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Fiard M, Militon C, Sylvi L, Migeot J, Michaud E, Jézéquel R, Gilbert F, Bihannic I, Devesa J, Dirberg G, Cuny P. Uncovering potential mangrove microbial bioindicators to assess urban and agricultural pressures on Martinique island in the eastern Caribbean Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172217. [PMID: 38583633 DOI: 10.1016/j.scitotenv.2024.172217] [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: 01/12/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Martinique's mangroves, which cover 1.85 ha of the island (<0.1 % of the total area), are considerably vulnerable to local urban, agricultural, and industrial pollutants. Unlike for temperate ecosystems, there are limited indicators that can be used to assess the anthropogenic pressures on mangroves. This study investigated four stations on Martinique Island, with each being subject to varying anthropogenic pressures. An analysis of mangrove sediment cores approximately 18 cm in depth revealed two primary types of pressures on Martinique mangroves: (i) an enrichment in organic matter in the two stations within the highly urbanized bay of Fort-de-France and (ii) agricultural pressure observed in the four studied mangrove stations. This pressure was characterized by contamination, exceeding the regulatory thresholds, with dieldrin, total DDT, and metals (As, Cu and Ni) found in phytosanitary products. The mangroves of Martinique are subjected to varying degrees of anthropogenic pressure, but all are subjected to contamination by organochlorine pesticides. Mangroves within the bay of Fort-de-France experience notably higher pressures compared to those in the island's northern and southern regions. In these contexts, the microbial communities exhibited distinct responses. The microbial biomass and the abundance of bacteria and archaea were higher in the two less-impacted stations, while in the mangrove of Fort-de-France, various phyla typically associated with polluted environments were more prevalent. These differences in the microbiota composition led to the identification of 65 taxa, including Acanthopleuribacteraceae, Spirochaetaceae, and Pirellulaceae, that could potentially serve as indicators of an anthropogenic influence on the mangrove sediments of Martinique Island.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Jonathan Migeot
- Impact Mer consulting, expertise, and R&D firm, 20 rue Karukéra, 97200 Fort de France, Martinique/FWI, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Ronan Jézéquel
- CEDRE, 715 rue Alain Colas, 29218 Brest CEDEX 2, France.
| | - Franck Gilbert
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier, Toulouse, France.
| | | | - Jeremy Devesa
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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Investigation on Metabolites in Structure and Biosynthesis from the Deep-Sea Sediment-Derived Actinomycete Janibacter sp. SCSIO 52865. Molecules 2023; 28:molecules28052133. [PMID: 36903380 PMCID: PMC10003874 DOI: 10.3390/molecules28052133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
For exploring structurally diverse metabolites and uniquely metabolic mechanisms, we systematically investigated the chemical constituents and putative biosynthesis of Janibacter sp. SCSIO 52865 derived from the deep-sea sediment based on the OSMAC strategy, molecular networking tool, in combination with bioinformatic analysis. As a result, one new diketopiperazine (1), along with seven known cyclodipeptides (2-8), trans-cinnamic acid (9), N-phenethylacetamide (10) and five fatty acids (11-15), was isolated from the ethyl acetate extract of SCSIO 52865. Their structures were elucidated by a combination of comprehensive spectroscopic analyses, Marfey's method and GC-MS analysis. Furthermore, the analysis of molecular networking revealed the presence of cyclodipeptides, and compound 1 was produced only under mBHI fermentation condition. Moreover, bioinformatic analysis suggested that compound 1 was closely related to four genes, namely jatA-D, encoding core non-ribosomal peptide synthetase and acetyltransferase.
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Nassar HN, Rabie AM, Abu Amr SS, El-Gendy NS. Kinetic and statistical perspectives on the interactive effects of recalcitrant polyaromatic and sulfur heterocyclic compounds and in-vitro nanobioremediation of oily marine sediment at microcosm level. ENVIRONMENTAL RESEARCH 2022; 209:112768. [PMID: 35085558 DOI: 10.1016/j.envres.2022.112768] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
A halotolerant biosurfactant producer Pseudomonas aeruginosa strain NSH3 (NCBI Gene Bank Accession No. MN149622) was isolated to degrade high concentrations of recalcitrant polyaromatic hydrocarbons (PAHs) and polyaromatic heterocyclic sulfur compounds (PASHs). In biphasic batch bioreactors, the biodegradation and biosurfactant-production activities of NSH3 have been significantly enhanced (p < 0.0001) by its decoration with eco-friendly prepared magnetite nanoparticles (MNPs). On an artificially contaminated sediment microcosm level, regression modeling and statistical analysis based on a 23 full factorial design of experiments were trendily applied to provide insights into the interactive impacts of such pollutants. MNPs-coated NSH3 were also innovatively applied for nanobioremediation (NBR) of in-vitro diesel oil-polluted sediment microcosms. Gravimetric, chromatographic, and microbial respiratory analyses proved the significantly enhanced biodegradation capabilities of MNPs-coated NSH3 (p < 0.001) and the complete mineralization of various recalcitrant diesel oil components. Kinetic analyses showed that the biodegradation of iso- and n-alkanes was best fitted with a second-order kinetic model equation. Nevertheless, PAHs and PASHs in biphasic batch bioreactors and sediment microcosms followed the first-order kinetic model equation. Sustainable NBR overcome the toxicity of low molecular weight hydrocarbons, mass transfer limitation, and steric hindrance of hydrophobic recalcitrant high molecular weight hydrocarbons and alkylated polyaromatic compounds.
