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Wang Q, Hou J, Huang Y, Liu W, Christie P. Metagenomics reveals mechanism of pyrene degradation by an enriched bacterial consortium from a coking site contaminated with PAHs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166759. [PMID: 37659531 DOI: 10.1016/j.scitotenv.2023.166759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
A bacterial consortium, termed WPB, was obtained from polycyclic aromatic hydrocarbons (PAHs) contaminated soil from a coking site. The consortium effectively degraded 100 mg L-1 pyrene by 94.8 % within 12 days. WPB was also able to degrade phenanthrene (98.3 %) and benzo[a]pyrene (24.6 %) in 12 days, while the individual isolates showed no PAHs degrading ability. Paracoccus sp. dominated the bacterial consortium (65.0-86.2 %) throughout the degradation process. Metagenomic sequencing reveals the proportion of sequences with xenobiotics biodegradation and metabolism increased throughout the degradation process indicating the great potential of WPB to degrade pollutants. The annotation of genes by metagenomic analysis help reconstruct the degradation pathways ("phthalate pathway" and "naphthalene degradation") and reveal how different bacteria contribute to the degradation process. Mycobacterium gilvum was found to carry nidAB genes that catalyze the first step of high-molecular-weight (HMW) PAHs in the degradation process despite Mycobacterium gilvum accounting for only 0.005-0.06 %. In addition, genomes of Paracoccus denitrificans and some other genera affiliated with Devosia, Pusillimonas caeni and Eoetvoesia caeni were successfully recovered and were found to carry genes responsible for the degradation of the intermediates of pyrene. These results enable further understanding of the metabolic patterns of pyrene-degrading consortia and provide direction for further cultivation and discovery of key players in complex microbial consortia.
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Affiliation(s)
- Qingling Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyu Hou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ya Huang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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Pulikova E, Ivanov F, Gorovtsov A, Dudnikova T, Zinchenko V, Minkina T, Mandzhieva S, Barahov A, Sherbakov A, Sushkova S. Microbiological status of natural and anthropogenic soils of the Taganrog Bay coast at different levels of combined pollution with heavy metals and PAHs. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:9373-9390. [PMID: 36436180 DOI: 10.1007/s10653-022-01405-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
The effect of heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) pollution on the microbiological status of soils on the coast of the Taganrog Bay and adjacent areas was studied. The content of total and exchangeable forms of HMs, the content of 16 priority PAHs and the abundance of several groups of culturable microorganisms was determined, namely copiotrophic, prototrophic, aerobic spore-forming bacteria, actinomycetes, molds and yeasts. The content of total and exchangeable forms of HMs in urban coastal soils in industrial zone significantly exceeded that in non-urban soils. The maximum concentrations of total forms of Mn, Cr, Ni, Cu, Zn, Pb and Cd are 1821, 871, 143, 89, 1390, 317 and 10 mg/kg, respectively. The median value of the total content of 16 PAHs in urban soils is 3 times higher than in the soils of natural areas and reached 4309 ng/g. The lowest numbers of copiotrophic bacteria, prototrophic bacteria and aerobic spore-forming bacteria were found in the soils of industrial zone: 6.8, 13.8 and 0.63 million CFU g-1 dry soil, respectively. The largest numbers of copiotrophic bacteria, prototrophic bacteria and aerobic spore-forming bacteria were recorded in the soils of natural areas-72.5, 136 and 5.73 million CFU g-1 dry soil, respectively. It was found that the abundance of copiotrophs, prototrophs, and aerobic spore-forming bacteria is more affected by the urbanization of coastal soils including the pollution of HMs and PAHs. Other groups of microorganisms (actinomycetes, molds and yeasts) turned out to be more resistant to anthropogenic factors.
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Affiliation(s)
| | - Fedor Ivanov
- Southern Federal University, Rostov-on-Don, Russian Federation, 344090
| | - Andrey Gorovtsov
- Southern Federal University, Rostov-on-Don, Russian Federation, 344090
| | - Tamara Dudnikova
- Southern Federal University, Rostov-on-Don, Russian Federation, 344090
| | | | - Tatiana Minkina
- Southern Federal University, Rostov-on-Don, Russian Federation, 344090
| | | | - Anatoly Barahov
- Southern Federal University, Rostov-on-Don, Russian Federation, 344090
| | - Alexey Sherbakov
- Southern Federal University, Rostov-on-Don, Russian Federation, 344090
| | - Svetlana Sushkova
- Southern Federal University, Rostov-on-Don, Russian Federation, 344090.
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Genomic Analysis of Surfactant-Producing Bacillus vallismortis TIM68: First Glimpse at Species Pangenome and Prediction of New Plipastatin-Like Lipopeptide. Appl Biochem Biotechnol 2023; 195:753-771. [PMID: 36166154 DOI: 10.1007/s12010-022-04154-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2022] [Indexed: 01/24/2023]
Abstract
Surfactants are applied in several industrial processes when the modification of interface activity and the stability of colloidal systems are required. Lipopeptides are a class of microbial biosurfactants produced by species of the Bacillus genus. The present study aimed at assembling and analyzing the genome of a new Bacillus vallismortis strain, TIM68, that was shown to produce surfactant lipopeptides. The draft genome was also screened for common virulence factors and antibiotics resistance genes to investigate the strain biosafety. Comparative genomics analyses, i.e., synteny, average nucleotide identity (ANI), and pangenome, were also carried out using strain TIM68 and publicly available B. vallismortis complete and partial genomes. Three peptide synthetase operons were found in TIM68 genome, and they were surfactin A, mojavensin, and a novel plipastatin-like lipopeptide named vallisin. No virulence factors that render pathogenicity to the strain have been identified, but a region of prophage, that may contain unknown pathogenic factors, has been predicted. The pangenome of the species was characterized as closed, with 57% of genes integrating the core genome. The results obtained here on the genetic potential of TIM68 strain should contribute to its exploration in biotechnological applications.
