcaliphila. CONCLUSIONS The first applicable vectors and a simple electroporation protocol enabling the manipulation of several Dietzia spp. are presented. SIGNIFICANCE AND IMPACT OF THE STUDY Dietzia spp. have clinical, industrial and great environmental importance; however, the analysis of the Dietzia genus is currently hampered by the lack of manipulation techniques. The presented basic tools allow the genetic analysis of several Dietzia species, including the human disease-associated Dietzia maris.
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Affiliation(s)
- A Szvetnik
- Institute for Biotechnology, Bay Zoltán Foundation for Applied Research, Szeged, Hungary.
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Hydrocarbon degradation by Dietzia sp. A14101 isolated from an oil reservoir model column. Antonie van Leeuwenhoek 2009; 96:459-69. [PMID: 19565350 DOI: 10.1007/s10482-009-9359-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 06/11/2009] [Indexed: 10/20/2022]
Abstract
The hydrocarbon-degrading strain Dietzia sp. A14101 was isolated from an oil reservoir model column inoculated with oil-field bacteria. The column was continuously injected with nitrate (0.5 mM) from the start of water flooding, which lead to a gradual development of nitrate reduction in the column. Strain A14101 was able to utilize a range of aliphatic hydrocarbons as sole carbon and energy source during aerobic growth. Whole oil gas chromatography analysis of the crude oil phase from aerobic pure cultures showed that strain A14101 utilized the near complete range of aliphatic components and aromatic components toluene and xylene. Longer n-alkanes >/=C(17) were utilized simultaneously with the shorter C(10) and C(15). After 120 days aerobic incubation, the whole oil gas chromatography profile of the crude oil phase was similar to that of heavily biodegraded oils. Anaerobic degradation of hydrocarbons with nitrate was not observed. Nitrate reduction was, however, observed during anaerobic growth on propionate, which suggests that strain A14101 grows on fatty acids in the column rather than on hydrocarbons.
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Koerner RJ, Goodfellow M, Jones AL. The genus Dietzia: a new home for some known and emerging opportunist pathogens. ACTA ACUST UNITED AC 2009; 55:296-305. [PMID: 19159434 DOI: 10.1111/j.1574-695x.2008.00513.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The genus Dietzia has only been established fairly recently. The Gram morphology and colony appearance of the species of this genus is remarkably similar to Rhodococcus equi. In the absence of simple, accurate methods for their identification, Dietzia spp. might have been misidentified as a Rhodococcus spp. and/or considered to be contaminants only. This MiniReview is designed to summarize current evidence on the clinical significance of Dietzia species, to consider their potential role as human pathogens, and to outline approaches that can be used to accurately classify and identify members of the genus, with the overall aim of alerting the medical microbiological community to a little known genus that contains clinically significant organisms.
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Affiliation(s)
- Roland J Koerner
- Department of Microbiology, Sunderland Royal Hospital, Sunderland, UK.
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Freitas D, Lima-Bittencourt C, Reis M, Costa P, Assis P, Chartone-Souza E, Nascimento A. Molecular characterization of early colonizer bacteria from wastes in a steel plant. Lett Appl Microbiol 2008; 47:241-9. [DOI: 10.1111/j.1472-765x.2008.02415.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Iwaki H, Nakai E, Nakamura S, Hasegawa Y. Isolation and Characterization of New Cyclohexylacetic Acid-Degrading Bacteria. Curr Microbiol 2008; 57:107-10. [DOI: 10.1007/s00284-008-9158-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 02/26/2008] [Indexed: 10/22/2022]
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Wentzel A, Ellingsen TE, Kotlar HK, Zotchev SB, Throne-Holst M. Bacterial metabolism of long-chain n-alkanes. Appl Microbiol Biotechnol 2007; 76:1209-21. [PMID: 17673997 DOI: 10.1007/s00253-007-1119-1] [Citation(s) in RCA: 207] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2007] [Revised: 07/10/2007] [Accepted: 07/11/2007] [Indexed: 10/23/2022]
Abstract
Degradation of alkanes is a widespread phenomenon in nature, and numerous microorganisms, both prokaryotic and eukaryotic, capable of utilizing these substrates as a carbon and energy source have been isolated and characterized. In this review, we summarize recent advances in the understanding of bacterial metabolism of long-chain n-alkanes. Bacterial strategies for accessing these highly hydrophobic substrates are presented, along with systems for their enzymatic degradation and conversion into products of potential industrial value. We further summarize the current knowledge on the regulation of bacterial long-chain n-alkane metabolism and survey progress in understanding bacterial pathways for utilization of n-alkanes under anaerobic conditions.
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Affiliation(s)
- Alexander Wentzel
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Saelandsvei 6/8, 7491 Trondheim, Norway.
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