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Affiliation(s)
- Hussein N Nassar
- Egyptian Petroleum Research Institute (EPRI), Nasr City, Cairo, PO, 11727, Egypt; Center of Excellence, October University for Modern Sciences and Arts (MSA), 6(th) of October City, Giza, PO, 12566, Egypt
| | - Abdelrahman M Rabie
- Egyptian Petroleum Research Institute (EPRI), Nasr City, Cairo, PO, 11727, Egypt
| | - Salem S Abu Amr
- Department of Chemical and Environmental Engineering, Faculty of Engineering, Karabuk University, Demir Campus, Karabuk, PO, 78050, Turkey
| | - Nour Sh El-Gendy
- Egyptian Petroleum Research Institute (EPRI), Nasr City, Cairo, PO, 11727, Egypt; Center of Excellence, October University for Modern Sciences and Arts (MSA), 6(th) of October City, Giza, PO, 12566, Egypt.
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Ezzat S, Ahmed NA. Short-Term Biodegradation of Crude Petroleum Oil in Water by Photostimulated Janibacter terrae Strain S1N1. ACS OMEGA 2022; 7:13976-13984. [PMID: 35559133 PMCID: PMC9089385 DOI: 10.1021/acsomega.2c00460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/30/2022] [Indexed: 06/01/2023]
Abstract
Biodegradation is a sustainable green strategy that gives the opportunity for remediation of water contaminated with petroleum products. In this study, 12 bacterial isolates were recovered from River Nile, Egypt and screened for their potential to degrade a mixture of paraffinic petroleum crude oil. The most promising isolate was identified according to 16S rRNA sequencing as Janibacter terrae strain S1N1 (GenBank accession No. KX570955.1). In order to boost the biodegradation efficiency, the bacterial suspension was photostimulated by exposure to different irradiation doses using a low-power helium-neon (He-Ne) laser (λ = 632.8 nm). Maximum biodegradation was achieved after 4 min of exposure (134.07 J cm-2) at optimized pH value (6) and temperature (35 °C). The gas chromatography-mass spectrometry (GC-MS) analysis revealed the biodegradation of 96.5% of the substrate after only 48 h of incubation. The n-C17/Pr and n-C18/Ph ratios indicated a preferential biodegradation of iso-paraffines over normal ones. Meanwhile, pristane/phytane (Pr/Ph) ratios were indicative of selective biodegradation for pristane. The carbon preference index (CPI) was nearly around unity indicating the ability of Janibacter terrae to attack the odd and even n-alkanes simultaneously. These results support the superiority of irradiated bacteria in optimizing the biodegradation efficiency and shortening the time of treatment, thus proposing an eco-friendly technique in water bioremediation programs.
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Affiliation(s)
- Safaa
M. Ezzat
- Microbiology
Department, Central Laboratory for Environmental Quality Monitoring
(CLEQM), National Water Research Center
(NWRC), El-Kanater, 13621/6, Egypt
| | - Nashwa A. Ahmed
- Microbiology
Department, Faculty of Applied Medical Sciences, October 6 University, Giza, 12585, Egypt
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Ghosh P, Mukherji S. Environmental contamination by heterocyclic Polynuclear aromatic hydrocarbons and their microbial degradation. BIORESOURCE TECHNOLOGY 2021; 341:125860. [PMID: 34614557 DOI: 10.1016/j.biortech.2021.125860] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Heterocyclic polynuclear aromatic hydrocarbons (PAHs) have been detected in all environmental matrices at few ppb to several ppm concentrations and they are characterized by high polarity. Some heterocyclic PAHs are mutagenic and carcinogenic to humans and various organisms. Despite being potent environmental pollutants, these compounds have received less attention. This paper focuses on the sources and occurrence of these compounds and their microbial degradation using diverse species of bacteria, fungi, and algae. Complete removal of 1.8 to 2614 mg/L of nitrogen heterocyclic PAH (PANH), 0.27 to 184 mg/L of sulfur heterocyclic PAH (PASH), and 0.6 to 120 mg/L of oxygen heterocyclic PAH (PAOH) compounds by various microbial species was observed between 3 h and 18 days, 8 h to 6 days, and 4 h to 250 h, respectively under aerobic condition. Strategies for enhancing the removal of heterocyclic PAHs from aquatic systems are also discussed along with the challenges.
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Affiliation(s)
- Prasenjit Ghosh
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; Department of Civil Engineering, NIT Tiruchirappalli, Tiruchirappalli, Tamil Nadu 620015, India
| | - Suparna Mukherji
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Ghosh P, Mukherji S. Elucidation of substrate interaction effects in multicomponent systems containing 3-ring homocyclic and heterocyclic polynuclear aromatic hydrocarbons. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:1394-1404. [PMID: 34382630 DOI: 10.1039/d1em00140j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial growth and degradation experiments were conducted on carbazole (CBZ), fluorene (FLU) and dibenzothiophene (DBT) individually and in various mixture combinations using an efficient polynuclear aromatic hydrocarbon (PAH) degrading bacterial strain, Pseudomonas aeruginosa RS1. In single component systems, bacterial growth on CBZ (specific growth rate, μ = 0.99 day-1) was much higher compared to that on FLU (μ = 0.38 day-1) and DBT (μ = 0.33 day-1) and bacterial growth was inhibited in the presence of FLU and DBT in binary (μ = 0.64 day-1) and ternary (μ = 0.75 day-1) mixtures. Multisubstrate additive modelling indicated growth inhibition in all the systems. The degradation of the compounds was significantly inhibited in binary mixtures. While the degradation of the compounds in binary mixtures varied from 35 ± 4% to 73 ± 3%, their degradation varied from 61 ± 5% to 91 ± 4%, when applied as sole substrates and from 77 ± 3% to 96 ± 3%, when applied in a ternary mixture. Degradation experiments were also conducted in ternary mixtures using a 23 full factorial design and the results were examined using analysis of variance (ANOVA) and Tukey's honest significant difference (HSD) tests. At a low concentration of the heterocyclics, CBZ and DBT (5 mg L-1 each), the degradation of the PAH, FLU, was significantly enhanced (from 81 ± 1% to 93 ± 0.3%) when its concentration was increased from 5 to 30 mg L-1. The full factorial design can provide valuable insights into substrate interaction effects in mixtures.