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Imam A, Suman SK, Vempatapu BP, Tripathi D, Ray A, Kanaujia PK. Pyrene remediation by Trametes maxima: an insight into secretome response and degradation pathway. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:44135-44147. [PMID: 35122201 DOI: 10.1007/s11356-022-18888-7] [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: 11/02/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
The rapid pace of economic development has resulted in the release of several polycyclic aromatic hydrocarbons (PAHs) into the environment. Microbial degradation using white-rot fungi is a promising method for the removal of PAHs from the environment. In the present study, biodegradation of recalcitrant PAH by a white-rot fungus, Trametes maxima IIPLC-32, was investigated using pyrene. The pyrene concentration decreased by 79.80%, 65.37%, and 56.37% within 16 days from the initial levels of 10 mg L-1, 25 mg L-1, and 50 mg L-1, respectively. Gas chromatographic-mass spectrometric identification of prominent metabolites 1-hydroxypyrene, 2-methyl-1-naphthyl acetic acid, di-n-butyl phthalate, and diethyl phthalate helped in determining the pyrene degradation pathway. The presence of 81 extracellular proteins was revealed by secretome analysis. The identified proteins up-regulated in response to pyrene degradation were classified into detoxification proteins (6.12%), redox proteins (6.12%), stress proteins (4.08%), metabolic-related proteins (26.53%), translation and transcriptional proteins (49%), catalytic proteins (49%), and other proteins (8.16%). Knowledge of secretome analysis in pyrene degradation helped to understand the degradation mechanism of pyrene. Also, the study suggests that T. maxima IIPLC-32 has the potential to be used in the bioremediation of PAH contaminated aquatic environment.
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Affiliation(s)
- Arfin Imam
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India
- Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, 201002, India
| | - Sunil Kumar Suman
- Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, 201002, India.
| | - Bhanu Prasad Vempatapu
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India
| | - Deependra Tripathi
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India
| | - Anjan Ray
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, 201002, India
| | - Pankaj K Kanaujia
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, 201002, India.
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Mai Z, Wang L, Li Q, Sun Y, Zhang S. Biodegradation and metabolic pathway of phenanthrene by a newly isolated bacterium Gordonia sp. SCSIO19801. Biochem Biophys Res Commun 2021; 585:42-47. [PMID: 34784550 DOI: 10.1016/j.bbrc.2021.10.069] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 11/17/2022]
Abstract
The bacterium Gordonia sp. SCSIO19801, which could effectively utilize phenanthrene as the sole carbon source, was isolated from the seawater of the South China Sea. Its biodegradation characteristics, whole genome sequence, and biodegradation pathway were investigated. The phenanthrene biodegradation process of Gordonia sp. SCSIO19801 was estimated to be a first-order kinetic model with a k value of 0.26/day. Based on the identification of metabolites, utilization of probable intermediates, and genomics analysis of related genes, the degradation of phenanthrene by Gordonia sp. SCSIO19801 was proposed to occur via the salicylate metabolic pathway. This is the first report of a phenanthrene degradation pathway in Gordonia species. In addition, the Gordonia sp. SCSIO19801 could use other aromatic compounds as the sole source of carbon and energy. These characteristics indicate that Gordonia sp. SCSIO19801 can be utilized for developing effective methods for the biodegradation of petroleum hydrocarbons in marine environments.
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Affiliation(s)
- Zhimao Mai
- State Key Laboratory of Tropical Oceanography and 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, 511458, China
| | - Lin Wang
- State Key Laboratory of Tropical Oceanography and 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, 511458, China
| | - Qiqi Li
- State Key Laboratory of Tropical Oceanography and CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yingting Sun
- State Key Laboratory of Tropical Oceanography and CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Si Zhang
- State Key Laboratory of Tropical Oceanography and 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, 511458, China.
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Wu P, Wang YS. Fluorene degradation by Rhodococcus sp. A2-3 isolated from hydrocarbon contaminated sediment of the Pearl River estuary, China. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:929-935. [PMID: 33797662 DOI: 10.1007/s10646-021-02379-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
The pollution of polycyclic aromatic hydrocarbons was serious in sediments of the Pearl River estuary, China. A fluorene-degrading bacterium, strain A2-3, was isolated from hydrocarbon contaminated sediment of this estuary and identified as Rhodococcus sp. based on the analyses of 16S rRNA gene sequence and morphology. Rhodococcus sp. A2-3 can take naphthalene, p-Teropheny, fluorene, pyrene, salicylic acid, citric acid, acetic acid, diethyletheranhydrous, methanol or 4,4'-dibromodiphenyl ether as sole carbon source. 100% of 100 mg/L fluorene or 89% of 400 mg/L fluorene was removed in 7 days by strain A2-3 at 30 °C and pH 7.5. The strain A2-3 showed a high degradation efficiency of fluorene when pH values ranged from 5.5 to 8.5. The proposed pathway of fluorene catabolism by strain A2-3 was initially attacked by 3,4 dioxygenation. Our results suggested Rhodococcus sp. A2-3 can degrade PAHs under aerobic conditions and can function in bioremediation, particularly for weakly acid environment.
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Affiliation(s)
- Peng Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
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Wang C, Luo Y, Tan H, Liu H, Xu F, Xu H. Responsiveness change of biochemistry and micro-ecology in alkaline soil under PAHs contamination with or without heavy metal interaction. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115296. [PMID: 32791476 DOI: 10.1016/j.envpol.2020.115296] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 07/16/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
Co-presence of organic pollutants and heavy metals in soil is causing increasing concerns, but the lack of knowledge of relation between soil ecology and pollutant fate is limiting the developing of specific control strategy. This study investigated soil change under pyrene stress and its interaction with cadmium (Cd). Soil physicochemical properties were not seriously influenced. However, pollutants' presence easily varied soil microbial activity, quantity, and diversity. Under high-level pyrene, Cd presence contributed to soil indigenous microorganisms' adaption and soil microbial community structure stability. Soils with both pyrene and Cd presented 7.11-12.0% higher pyrene degradation compared with single pyrene treatment. High-throughput sequencing analysis indicated the proportion of Mycobacterium sp., a commonly known PAHs degrader, increased to 25.2-48.5% in treatments from 0.52% in control. This phenomenon was consistent with the increase of PAHs probable degraders (the ratio increased to 2.86-6.57% from 0.24% in control). Higher Cd bioavailability was also observed in soils with both pollutants than that with Cd alone. And Cd existence caused the elevation of Cd resistant bacterium Limnobacter sp. (increased to 12.2% in CdCK from 2.06% in control). Functional gene prediction also indicated that abundance of genes related to nutrient metabolism decreased dramatically with pollutants, while the abundances of energy metabolism, lipid metabolism, secondary metabolites biosynthesis-related genes increased (especially for aromatic compound degradation related genes). These results indicated the mutual effect and internal-interaction existed between pollutants and soils resulted in pollutants' fate and soil microbial changes, providing further information regarding pollutants dissipation and transformation under soil microbial response.
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Affiliation(s)
- Can Wang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China; Key Laboratory of Environment Protection, Soil Ecological Protection and Pollution Control, Sichuan University & Department of Ecology and Environment of Sichuan, Chengdu, 610065, Sichuan, PR China.
| | - Yao Luo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Hang Tan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Huakang Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Fei Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Heng Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China; Key Laboratory of Environment Protection, Soil Ecological Protection and Pollution Control, Sichuan University & Department of Ecology and Environment of Sichuan, Chengdu, 610065, Sichuan, PR China.
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Nurzhanova A, Mukasheva T, Berzhanova R, Kalugin S, Omirbekova A, Mikolasch A. Optimization of microbial assisted phytoremediation of soils contaminated with pesticides. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2020; 23:482-491. [PMID: 33000955 DOI: 10.1080/15226514.2020.1825330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
580 microbial strains were isolated from the rhizosphere of the plants Cucurbita pepo L. and Xanthium strumarium grown on soil contaminated with dichlorodiphenyltrichloroethane (DDT) and its metabolites. During the cultivation, two bacterial strains were selected because of their ability to grow on media containing 0.5-5.0 mg L-1 of dichlorodiphenyldichloroethylene (DDE) as the sole carbon source. They were identified as Bacillus vallismortis and Bacillus aryabhattai. Both of these species were shown to have a high capacity for the utilization of DDE - more than 90% of which was consumed after 21 days of cultivation. Laboratory experiments were carried out then to assess the possibility of using these strains for the decontamination of organochlorine pesticides (OCPs) contaminated soils. Inoculation of C. pepo and X. strumarium with our isolates B. vallismortis and B. aryabhattai resulted in a reduction of the pollutant stress to the plants as shown by an increase both in aboveground and in root biomass. The microorganisms enhanced the uptake and phytostabilization potential of C. pepo and X. strumarium and can be applied for the treatment of DDE contaminated soils.
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Affiliation(s)
- Asil Nurzhanova
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Togzhan Mukasheva
- Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Ramza Berzhanova
- Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Sergey Kalugin
- Faculty of Chemistry and Chemical Technology, al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anel Omirbekova
- Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Annett Mikolasch
- Institute of Microbiology, University Greifswald, Greifswald, Germany
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Xu X, Liu W, Wang W, Tian S, Jiang P, Qi Q, Li F, Li H, Wang Q, Li H, Yu H. Potential biodegradation of phenanthrene by isolated halotolerant bacterial strains from petroleum oil polluted soil in Yellow River Delta. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 664:1030-1038. [PMID: 30901777 DOI: 10.1016/j.scitotenv.2019.02.080] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
The Yellow River Delta (YRD), being close to Shengli Oilfield, is at high risk for petroleum oil pollution. The aim of this study was to isolate halotolerant phenanthrene (PHE) degrading bacteria for dealing with this contaminates in salinity environment. Two bacterial strains assigned as FM6-1 and FM8-1 were successfully screened from oil contaminated soil in the YRD. Morphological and molecular analysis suggested that strains FM6-1 and FM8-1 were belonging to Delftia sp. and Achromobacter sp., respectively. Bacterial growth of both strains was not dependent on NaCl, however, grew well under extensive NaCl concentration. The optimum NaCl concentration for bacterial production of strain FM8-1 was 4% (m/v), whereas for strain FM6-1, growth was not affected within 2.5% NaCl. Both strains could use the tested aromatic hydrocarbons (naphthalene, phenanthrene, fluoranthene and pyrene) and aliphatic hydrocarbons (C12, C16, C20 and C32) as sole carbon source. The optimized biodegradation conditions for strain FM6-1 were pH 7, 28 °C and 2% NaCl, for strain FM8-1 were pH 8, 28 °C and 2.5% NaCl. The highest biodegradation rate of strains FM6-1 and FM8-1 was found at 150 mg/L PHE and 200 mg/L, respectively. In addition, strainsFM8-1 showed a superior biodegradation ability to strain FM6-1 at each optimized condition. The PHE biodegradation process by both strains well fitted to first-order kinetic models and the k1 values were calculated to be 0.1974 and 0.1070 per day. Strain FM6-1 metabolized PHE via a "phthalic acid" route, while strain FM8-1 metabolized PHE through the "naphthalene" route. This project not only obtained two halotolerant petroleum hydrocarbon degraders but also provided a promising remediation approach for solving oil pollutants in salinity environments.
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Affiliation(s)
- Xingjian Xu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, Inner Mongolia 137400, China.
| | - Wenming Liu
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, Inner Mongolia 137400, China
| | - Wei Wang
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, Inner Mongolia 137400, China
| | - Shuhua Tian
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, Inner Mongolia 137400, China
| | - Pan Jiang
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, Inner Mongolia 137400, China
| | - Qige Qi
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, Inner Mongolia 137400, China
| | - Fengjiao Li
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, Inner Mongolia 137400, China
| | - Haiyan Li
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; Changchun University of Science and Technology, Changchun 130022, China
| | - Quanying Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Huai Li
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Hongwen Yu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; Changchun University of Science and Technology, Changchun 130022, China
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Zeng J, Zhu Q, Li Y, Dai Y, Wu Y, Sun Y, Miu L, Chen H, Lin X. Isolation of diverse pyrene-degrading bacteria via introducing readily utilized phenanthrene. CHEMOSPHERE 2019; 222:534-540. [PMID: 30721812 DOI: 10.1016/j.chemosphere.2019.01.189] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 01/17/2019] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
Bacteria able to degrade pyrene play a critical role in the biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons (PAHs). However, the traditional isolation procedure only obtains strains related to the genus Mycobacterium. The aim of the present study was to develop a modified method to isolate taxonomically distinct pyrene-degrading strains. The results indicated that replacing pyrene with phenanthrene in the isolation step improved the isolation efficiency. Using the modified method, six PAH degraders belonging to the genera Bosea, Arthrobacter, Paenibacillus, Bacillus, and Rhodococcus were obtained. They were capable of effectively utilizing pyrene (∼100%) as their sole carbon source, and could co-metabolize the degradation of benzo [a]pyrene (26.9-71.5%). In contrast, a small amount of pyrene (5.6%) and benzo [a]pyrene (8.6%) were degraded by a phenanthrene-degrading Sphingobium sp. NS7 under the same conditions. The difference in PAHs degradation between agar plate culture and liquid culture may lead to the low isolation efficiency in the traditional procedure. Hereditary stability analysis showed that PAH degradation capability of the Bosea, Paenibacillus, and Rhodococcus strains were easily lost without PAH pressure, which may partly explain why those strains were difficult to obtain using the traditional method.