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Affiliation(s)
- Prasenjit Ghosh
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Department of Civil Engineering, National Institute of Technology Goa, Farmagudi, Ponda, Goa 403401, India.
| | - Suparna Mukherji
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Pei S, Xie F, Zhang R, Zhang G. Complete genome sequence of Janibaecter indicus YB324 from an Atlantic marine sediment. Mar Genomics 2020; 58:100833. [PMID: 33341425 DOI: 10.1016/j.margen.2020.100833] [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: 09/17/2020] [Revised: 11/03/2020] [Accepted: 12/01/2020] [Indexed: 11/18/2022]
Abstract
Janibacter indicus YB324, a gram-positive, aerobic and non-motile actinobacterium isolated from south Atlantic sediment at a depth of 2875 m. The complete genome sequence of the strain YB324 was obtained using PacBio Sequel HGAP.4 and comprised of 3,369,845 base pairs with a 71.3 mol% G + C content, 3225 protein-coding genes, 53 RNAs. In silico analysis confirmed the genes associated with polysaccharide hydrolyzation, nitrite reduction, and phenol degradation. Multiple natural product biosynthesis gene clusters were identified as well. The complete genome sequence will provide insight into the potential use of this strain in biotechnological and natural product biosynthesis applications.
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Affiliation(s)
- Shengxiang Pei
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China; State Key Laboratory of Marine Environmental Science, College of Ocean and EarthSciences, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Fuquan Xie
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and EarthSciences, Xiamen University, Xiamen 361102, Fujian, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, PR China
| | - Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, PR China.
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Zhao Q, Jin M, Zhou Z, Zhu L, Zhang Z, Jiang L. Complete Genome Sequence of Janibacter melonis M714, a Janus-Faced Bacterium with Both Human Health Impact and Industrial Applications. Curr Microbiol 2020; 77:1883-1889. [PMID: 32346782 DOI: 10.1007/s00284-020-01951-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 03/09/2020] [Indexed: 10/24/2022]
Abstract
Janibacter, a member of the Intrasporangiaceae family of Actinobacteria, is a Janus-faced bacterium that has both antibiotic resistance/pathogenicity and the ability to degrade pollutants, with significant research value. Here, we isolated the novel strain Janibacter melonis M714 from an irradiated area in Xinjiang Uygur Autonomous Region, China. J. melonis M714 contains one circular chromosome of 3,426,637 bp with a GC content of 72.98% and one plasmid of 54,436 bp with a GC content of 67.80%. The genome of J. melonis M714 contains 2,859 CDSs, 47 tRNA genes, and 6 rRNA genes. Genome assembly and annotation indicated that strain M714 has a high GC content and contains multiple notable functional genes, including a beta-lactam resistance gene and dioxygenase gene, which may be the key determinants of the strain's antibiotic resistance and xenobiotic degradation ability, respectively. The whole genome sequences of J. melonis M714 provide information that is useful for its potential applications in the degradation of pollutants and environmental remediation.
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Affiliation(s)
- Qianru Zhao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 210009, People's Republic of China
| | - Mengmeng Jin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 210009, People's Republic of China
| | - Zhi Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 210009, People's Republic of China.
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing, 210009, People's Republic of China
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Uigur Autonomous Region, Xinjiang Academy of Agricultural Sciences, Urumqi, People's Republic of China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 210009, People's Republic of China.
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Saibu S, Adebusoye SA, Oyetibo GO, Rodrigues DF. Aerobic degradation of dichlorinated dibenzo-p-dioxin and dichlorinated dibenzofuran by bacteria strains obtained from tropical contaminated soil. Biodegradation 2020; 31:123-137. [PMID: 32342243 DOI: 10.1007/s10532-020-09898-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/07/2020] [Indexed: 11/26/2022]
Abstract
Bacterial diversity and aerobic catabolic competence of dioxin-degrading bacterial strains isolated from a polluted soil in the tropics were explored. Isolation of bacteria occurred after 12 months of consecutive enrichment, with dioxin congeners serving as the only sources of carbon and energy. Seventeen strains that were isolated were subsequently screened for dioxin metabolic competence. Among these isolates, five had unique amplified ribosomal DNA restriction analysis (ARDRA) patterns out of which two exhibiting good metabolic competence were selected for further investigation. The two strains were identified as Bacillus sp. SS2 and Serratia sp. SSA1, based on their 16S rRNA gene sequences. Bacterial growth co-occurred with dioxin disappearance and near stoichiometric release of chloride for one ring of the chlorinated congeners. The overall percentage removal of dibenzofuran (DF) by strain SS2 was 93.87%; while corresponding values for 2,8-dichlorodibenzofuran (2,8-diCDF) and 2,7-dichlorodibenzo-p-dioxin (2,7-diCDD) were 86.22% and 82.30% respectively. In the case of strain SSA1, percentage removal for DF, 2,8-diCDF and 2,7-diCDD were respectively 98.9%, 80.97% and 70.80%. The presence of two dioxin dioxygenase catabolic genes (dxnA1 and dbfA1) was investigated. Only the dbfA1 gene could be amplified in SS2 strain. Results further revealed that strain SS2 presented higher expression levels for the alpha-subunit of DF dioxygenase (dbfA1) gene during growth with dioxins. The expression level for dbfA1 gene was higher when growing on DF than on the other chlorinated analogs. This study gives an insight into dioxin degradation, with the catabolic potential of strains SS2 and SSA1 (an enteric bacterium) within the sub-Sahara Africa. It further shows that dioxin catabolic potential might be more prevalent in different groups of microorganisms than previously believed. Few reports have demonstrated the degradation of chlorinated congeners of dioxins, particularly from sub-Saharan African contaminated systems.