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Affiliation(s)
- Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, PR China
| | - Qinghe Zhu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, PR China
| | - Yanjie Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, PR China
| | - Yeliang Dai
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, PR China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, PR China
| | - Yuhan Sun
- High School Affiliated To Nanjing Normal University, Chahaer Road, 37, Nanjing, 210003, PR China
| | - Luyi Miu
- High School Affiliated To Nanjing Normal University, Chahaer Road, 37, Nanjing, 210003, PR China
| | - Hong Chen
- Soil and Environment Analysis Center, Institute of Soil Science, Chinese Academy of Science, PR China
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, PR China.
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Perchlorate-Reducing Bacteria from Hypersaline Soils of the Colombian Caribbean. Int J Microbiol 2019; 2019:6981865. [PMID: 30906324 PMCID: PMC6398020 DOI: 10.1155/2019/6981865] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/24/2018] [Accepted: 12/11/2018] [Indexed: 11/17/2022] Open
Abstract
Perchlorate (ClO4 -) has several industrial applications and is frequently detected in environmental matrices at relevant concentrations to human health. Currently, perchlorate-degrading bacteria are promising strategies for bioremediation in polluted sites. The aim of this study was to isolate and characterize halophilic bacteria with the potential for perchlorate reduction. Ten bacterial strains were isolated from soils of Galerazamba-Bolivar, Manaure-Guajira, and Salamanca Island-Magdalena, Colombia. Isolates grew at concentrations up to 30% sodium chloride. The isolates tolerated pH variations ranging from 6.5 to 12.0 and perchlorate concentrations up to 10000 mg/L. Perchlorate was degraded by these bacteria on percentages between 25 and 10. 16S rRNA gene sequence analysis indicated that the strains were phylogenetically related to Vibrio, Bacillus, Salinovibrio, Staphylococcus, and Nesiotobacter genera. In conclusion, halophilic-isolated bacteria from hypersaline soils of the Colombian Caribbean are promising resources for the bioremediation of perchlorate contamination.
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12
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Hosseini-Abari A, Emtiazi G, Jazini M, Kim J, Kim BG. LC/MS detection of oligogalacturonic acids obtained from tragacanth degradation by pectinase producing bacteria. J Basic Microbiol 2018; 59:249-255. [PMID: 30548881 DOI: 10.1002/jobm.201800332] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/12/2018] [Accepted: 11/15/2018] [Indexed: 01/17/2023]
Abstract
Tragacanth, a highly branched carbohydrate polymer isolated from Astragalus, is one of the most commonly used gums in food industry. The primary structure of tragacanth is composed of galacturonic acid monomers connected with α 1-4 links, and it is very similar to the pectin. Tragacanth degradation by microorganisms is significant in two aspects: first, food preservation and microbial growth control due to too much use of tragacanth in the food industry, second, therapeutic and pharmaceutical potential of obtained oligosaccharides. In the present study, we report three new strains of bacteria, Acinetobacter guillouiae strain TD1, Kosakonia sacchari strain TD2, and Bacillus vallismortis strain PD1 with the capability of growing in tragacanth as an only source of carbon and energy. The evolutionary history of the isolated strains was analyzed based on 16S rRNA gene sequences in MEGA7 using the neighbor-joining method. The production of di and tri galacturonic acid due to pectinase activities of the strains were detected by thin layer chromatography (TLC) and liquid chromatography/Mass spectroscopy (LC/MS) analysis. Here is the first report of the ability to grow in tragacanth and pectinase activity monitoring in bacteria. Our results revealed that all of the isolated strains are capable of degrading pectin and tragacanth to oligo-galacturonic acids. The obtained products, which have different structures depending on the tragacanth structures and types of pectinolytic enzymes, would show therapeutic and pharmaceutical potentials.
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Affiliation(s)
- Afrouzossadat Hosseini-Abari
- Faculty of Sciences, Department of Biology, University of Isfahan, Isfahan, Iran.,Environmental Research Institute, University of Isfahan, Isfahan, Iran
| | - Giti Emtiazi
- Faculty of Sciences, Department of Biology, University of Isfahan, Isfahan, Iran.,Faculty of Sciences and Technology, Department of Biotechnology, Shahid Ashrafi Esfahani University, Isfahan, Iran
| | - Mahboubeh Jazini
- Faculty of Sciences, Department of Biology, University of Isfahan, Isfahan, Iran
| | - Joonwon Kim
- School of Chemical and Biological Engineering, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
| | - Byung Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
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Dasgupta D, Jasmine J, Mukherji S. Characterization, phylogenetic distribution and evolutionary trajectories of diverse hydrocarbon degrading microorganisms isolated from refinery sludge. 3 Biotech 2018; 8:273. [PMID: 29868311 DOI: 10.1007/s13205-018-1297-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/20/2018] [Indexed: 12/01/2022] Open
Abstract
Phylogenic association between bacteria living under harsh conditions can provide important information on adaptive mechanism, survival strategy and their potential application. Indigenous microorganisms isolated from toxic refinery oily sludge with ability to degrade a diverse range of hydrocarbons were identified and characterized. The strains including Pseudomonas aeruginosa RS1, Microbacterium sp. RS2, Bacillus sp. RS3, Acinetobacter baumannii RS4 and Stenotrophomonas sp. RS5 could utilize n-alkanes, cycloalkanes, polynuclear aromatic hydrocarbons (PAHs) with 2-4 rings and also substituted PAHs as sole substrate. The phylogenetic position of Bacillus sp. RS3 and Pseudomonas sp. RS1 was tested by applying the maximum likelihood (ML) method to the aligned 16S rRNA nucleotide sequences of PAH and aliphatic hydrocarbon degrading strains belonging to the corresponding genus. The base substitution matrix created with each set of organisms capable of degrading aromatic and aliphatic hydrocarbons showed significant transitional event with high values of transition: transversion ratio (R) under all conditions. The guanine-cytosine (GC) content of the hydrocarbon degrading test strains was also found to be highest for the clade which harbored them. The test strains consistently occupied a distinct terminal end within the phylogenetic tree constructed by ML analysis. This study reveals that the refinery sludge imposed environmental stress on the bacterial strains which possibly caused significant genetic alteration and phenotypic adaptation. Due to the divergent evolution of the Pseudomonas and Bacillus strains in the sludge, they appeared distinctly different from other hydrocarbon degrading strains of the same genus.