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Affiliation(s)
- Salametu Saibu
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos, Nigeria
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77204-4003, USA
| | - Sunday A Adebusoye
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos, Nigeria.
| | - Ganiyu O Oyetibo
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos, Nigeria
| | - Debora F Rodrigues
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77204-4003, USA
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Ji M, Sang W, Tsang DCW, Usman M, Zhang S, Luo G. Molecular and microbial insights towards understanding the effects of hydrochar on methane emission from paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 714:136769. [PMID: 31982762 DOI: 10.1016/j.scitotenv.2020.136769] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Directly returning rice straw to the paddy soil would significantly stimulate methane emission, and hydrochar has potential to be used as soil conditioner. However, the effects of hydrochar on the methane emission from paddy soil and the related mechanisms are still unclear. In the present study, straw-based hydrochar obtained at 200 °C (HC200), 250 °C (HC250) and 300 °C (HC300) and hydrochar after removal of bio-oil at these temperatures (CHC200, CHC250, and CHC300) were prepared and added to the paddy soil. The application of HC200, HC250 and HC300 resulted in the enhanced methane production compared to the control, showing 4.3, 1.6 and 1.5-fold higher methane production, respectively. It was related to the large amount of dissolved organic matter (DOM) released from hydrochar. Excitation-emission matrix fluorescence spectroscopy with parallel factor analysis (EEM-PARAFAC) showed that the hydrochar-derived DOM mainly included humic-like, phenolic and less aromatic structures, and with the increase of hydrothermal temperature, the content of humic-like substances and phenols increased, while biodegradable organics decreased. This was consistent with the maximum methane production by HC200. After incubation, there was no low-aromatic structures observed in the soil leachate, and the residual organics were mainly humus. The EEM-PARAFAC results were supported by compositional characterization of soil leachate by high-resolution mass spectrometry, and the refractory organics released from hydrochar was mainly lignins or (CRAM)-like structures in the range of H/C = 0.8-1.6 and O/C = 0.1-0.5. The organics dissolved from the washed hydrochar was significantly reduced, and some washed hydrochar (CHC250 and CHC300) even inhibited methane emission possibly due to their ability to adsorb organics. Microbial analysis further showed that the increased methane production resulted from hydrochar was associated with the enrichment of Janibacter, Anaeromyxobacter, Anaerolinea and Sporacetigenium. This present study provided a better understanding to the effect of hydrochar on methanogenesis in paddy soil.
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Affiliation(s)
- Mengyuan Ji
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China; Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Wenjing Sang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China.
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Muhammad Usman
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China.
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Saibu S, Adebusoye SA, Oyetibo GO. Aerobic bacterial transformation and biodegradation of dioxins: a review. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-0294-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractWaste generation tends to surge in quantum as the population and living conditions grow. A group of structurally related chemicals of dibenzofurans and dibenzo-p-dioxins including their chlorinated congeners collectively known as dioxins are among the most lethal environmental pollutants formed during different anthropogenic activities. Removal of dioxins from the environment is challenging due to their persistence, recalcitrance to biodegradation, and prevalent nature. Dioxin elimination through the biological approach is considered both economically and environmentally as a better substitute to physicochemical conventional approaches. Bacterial aerobic degradation of these compounds is through two major catabolic routes: lateral and angular dioxygenation pathways. Information on the diversity of bacteria with aerobic dioxin degradation capability has accumulated over the years and efforts have been made to harness this fundamental knowledge to cleanup dioxin-polluted soils. This paper covers the previous decades and recent developments on bacterial diversity and aerobic bacterial transformation, degradation, and bioremediation of dioxins in contaminated systems.
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Thanh LTH, Thi TVN, Shintani M, Moriuchi R, Dohra H, Loc NH, Kimbara K. Isolation and characterization of a moderate thermophilic Paenibacillus naphthalenovorans strain 4B1 capable of degrading dibenzofuran from dioxin-contaminated soil in Vietnam. J Biosci Bioeng 2019; 128:571-577. [DOI: 10.1016/j.jbiosc.2019.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/19/2019] [Accepted: 05/07/2019] [Indexed: 10/26/2022]
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Kosek K, Kozioł K, Luczkiewicz A, Jankowska K, Chmiel S, Polkowska Ż. Environmental characteristics of a tundra river system in Svalbard. Part 2: Chemical stress factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:1585-1596. [PMID: 30446169 DOI: 10.1016/j.scitotenv.2018.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 06/09/2023]
Abstract
Bacterial communities in the Arctic environment are subject to multiple stress factors, including contaminants, although typically their concentrations are small. The Arctic contamination research has focused on persistent organic pollutants (POPs) because they are bioaccumulative, resistant to degradation and toxic for all organisms. Pollutants have entered the Arctic predominantly by atmospheric and oceanic long-range transport, and this was facilitated by their volatile or semi-volatile properties, while their chemical stability extended their lifetimes following emission. Chemicals present in the Arctic at detectable and quantifiable concentrations testify to their global impact. Chemical contamination may induce serious disorders in the integrity of polar ecosystems influencing the growth of bacterial communities. In this study, the abundance and the types of bacteria in the Arctic freshwater were examined and the microbial characteristics were compared to the amount of potentially harmful chemical compounds in particular elements of the Arctic catchment. The highest concentrations of all determined PAHs were observed in two samples in the vicinity of the estuary both in June and September 2016 and were 1964 ng L-1 (R12) and 3901 ng L-1 (R13) in June, and 2179 ng L-1 (R12) and 1349 ng L-1 (R13) in September. Remarkable concentrations of the sum of phenols and formaldehyde were detected also at the outflow of the Revelva river into the sea (R12) and were 0.24 mg L-1 in June and 0.35 mg L-1 in September 2016. The elevated concentrations of chemical compounds near the estuary suggest a potential impact of the water from the lower tributaries (including the glacier-fed stream measured at R13) or the sea currents and the sea aerosol as pollutant sources. The POPs' degradation at low temperature is not well understood but bacteria capable to degrading such compounds were noted in each sampling point.