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Affiliation(s)
- Debdeep Dasgupta
- 1Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076 India
- 2Present Address: Amity Institute of Biotechnology, Amity University Mumbai, Bhatan, Post-Somathne, Panvel, Mumbai, Maharashtra 410206 India
| | - Jublee Jasmine
- 1Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076 India
| | - Suparna Mukherji
- 1Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076 India
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Skariyachan S, Setlur AS, Naik SY, Naik AA, Usharani M, Vasist KS. Enhanced biodegradation of low and high-density polyethylene by novel bacterial consortia formulated from plastic-contaminated cow dung under thermophilic conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:8443-8457. [PMID: 28188552 DOI: 10.1007/s11356-017-8537-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/31/2017] [Indexed: 05/06/2023]
Abstract
The current study aimed to devise eco-friendly, safe, and cost-effective strategies for enhanced degradation of low- and high-density polyethylene (LDPE and HDPE) using newly formulated thermophilic microbial consortia from cow dung and to assess the biodegradation end products. The plastic-degrading bacteria from cow dung samples gathered from highly plastic-acclimated environments were enriched by standard protocols. The degradation ability was comprehended by zone of clearance method, and the percentage of degradation was monitored by weight reduction process. The best isolates were characterized by standard microbiological and molecular biology protocols. The best isolates were employed to form several combinations of microbial consortia, and the degradation end products were analyzed. The stability of 16S ribosomal DNA (rDNA) was predicted by bioinformatics approach. This study identified 75 ± 2, 55 ± 2, 60 ± 3, and 43 ± 3% degradation for LDPE strips, pellets, HDPE strips, and pellets, respectively, for a period of 120 days (p < 0.05) at 55 °C by the formulated consortia of IS1-IS4, and the degradation efficiency was found to be better in comparison with other formulations. The end product analysis by Fourier transform infrared, scanning electron microscopy, energy-dispersive spectroscopy, and nuclear magnetic resonance showed major structural changes and formation of bacterial biofilm on plastic surfaces. These novel isolates were designated as Bacillus vallismortis bt-dsce01, Psuedomonas protegens bt-dsce02, Stenotrophomonas sp. bt-dsce03, and Paenibacillus sp.bt-dsce04 by 16S rDNA sequencing and suggested good gene stability with minimum Gibb's free energy. Therefore, this study imparts substantial information regarding the utilization of these thermophilic microbial consortia from cow dung for rapid polyethylene removal.
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Affiliation(s)
- Sinosh Skariyachan
- R&D Centre, Department of Biotechnology Engineering, Dayananda Sagar Institutions, Bangalore, 560 078, India.
- Visvesvaraya Technological University, Belagavi, Karnataka, India.
| | - Anagha Shamsundar Setlur
- R&D Centre, Department of Biotechnology Engineering, Dayananda Sagar Institutions, Bangalore, 560 078, India
- Visvesvaraya Technological University, Belagavi, Karnataka, India
| | - Sujay Yashwant Naik
- R&D Centre, Department of Biotechnology Engineering, Dayananda Sagar Institutions, Bangalore, 560 078, India
- Visvesvaraya Technological University, Belagavi, Karnataka, India
| | - Ashwini Amaresh Naik
- R&D Centre, Department of Biotechnology Engineering, Dayananda Sagar Institutions, Bangalore, 560 078, India
- Visvesvaraya Technological University, Belagavi, Karnataka, India
| | - Makam Usharani
- R&D Centre, Department of Biotechnology Engineering, Dayananda Sagar Institutions, Bangalore, 560 078, India
- Visvesvaraya Technological University, Belagavi, Karnataka, India
| | - Kiran S Vasist
- R&D Centre, Department of Biotechnology Engineering, Dayananda Sagar Institutions, Bangalore, 560 078, India
- Visvesvaraya Technological University, Belagavi, Karnataka, India
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15
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Mikolasch A, Reinhard A, Alimbetova A, Omirbekova A, Pasler L, Schumann P, Kabisch J, Mukasheva T, Schauer F. From oil spills to barley growth - oil-degrading soil bacteria and their promoting effects. J Basic Microbiol 2016; 56:1252-1273. [PMID: 27624187 DOI: 10.1002/jobm.201600300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/06/2016] [Indexed: 12/30/2022]
Abstract
Heavy contamination of soils by crude oil is omnipresent in areas of oil recovery and exploitation. Bioremediation by indigenous plants in cooperation with hydrocarbon degrading microorganisms is an economically and ecologically feasible means to reclaim contaminated soils. To study the effects of indigenous soil bacteria capable of utilizing oil hydrocarbons on biomass production of plants growing in oil-contaminated soils eight bacterial strains were isolated from contaminated soils in Kazakhstan and characterized for their abilities to degrade oil components. Four of them, identified as species of Gordonia and Rhodococcus turned out to be effective degraders. They produced a variety of organic acids from oil components, of which 59 were identified and 7 of them are hitherto unknown acidic oil metabolites. One of them, Rhodococcus erythropolis SBUG 2054, utilized more than 140 oil components. Inoculating barley seeds together with different combinations of these bacterial strains restored normal growth of the plants on contaminated soils, demonstrating the power of this approach for bioremediation. Furthermore, we suggest that the plant promoting effect of these bacteria is not only due to the elimination of toxic oil hydrocarbons but possibly also to the accumulation of a variety of organic acids which modulate the barley's rhizosphere environment.
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Affiliation(s)
- Annett Mikolasch
- Department of Applied Microbiology, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Anne Reinhard
- Department of Applied Microbiology, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Anna Alimbetova
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anel Omirbekova
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Lisa Pasler
- Department of Applied Microbiology, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Johannes Kabisch
- Institute of Biochemistry, University Greifswald, 17487, Greifswald, Germany
| | - Togzhan Mukasheva
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Frieder Schauer
- Department of Applied Microbiology, Institute of Microbiology, University Greifswald, Greifswald, Germany
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16
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Shekoohiyan S, Moussavi G, Naddafi K. The peroxidase-mediated biodegradation of petroleum hydrocarbons in a H2O2-induced SBR using in-situ production of peroxidase: Biodegradation experiments and bacterial identification. JOURNAL OF HAZARDOUS MATERIALS 2016; 313:170-178. [PMID: 27060866 DOI: 10.1016/j.jhazmat.2016.03.081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 03/26/2016] [Accepted: 03/28/2016] [Indexed: 06/05/2023]
Abstract
A bacterial peroxidase-mediated oxidizing process was developed for biodegrading total petroleum hydrocarbons (TPH) in a sequencing batch reactor (SBR). Almost complete biodegradation (>99%) of high TPH concentrations (4g/L) was attained in the bioreactor with a low amount (0.6mM) of H2O2 at a reaction time of 22h. A specific TPH biodegradation rate as high as 44.3mgTPH/gbiomass×h was obtained with this process. The reaction times required for complete biodegradation of TPH concentrations of 1, 2, 3, and 4g/L were 21, 22, 28, and 30h, respectively. The catalytic activity of hydrocarbon catalyzing peroxidase was determined to be 1.48U/mL biomass. The biodegradation of TPH in seawater was similar to that in fresh media (no salt). A mixture of bacteria capable of peroxidase synthesis and hydrocarbon biodegradation including Pseudomonas spp. and Bacillus spp. were identified in the bioreactor. The GC/MS analysis of the effluent indicated that all classes of hydrocarbons could be well-degraded in the H2O2-induced SBR. Accordingly, the peroxidase-mediated process is a promising method for efficiently biodegrading concentrated TPH-laden saline wastewater.
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Affiliation(s)
- Sakine Shekoohiyan
- Department of Environmental Health Engineering, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Gholamreza Moussavi
- Department of Environmental Health Engineering, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Kazem Naddafi
- Department of Environmental Health Engineering, Faculty of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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17
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Pal S, Banat F, Almansoori A, Abu Haija M. Review of technologies for biotreatment of refinery wastewaters: progress, challenges and future opportunities. ACTA ACUST UNITED AC 2016. [DOI: 10.1080/21622515.2016.1164252] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sreela Pal
- Department of Chemical Engineering, The Petroleum Institute, Abu Dhabi, UAE
| | - Fawzi Banat
- Department of Chemical Engineering, The Petroleum Institute, Abu Dhabi, UAE
| | - Ali Almansoori
- Department of Chemical Engineering, The Petroleum Institute, Abu Dhabi, UAE
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18
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Chen C, Lei W, Lu M, Zhang J, Zhang Z, Luo C, Chen Y, Hong Q, Shen Z. Characterization of Cu(II) and Cd(II) resistance mechanisms in Sphingobium sp. PHE-SPH and Ochrobactrum sp. PHE-OCH and their potential application in the bioremediation of heavy metal-phenanthrene co-contaminated sites. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:6861-6872. [PMID: 26670028 DOI: 10.1007/s11356-015-5926-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/03/2015] [Indexed: 06/05/2023]
Abstract
Soil that is co-contaminated with heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) is difficult to bioremediate due to the ability of toxic metals to inhibit PAH degradation by bacteria. We demonstrated the resistance mechanisms to Cu(II) and Cd(II) of two newly isolated strains of Sphingobium sp. PHE-SPH and Ochrobactrum sp. PHE-OCH and further tested their potential application in the bioremediation of HM-phenanthrene (PhA) co-contaminated sites. The PHE-SPH and PHE-OCH strains tolerated 4.63 and 4.34 mM Cu(II) and also showed tolerance to 0.48 and 1.52 mM Cd(II), respectively. Diverse resistance patterns were detected between the two strains. In PHE-OCH cells, the maximum accumulation of Cu(II) occurred in the cell wall, while the maximum accumulation was in the cytoplasm of PHE-SPH cells. This resulted in a sudden suppression of growth in PHE-OCH and a gradual inhibition in PHE-SPH as the concentration of Cu(II) increased. Organic acid production was markedly higher in PHE-OCH than in PHE-SPH, which may also have a role in the resistance mechanisms, and contributes to the higher Cd(II) tolerance of PHE-OCH. The factors involved in the absorption of Cu(II) or Cd(II) in PHE-SPH and PHE-OCH were identified as proteins and carbohydrates by Fourier transform infrared (FT-IR) spectroscopy. Furthermore, both strains showed the ability to efficiently degrade PhA and maintained this high degradation efficiency under HM stress. The high tolerance to HMs and the PhA degradation capacity make Sphingobium sp. PHE-SPH and Ochrobactrum sp. PHE-OCH excellent candidate organisms for the bioremediation of HM-PhA co-contaminated sites.
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Affiliation(s)
- Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Wenrui Lei
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Min Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jianan Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zhou Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, People's Republic of China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qing Hong
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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19
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Daghio M, Vaiopoulou E, Patil SA, Suárez-Suárez A, Head IM, Franzetti A, Rabaey K. Anodes Stimulate Anaerobic Toluene Degradation via Sulfur Cycling in Marine Sediments. Appl Environ Microbiol 2016; 82:297-307. [PMID: 26497463 PMCID: PMC4702649 DOI: 10.1128/aem.02250-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 10/17/2015] [Indexed: 11/20/2022] Open
Abstract
Hydrocarbons released during oil spills are persistent in marine sediments due to the absence of suitable electron acceptors below the oxic zone. Here, we investigated an alternative bioremediation strategy to remove toluene, a model monoaromatic hydrocarbon, using a bioanode. Bioelectrochemical reactors were inoculated with sediment collected from a hydrocarbon-contaminated marine site, and anodes were polarized at 0 mV and +300 mV (versus an Ag/AgCl [3 M KCl] reference electrode). The degradation of toluene was directly linked to current generation of up to 301 mA m(-2) and 431 mA m(-2) for the bioanodes polarized at 0 mV and +300 mV, respectively. Peak currents decreased over time even after periodic spiking with toluene. The monitoring of sulfate concentrations during bioelectrochemical experiments suggested that sulfur metabolism was involved in toluene degradation at bioanodes. 16S rRNA gene-based Illumina sequencing of the bulk anolyte and anode samples revealed enrichment with electrocatalytically active microorganisms, toluene degraders, and sulfate-reducing microorganisms. Quantitative PCR targeting the α-subunit of the dissimilatory sulfite reductase (encoded by dsrA) and the α-subunit of the benzylsuccinate synthase (encoded by bssA) confirmed these findings. In particular, members of the family Desulfobulbaceae were enriched concomitantly with current production and toluene degradation. Based on these observations, we propose two mechanisms for bioelectrochemical toluene degradation: (i) direct electron transfer to the anode and/or (ii) sulfide-mediated electron transfer.