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Affiliation(s)
- Klaudia Kosek
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Krystyna Kozioł
- Institute of Geography, Faculty of Geography and Biology, Pedagogical University in Cracow, Podchorążych 2, Cracow 30-084, Poland; Institute of Geophysics, Polish Academy of Sciences, 64 Księcia Janusza St., Warsaw 01-452, Poland
| | - Aneta Luczkiewicz
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Katarzyna Jankowska
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Stanisław Chmiel
- Faculty of Earth Sciences and Spatial Management, Maria Curie-Skłodowska University, 2 C-D Kraśnicka Ave., Lublin 20-718, Poland
| | - Żaneta Polkowska
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
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Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi. Sci Rep 2018; 8:14281. [PMID: 30250138 PMCID: PMC6155181 DOI: 10.1038/s41598-018-32688-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/11/2018] [Indexed: 02/08/2023] Open
Abstract
Organic and inorganic xenobiotic compounds can affect the potential ecological function of the soil, altering its biodiversity. Therefore, the response of microbial communities to environmental pollution is a critical issue in soil ecology. Here, a high-throughput sequencing approach was used to investigate the indigenous bacterial and fungal community structure as well as the impact of pollutants on their diversity and richness in contaminated and noncontaminated soils of a National Interest Priority Site of Campania Region (Italy) called "Terra dei Fuochi". The microbial populations shifted in the polluted soils via their mechanism of adaptation to contamination, establishing a new balance among prokaryotic and eukaryotic populations. Statistical analyses showed that the indigenous microbial communities were most strongly affected by contamination rather than by site of origin. Overabundant taxa and Actinobacteria were identified as sensitive biomarkers for assessing soil pollution and could provide general information on the health of the environment. This study has important implications for microbial ecology in contaminated environments, increasing our knowledge of the capacity of natural ecosystems to develop microbiota adapted to polluted soil in sites with high agricultural potential and providing a possible approach for modeling pollution indicators for bioremediation purposes.
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Liu X, Wang W, Hu H, Lu X, Zhang L, Xu P, Tang H. 2-Hydroxy-4-(3′-oxo-3′H-benzofuran-2′-yliden)but-2-enoic acid biosynthesis from dibenzofuran using lateral dioxygenation in a Pseudomonas putida strain B6-2 (DSM 28064). BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0209-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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16
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Ortega RA, Mahnert A, Berg C, Müller H, Berg G. The plant is crucial: specific composition and function of the phyllosphere microbiome of indoor ornamentals. FEMS Microbiol Ecol 2016; 92:fiw173. [PMID: 27624084 DOI: 10.1093/femsec/fiw173] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2016] [Indexed: 11/14/2022] Open
Abstract
The plant microbiome is a key determinant of plant health. Less is known about the phyllosphere microbiota and its driving factors in built environments. To study the variability of the microbiome in relation to plant genotype and climate under different controlled conditions, we investigated 14 phylogenetically diverse plant species grown in the greenhouses of the Botanical Garden in Graz (Austria). All investigated plants showed specific bacterial abundances of up to 10(6) CFU cm(-2) on their leaves. Bacterial diversity (H('): 2.4-7.9) and number of putative OTUs (461-2013) were strongly plant species dependent. Statistical analysis showed a significantly higher correlation of community composition to plant genotype in comparison to the ambient climatic variables. In addition to the microbiome structure, we studied the antagonistic potential towards the foliar pathogen Botrytis cinerea as functional indicator. A high proportion of isolates (up to 58%) were able to inhibit pathogen growth by production of volatile organic compounds (VOCs). Data of structure and function were linked: frequently isolated VOCs producers (e.g. Bacillus and Stenotrophomonas) were highly present in phyllosphere communities, which were dominated by members of Firmicutes This study indicates that indoor ornamentals feature a distinct, stable microbiota on leaves irrespective of the indoor climate.
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Affiliation(s)
- Rocel Amor Ortega
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria University of the Philippines Baguio, 2600 Baguio City, Philippines
| | - Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Christian Berg
- Institute of Plant Sciences, University of Graz, 8010 Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria
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Chakraborty J, Das S. Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:16883-16903. [PMID: 27234838 DOI: 10.1007/s11356-016-6887-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/11/2016] [Indexed: 06/05/2023]
Abstract
Nutrition and pollution stress stimulate genetic adaptation in microorganisms and assist in evolution of diverse metabolic pathways for their survival on several complex organic compounds. Persistent organic pollutants (POPs) are highly lipophilic in nature and cause adverse effects to the environment and human health by biomagnification through the food chain. Diverse microorganisms, harboring numerous plasmids and catabolic genes, acclimatize to these environmentally unfavorable conditions by gene duplication, mutational drift, hypermutation, and recombination. Genetic aspects of some major POP catabolic genes such as biphenyl dioxygenase (bph), DDT 2,3-dioxygenase, and angular dioxygenase assist in degradation of biphenyl, organochlorine pesticides, and dioxins/furans, respectively. Microbial metagenome constitutes the largest genetic reservoir with miscellaneous enzymatic activities implicated in degradation. To tap the metabolic potential of microorganisms, recent techniques like sequence and function-based screening and substrate-induced gene expression are proficient in tracing out novel catabolic genes from the entire metagenome for utilization in enhanced biodegradation. The major endeavor of today's scientific world is to characterize the exact genetic mechanisms of microbes for bioremediation of these toxic compounds by excavating into the uncultured plethora. This review entails the effect of POPs on the environment and involvement of microbial catabolic genes for their removal with the advanced techniques of bioremediation.
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Affiliation(s)
- Jaya Chakraborty
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India.
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Ettoumi B, Chouchane H, Guesmi A, Mahjoubi M, Brusetti L, Neifar M, Borin S, Daffonchio D, Cherif A. Diversity, ecological distribution and biotechnological potential of Actinobacteria inhabiting seamounts and non-seamounts in the Tyrrhenian Sea. Microbiol Res 2016; 186-187:71-80. [DOI: 10.1016/j.micres.2016.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 03/31/2016] [Indexed: 11/26/2022]
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Chakraborty J, Das S. Characterization of the metabolic pathway and catabolic gene expression in biphenyl degrading marine bacterium Pseudomonas aeruginosa JP-11. CHEMOSPHERE 2016; 144:1706-1714. [PMID: 26519802 DOI: 10.1016/j.chemosphere.2015.10.059] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 06/05/2023]
Abstract
Metabolic pathway of biphenyl assimilation and the catabolic gene expression in a marine bacterium Pseudomonas aeruginosa JP-11, isolated from the coastal sediments of Odisha, India have been studied. This strain utilized 98.86% ± 2.29% of biphenyl within 72 h when supplied as the sole source of carbon, however, preferential utilization of glucose was observed over catechol and biphenyl when grown in a complex medium. Combination of chromatographic and spectrophotometric techniques confirmed the catechol pathway and identified 2-Hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate as the intermediate metabolic product. Assimilation of biphenyl was initiated by its dioxygenation, forming cis-2, 3-dihydro-2, 3-dihydroxybiphenyl subsequently transformed to 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate. In the lower pathway, cis-1, 6-dihydroxy-2, 4-cyclohexadiene-1-carboxylic acid was detected which formed catechol before entering into the Krebs cycle. Detection of key enzyme catechol-1, 2-dioxygenase in the cell-free extract of P. aeruginosa JP-11 supported the proposed degradation pathway. The primary enzyme for biphenyl assimilation, biphenyl dioxygenase encoded by bphA gene was found in the genome of the isolate. On increasing biphenyl stress (50, 100, 150 and 200 mg L(-1)), bphA gene showed a significant (P < 0.01) up-regulation upto 43.5 folds. Production of biosurfactant was confirmed and the rhamnolipid synthesizing gene rhlAB was amplified. This gene also showed a significant (P < 0.01) up-regulation upto 258 folds on increasing biphenyl stress.
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Affiliation(s)
- Jaya Chakraborty
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India.
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20
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Colonization on root surface by a phenanthrene-degrading endophytic bacterium and its application for reducing plant phenanthrene contamination. PLoS One 2014; 9:e108249. [PMID: 25247301 PMCID: PMC4172705 DOI: 10.1371/journal.pone.0108249] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 08/27/2014] [Indexed: 11/19/2022] Open
Abstract
A phenanthrene-degrading endophytic bacterium, Pn2, was isolated from Alopecurus aequalis Sobol grown in soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Based on morphology, physiological characteristics and the 16S rRNA gene sequence, it was identified as Massilia sp. Strain Pn2 could degrade more than 95% of the phenanthrene (150 mg·L−1) in a minimal salts medium (MSM) within 48 hours at an initial pH of 7.0 and a temperature of 30°C. Pn2 could grow well on the MSM plates with a series of other PAHs, including naphthalene, acenaphthene, anthracene and pyrene, and degrade them to different degrees. Pn2 could also colonize the root surface of ryegrass (Lolium multiflorum Lam), invade its internal root tissues and translocate into the plant shoot. When treated with the endophyte Pn2 under hydroponic growth conditions with 2 mg·L−1 of phenanthrene in the Hoagland solution, the phenanthrene concentrations in ryegrass roots and shoots were reduced by 54% and 57%, respectively, compared with the endophyte-free treatment. Strain Pn2 could be a novel and useful bacterial resource for eliminating plant PAH contamination in polluted environments by degrading the PAHs inside plants. Furthermore, we provide new perspectives on the control of the plant uptake of PAHs via endophytic bacteria.
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Khessairi A, Fhoula I, Jaouani A, Turki Y, Cherif A, Boudabous A, Hassen A, Ouzari H. Pentachlorophenol degradation by Janibacter sp., a new actinobacterium isolated from saline sediment of arid land. BIOMED RESEARCH INTERNATIONAL 2014; 2014:296472. [PMID: 25313357 PMCID: PMC4182692 DOI: 10.1155/2014/296472] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 08/17/2014] [Indexed: 11/17/2022]
Abstract
Many pentachlorophenol- (PCP-) contaminated environments are characterized by low or elevated temperatures, acidic or alkaline pH, and high salt concentrations. PCP-degrading microorganisms, adapted to grow and prosper in these environments, play an important role in the biological treatment of polluted extreme habitats. A PCP-degrading bacterium was isolated and characterized from arid and saline soil in southern Tunisia and was enriched in mineral salts medium supplemented with PCP as source of carbon and energy. Based on 16S rRNA coding gene sequence analysis, the strain FAS23 was identified as Janibacter sp. As revealed by high performance liquid chromatography (HPLC) analysis, FAS23 strain was found to be efficient for PCP removal in the presence of 1% of glucose. The conditions of growth and PCP removal by FAS23 strain were found to be optimal in neutral pH and at a temperature of 30 °C. Moreover, this strain was found to be halotolerant at a range of 1-10% of NaCl and able to degrade PCP at a concentration up to 300 mg/L, while the addition of nonionic surfactant (Tween 80) enhanced the PCP removal capacity.