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Affiliation(s)
- Matteo Daghio
- Laboratory of Microbial Ecology and Technology, Ghent University, Ghent, Belgium Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Eleni Vaiopoulou
- Laboratory of Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Sunil A Patil
- Laboratory of Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Ana Suárez-Suárez
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ian M Head
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Korneel Rabaey
- Laboratory of Microbial Ecology and Technology, Ghent University, Ghent, Belgium
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20
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Hanafy AAELMEL, Anwar Y, Mohamed SA, Al-Garni SMS, Sabir JSM, AbuZinadah OA, Mehdar HA, Alfaidi AW, Ahmed MMM. Isolation and identification of bacterial consortia responsible for degrading oil spills from the coastal area of Yanbu, Saudi Arabia. BIOTECHNOL BIOTEC EQ 2015. [DOI: 10.1080/13102818.2015.1086282] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Singh S, Thavamani P, Megharaj M, Naidu R. Multifarious activities of cellulose degrading bacteria from Koala (Phascolarctos cinereus) faeces. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2015; 57:23. [PMID: 26290743 PMCID: PMC4540270 DOI: 10.1186/s40781-015-0056-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 05/25/2015] [Indexed: 11/10/2022]
Abstract
Cellulose degrading bacteria from koala faeces were isolated using caboxymethylcellulose-Congo red agar, screened in vitro for different hydrolytic enzyme activities and phylogenetically characterized using molecular tools. Bacillus sp. and Pseudomonas sp. were the most prominent bacteria from koala faeces. The isolates demonstrated good xylanase, amylase, lipase, protease, tannase and lignin peroxidase activities apart from endoglucanase activity. Furthermore many isolates grew in the presence of phenanthrene, indicating their probable application for bioremediation. Potential isolates can be exploited further for industrial enzyme production or in bioremediation of contaminated sites.
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Affiliation(s)
- Surender Singh
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Palanisami Thavamani
- University of Newcastle, Callaghan, New South Wales Australia ; formerly, Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, Adelaide, South Australia Australia ; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), Adelaide, 5095 South Australia Australia
| | - Mallavarapu Megharaj
- University of Newcastle, Callaghan, New South Wales Australia ; formerly, Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, Adelaide, South Australia Australia ; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), Adelaide, 5095 South Australia Australia
| | - Ravi Naidu
- University of Newcastle, Callaghan, New South Wales Australia ; formerly, Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, Adelaide, South Australia Australia ; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), Adelaide, 5095 South Australia Australia
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22
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Ren G, Ren W, Teng Y, Li Z. Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil. Front Microbiol 2015; 6:22. [PMID: 25688237 PMCID: PMC4311681 DOI: 10.3389/fmicb.2015.00022] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/08/2015] [Indexed: 11/13/2022] Open
Abstract
Understanding the potential for Polycyclic aromatic hydrocarbons (PAH) degradation by indigenous microbiota and the influence of PAHs on native microbial communities is of great importance for bioremediation and ecological evaluation. Various studies have focused on the bacterial communities in the environment where obvious PAH degradation was observed, little is known about the microbiota in the soil where poor degradation was observed. Soil microcosms were constructed with a red soil by supplementation with a high-molecular-weight PAH (pyrene) at three dosages (5, 30, and 70 mg ⋅ kg(-1)). Real-time PCR was used to evaluate the changes in bacterial abundance and pyrene dioxygenase gene (nidA) quantity. Illumina sequencing was used to investigate changes in diversity, structure, and composition of bacterial communities. After 42 days of incubation, no evident degradation was observed. The poor degradation ability was associated with the stability or significant decrease of abundance of the nidA gene. Although the abundance of the bacterial 16S rRNA gene was not affected by pyrene, the bacterial richness and diversity were decreased with increasing dosage of pyrene and the community structure was changed. Phylotypes affected by pyrene were comprehensively surveyed: (1) at the high taxonomic level, seven of the abundant phyla/classes (relative abundance >1.0%) including Chloroflexi, AD3, WPS-2, GAL5, Alphaproteobacteria, Actinobacteria, and Deltaproteobacteria and one rare phylum Crenarchaeota were significantly decreased by at least one dosage of pyrene, while three phyla/classes (Acidobacteria, Betaproteobacteria, and Gammaproteobacteria) were significantly increased; and (2) at the lower taxonomic level, the relative abundances of twelve orders were significantly depressed, whereas those of nine orders were significantly increased. This work enhanced our understanding of the biodegradation potential of pyrene in red soil and the effect of pyrene on soil ecosystems at the microbial community level.
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Affiliation(s)
- Gaidi Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
| | - Zhengao Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
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23
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Li Y, Wang H, Hua F. Uptake Modes of Fluoranthene by StrainRhodococcusSp. Bap-1. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2013.0102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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24
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Yuan H, Yao J, Masakorala K, Wang F, Cai M, Yu C. Isolation and characterization of a newly isolated pyrene-degrading Acinetobacter strain USTB-X. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:2724-2732. [PMID: 24122268 DOI: 10.1007/s11356-013-2221-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 10/04/2013] [Indexed: 06/02/2023]
Abstract
The pryene-degradation bacterium strain USTB-X was newly isolated from the polycyclic aromatic hydrocarbon (PAH)-contaminated soil in Beijing Coking Plant, China. The strain was identified as Acinetobacter with respect to its 16S rDNA and morphological and physiological characteristics. The strain was Gram-negative, non-mobile, non-acid-fast, and non-spore-forming, short rods in young culture and 0.8-1.6 μm in diameter and 1.2-2.5 μm long in the stationary phase of growth. Strain USTB-X could utilize pyrene, naphthalene, fluorene, phenanthrene, benzene, toluene, ethylbenzene, ethanol, methanol, and Tween 80 as sole source of carbon and energy. The strain could produce biosurfactants which enhanced the removal of pyrene and could remove 63 % of pyrene with an initial concentration of 100 mg·L-1 in 16 days without other substrates. Based on the intermediates analyzed by gas chromatography-mass spectrometry, we also deduced the possible metabolic pathway of strain USTBX for pyrene biodegradation. Results indicated that the strain USTB-X had high potential to enhance the removal of PAHs in contaminated sites.
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Masakorala K, Yao J, Cai M, Chandankere R, Yuan H, Chen H. Isolation and characterization of a novel phenanthrene (PHE) degrading strain Psuedomonas sp. USTB-RU from petroleum contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2013; 263 Pt 2:493-500. [PMID: 24225588 DOI: 10.1016/j.jhazmat.2013.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 05/15/2023]
Abstract
The phenanthrene degrading novel bacterium strain USTB-RU was isolated from petroleum contaminated soil in Dagan oilfield, southeast of Tianjin, northeast China. The novel isolate was identified as Pseudomonas sp. USTB-RU on the basis of morphological, physicochemical characteristics and analysis of 16S rDNA gene sequence. The strain could degrade 86.65% of phenanthrene at an initial concentration of 100 mg L(-1) in 8 days and identified intermediate metabolite evident the biodegradation of phenanthrene through protocatechuate metabolic pathway. The strain showed the potential to produce surface-active compounds that may have caused for the resulted efficient biodegradation through enhancing the substrate bioavailability. The results highlighted that the adaptability of USTB-RU to grow in a range of temperature, pH and potential to utilize various commonly co-exist pollutants in contaminated site other than phenanthrene as sole carbon and energy source. Further, susceptibility of the strain for the tested antibiotics inferred the possibility to absence of risk of spreading drug resistant factor to other indigenous bacteria. Therefore, the isolated novel strain USTB-RU may have a high potential for application in in situ bioremediation of phenanthrene contaminated environment.
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Affiliation(s)
- Kanaji Masakorala
- School of Civil and Environmental Engineering, and National "International Cooperation Based on Environment and Energy", and Key Laboratory of "Metal and Mine Efficiently Exploiting and Safety" Ministry of Education, University of Science and Technology Beijing, 100083 Beijing, PR China; Department of Botany, Faculty of Science, University of Ruhuna, Matara, Sri Lanka
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Dunlevy SR, Singleton DR, Aitken MD. Biostimulation Reveals Functional Redundancy of Anthracene-Degrading Bacteria in Polycyclic Aromatic Hydrocarbon-Contaminated Soil. ENVIRONMENTAL ENGINEERING SCIENCE 2013; 30:697-705. [PMID: 24302851 PMCID: PMC3833303 DOI: 10.1089/ees.2013.0067] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/28/2013] [Indexed: 05/25/2023]
Abstract
Stable-isotope probing was previously used to identify bacterial anthracene-degraders in untreated soil from a former manufactured gas plant site. However, subsequent pyrosequence analyses of total bacterial communities and quantification of 16S rRNA genes indicated that relative abundances of the predominant anthracene-degrading bacteria (designated Anthracene Group 1) diminished as a result of biological treatment conditions in lab-scale, aerobic bioreactors. This study identified Alphaproteobacterial anthracene-degrading bacteria in bioreactor-treated soil which were dissimilar to those previously identified. The largest group of sequences was from the Alterythrobacter genus while other groups of sequences were associated with bacteria within the order Rhizobiales and the genus Bradyrhizobium. Conditions in the bioreactor enriched for organisms capable of degrading anthracene which were not the same as those identified as dominant degraders in the untreated soil. Further, these data suggest that identification of polycyclic aromatic hydrocarbon-degrading bacteria in contaminated but untreated soil may be a poor indicator of the most active degraders during biological treatment.
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Affiliation(s)
| | - David R. Singleton
- Corresponding author: David R. Singleton, Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Room 0030 Michael Hooker Research Center, Chapel Hill, NC 27599-7431. Phone: 1-919-966-5452; Fax: 1-919-966-7911; E-mail:
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Kolb S, Stacheter A. Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment. Front Microbiol 2013; 4:268. [PMID: 24046766 PMCID: PMC3763247 DOI: 10.3389/fmicb.2013.00268] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 08/19/2013] [Indexed: 01/06/2023] Open
Abstract
The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH; mxaF) has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2), of the nicotinamide adenine dinucleotide-dependent MDH (mdh), of the methanol oxidoreductase of Actinobacteria (mdo), of the fungal flavin adenine nucleotide-dependent alcohol oxidase (mod1, mod2, and homologs), and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC) in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.
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Affiliation(s)
- Steffen Kolb
- Department of Ecological Microbiology, University of Bayreuth Bayreuth, Germany
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Aulenta F, Verdini R, Zeppilli M, Zanaroli G, Fava F, Rossetti S, Majone M. Electrochemical stimulation of microbial cis-dichloroethene (cis-DCE) oxidation by an ethene-assimilating culture. N Biotechnol 2013; 30:749-55. [DOI: 10.1016/j.nbt.2013.04.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/11/2013] [Accepted: 04/13/2013] [Indexed: 10/26/2022]
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Feng TC, Cui CZ, Dong F, Feng YY, Liu YD, Yang XM. Phenanthrene biodegradation by halophilic Martelella sp. AD-3. J Appl Microbiol 2012; 113:779-89. [PMID: 22762374 DOI: 10.1111/j.1365-2672.2012.05386.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 06/10/2012] [Accepted: 06/27/2012] [Indexed: 11/30/2022]
Abstract
AIMS To investigate the phenanthrene-degrading abilities of the halophilic Martelella species AD-3 under different conditions and to propose a possible metabolic pathway. METHODS AND RESULTS Using HPLC and GC-MS analyses, the phenanthrene-degrading properties of the halophilic strain AD-3 and its metabolites were analysed. This isolate efficiently degraded phenanthrene under multiple conditions characterized by different concentrations of phenanthrene (100-400 mg l(-1) ), a broad range of salinities (0·1-15%) and varying pHs (6·0-10·0). Phenanthrene (200 mg l(-1) ) was completely depleted under 3% salinity and a pH of 9·0 within 6 days. The potential toxicity of phenanthrene and its generated metabolites towards the bacterium Vibrio fischeri was significantly reduced 10 days after the bioassay. On the basis of the identified metabolites, enzyme activities and the utilization of probable intermediates, phenanthrene degradation by strain AD-3 was proposed in two distinct routes. In route I, metabolism of phenanthrene was initiated by the dioxygenation at C-3,4 via 1-hydroxy-2-naphthoic acid, 1-naphthol, salicylic acid and gentisic acid. In route II, phenanthrene was metabolized to 9-phenanthrol and 9,10-phenanthrenequinone. Further study indicated that strain AD-3 exhibited a wide spectrum of substrate utilization including other polycyclic aromatic hydrocarbons (PAHs). CONCLUSIONS The results suggest that strain AD-3 possesses a high phenanthrene biodegradability and that the degradation occurs via two routes that remarkably reduce toxicity. SIGNIFICANCE AND IMPACT OF THE STUDY To the best of our knowledge, this work presents the first report of phenanthrene degradation by a halophilic PAH-degrading strain via two routes. In the future, the use of halophilic strain AD-3 provides a potential application for efficient PAH-contaminated hypersaline field remediation.
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Affiliation(s)
- T-C Feng
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
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Viability of phenanthrene biodegradation by an isolated bacterial consortium: optimization and scale-up. Bioprocess Biosyst Eng 2012; 36:133-41. [DOI: 10.1007/s00449-012-0768-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 06/03/2012] [Indexed: 10/28/2022]
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Isolation of novel benzo[a]anthracene-degrading microorganisms and continuous bioremediation in an expanded-bed bioreactor. Bioprocess Biosyst Eng 2011; 35:851-5. [DOI: 10.1007/s00449-011-0669-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 12/04/2011] [Indexed: 10/14/2022]
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