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Affiliation(s)
- Amel Khessairi
- Université Tunis El Manar, Faculté des Sciences de Tunis (FST), LR03ES03 Laboratoire de Microorganisme et Biomolécules Actives, Campus Universitaire, 2092 Tunis, Tunisia
- Laboratoire de Traitement et Recyclage des Eaux, Centre des Recherches et Technologie des Eaux (CERTE), Technopôle Borj-Cédria, B.P. 273, 8020 Soliman, Tunisia
| | - Imene Fhoula
- Université Tunis El Manar, Faculté des Sciences de Tunis (FST), LR03ES03 Laboratoire de Microorganisme et Biomolécules Actives, Campus Universitaire, 2092 Tunis, Tunisia
| | - Atef Jaouani
- Université Tunis El Manar, Faculté des Sciences de Tunis (FST), LR03ES03 Laboratoire de Microorganisme et Biomolécules Actives, Campus Universitaire, 2092 Tunis, Tunisia
| | - Yousra Turki
- Laboratoire de Traitement et Recyclage des Eaux, Centre des Recherches et Technologie des Eaux (CERTE), Technopôle Borj-Cédria, B.P. 273, 8020 Soliman, Tunisia
| | - Ameur Cherif
- Université de Manouba, Institut Supérieur de Biotechnologie de Sidi Thabet, LR11ES31 Laboratoire de Biotechnologie et Valorization des Bio-Geo Resources, Biotechpole de Sidi Thabet, 2020 Ariana, Tunisia
| | - Abdellatif Boudabous
- Université Tunis El Manar, Faculté des Sciences de Tunis (FST), LR03ES03 Laboratoire de Microorganisme et Biomolécules Actives, Campus Universitaire, 2092 Tunis, Tunisia
| | - Abdennaceur Hassen
- Laboratoire de Traitement et Recyclage des Eaux, Centre des Recherches et Technologie des Eaux (CERTE), Technopôle Borj-Cédria, B.P. 273, 8020 Soliman, Tunisia
| | - Hadda Ouzari
- Université Tunis El Manar, Faculté des Sciences de Tunis (FST), LR03ES03 Laboratoire de Microorganisme et Biomolécules Actives, Campus Universitaire, 2092 Tunis, Tunisia
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Jiang B, Li A, Cui D, Cai R, Ma F, Wang Y. Biodegradation and metabolic pathway of sulfamethoxazole by Pseudomonas psychrophila HA-4, a newly isolated cold-adapted sulfamethoxazole-degrading bacterium. Appl Microbiol Biotechnol 2014; 98:4671-81. [DOI: 10.1007/s00253-013-5488-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/19/2013] [Accepted: 12/20/2013] [Indexed: 10/25/2022]
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Le T, Murugesan K, Nam IH, Jeon JR, Chang YS. Degradation of dibenzofuran via multiple dioxygenation by a newly isolated Agrobacterium
sp. PH-08. J Appl Microbiol 2013; 116:542-53. [DOI: 10.1111/jam.12403] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 11/05/2013] [Accepted: 11/19/2013] [Indexed: 11/30/2022]
Affiliation(s)
- T.T. Le
- School of Environmental Science and Engineering; Pohang University of Science and Technology (POSTECH); Pohang Korea
| | - K. Murugesan
- School of Environmental Science and Engineering; Pohang University of Science and Technology (POSTECH); Pohang Korea
| | - I.-H. Nam
- School of Environmental Science and Engineering; Pohang University of Science and Technology (POSTECH); Pohang Korea
| | - J.-R. Jeon
- School of Environmental Science and Engineering; Pohang University of Science and Technology (POSTECH); Pohang Korea
| | - Y.-S. Chang
- School of Environmental Science and Engineering; Pohang University of Science and Technology (POSTECH); Pohang Korea
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Jin HM, Choi EJ, Jeon CO. Isolation of a BTEX-degrading bacterium, Janibacter sp. SB2, from a sea-tidal flat and optimization of biodegradation conditions. BIORESOURCE TECHNOLOGY 2013; 145:57-64. [PMID: 23453980 DOI: 10.1016/j.biortech.2013.02.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 02/01/2013] [Accepted: 02/02/2013] [Indexed: 06/01/2023]
Abstract
An enrichment culture was established using seawater containing BTEX (benzene, toluene, ethylbenzene and xylene) compounds to isolate a BTEX-degrading bacterium from contaminated sea-tidal flat. The enriched microbial communities were characterized by 16S rRNA-based DGGE profiling, which indicated that a Janibacter species was dominant during the enrichment. Strain SB2, corresponding to the major band and able to degrade all BTEX compounds, was isolated and characterized. NH4Cl, NaH2PO4, cell mass and BTEX concentrations were used as independent variables to optimize the degradation of BTEX by strain SB2 in a tidal flat and a statistically significant (R(2)=0.8933, p<0.0001) quadratic polynomial mathematical model was suggested. For the initial concentration of 240 mg/L BTEX in a slurry system containing 3.0×10(7) cells/L, 45.5% BTEX removal was observed under the optimum condition of NH4Cl and NaH2PO4, while 32.2% BTEX removal was observed under the untreated condition of NH4Cl and NaH2PO4.
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Affiliation(s)
- Hyun Mi Jin
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
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Peng P, Yang H, Jia R, Li L. Biodegradation of dioxin by a newly isolated Rhodococcus sp. with the involvement of self-transmissible plasmids. Appl Microbiol Biotechnol 2012; 97:5585-95. [DOI: 10.1007/s00253-012-4363-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 08/07/2012] [Accepted: 08/09/2012] [Indexed: 10/27/2022]
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DeBruyn JM, Mead TJ, Sayler GS. Horizontal transfer of PAH catabolism genes in Mycobacterium: evidence from comparative genomics and isolated pyrene-degrading bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:99-106. [PMID: 21899303 DOI: 10.1021/es201607y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Biodegradation of high molecular weight polycyclic aromatic hydrocarbons (PAHs), such as pyrene and benzo[a]pyrene, has only been observed in a few genera, namely fast-growing Mycobacterium and Rhodococcus. In M. vanbaalenii PYR-1, multiple aromatic ring hydroxylating dioxygenase (ARHDOs) genes including pyrene dioxygenases nidAB and nidA3B3 are localized in one genomic region. Here we examine the homologous genomic regions in four other PAH-degrading Mycobacterium (strains JLS, KMS, and MCS, and M. gilvum PYR-GCK), presenting evidence for past horizontal gene transfer events. Seven distinct types of ARHDO genes are present in all five genomes, and display conserved syntenic architecture with respect to gene order, orientation, and association with other genes. Duplications and putative integrase and transposase genes suggest past gene shuffling. To corroborate these observations, pyrene-degrading strains were isolated from two PAH-contaminated sediments: Chattanooga Creek (Tennessee) and Lake Erie (western basin). Some were related to fast-growing Mycobacterium spp. and carried both nidA and nidA3 genes. Other isolates belonged to Microbacteriaceae and Intrasporangiaceae presenting the first evidence of pyrene degradation in these families. These isolates had nidA (and some, nidA3) genes that were homologous to Mycobacterial ARHDO genes, suggesting that horizontal gene transfer events have occurred.
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Affiliation(s)
- Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Tennessee, United States
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27
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Stable isotope probing identifies anthracene degraders under methanogenic conditions. Biodegradation 2011; 23:221-30. [DOI: 10.1007/s10532-011-9501-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Accepted: 07/22/2011] [Indexed: 10/17/2022]
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Zhang GY, Ling JY, Sun HB, Luo J, Fan YY, Cui ZJ. Isolation and characterization of a newly isolated polycyclic aromatic hydrocarbons-degrading Janibacter anophelis strain JY11. JOURNAL OF HAZARDOUS MATERIALS 2009; 172:580-586. [PMID: 19660861 DOI: 10.1016/j.jhazmat.2009.07.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 07/10/2009] [Accepted: 07/10/2009] [Indexed: 05/28/2023]
Abstract
The PAHs-degradation bacterium strain JY11 was newly isolated from the polluted soil in Jinan Oil Refinery Factory, Shandong Province of China. The isolate was identified as Janibacter anophelis with respect to its 16S rDNA sequence, DNA-DNA relatedness and fatty acid profiles, as well as various physiological characteristics. The strain was Gram-positive, non-motile, non-spore-forming, short rods in young culture, 0.8-1.0 microm in diameter and 1.3-1.6 microm long, and coccoid cells in the stationary phase of growth that are 1.0-1.2 microm in diameter and 1.3-1.5 microm long, occurred in pairs and sometimes in chains or in group, aerobic, oxidase-week positive, catalase-positive. J. anophelis strain JY11 can utilize naphthalene, phenanthrene, anthracene, pyrene, xylene, methanol, ethanol and salicylic acid as sole carbon source. The strain could remove 98.5% of phenanthrene, 82.1% of anthracene, and 97.7% of pyrene with an initial concentration of 500 ppm in five days without adding co-metabolism substrates and surfactants.
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Affiliation(s)
- Guo-Ying Zhang
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
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Kimura N, Kamagata Y. Impact of dibenzofuran/dibenzo-p-dioxin amendment on bacterial community from forest soil and ring-hydroxylating dioxygenase gene populations. Appl Microbiol Biotechnol 2009; 84:365-73. [PMID: 19513710 DOI: 10.1007/s00253-009-2046-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 05/11/2009] [Accepted: 05/12/2009] [Indexed: 10/20/2022]
Abstract
The impact of dibenzofuran (DF) and dibenzo-p-dioxin (DD) on the changes in bacterial community structure and the transition of catabolic genes were studied using forest soil. The bacterial community structure of soil suspensions amended with 1 microg/g of either DF or DD was analyzed by 16S rRNA and functional gene sequencing. To analyze the functional genes in the communities, we targeted a gene sequence that functions as the binding site of Rieske iron sulfur center common to ring-hydroxylating dioxygenases (RHDs) for monocyclic, bicyclic, and tricyclic aromatic compounds. The gene fragments were polymerase chain reaction-amplified from DNAs extracted from soil suspensions spiked with either DF or DD, cloned, and sequenced (70 clones). Bacterial community analysis based on 16S rRNA genes revealed that specific 16S rRNA gene sequences, in particular, phylotypes within alpha-Proteobacteria, increased in the soil suspension amended with DF or DD. RHD gene-based functional community analysis showed that, in addition to two groups of RHD genes that were also detected in unamended soil suspensions, another two groups of RHD genes, each of which is specific to DF- and DD-amended soil, respectively, emerged to a great extent. The DD-specific genotype is phylogenetically distant from any known RHDs. These results strongly suggest that soil microbial community potentially harbors a wide array of organisms having diverse RHDs including those previously unknown, and that they could quickly respond to an impact of contamination of hazardous chemicals by changing the microbial community and gene diversity.
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Affiliation(s)
- Nobutada Kimura
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan.
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Bacterial degradation of aromatic compounds. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2009; 6:278-309. [PMID: 19440284 PMCID: PMC2672333 DOI: 10.3390/ijerph6010278] [Citation(s) in RCA: 459] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 01/06/2009] [Indexed: 11/21/2022]
Abstract
Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.
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Li A, Qu Y, Zhou J, Gou M. Isolation and characteristics of a novel biphenyl-degrading bacterial strain, Dyella ginsengisoli LA-4. J Environ Sci (China) 2009; 21:211-217. [PMID: 19402424 DOI: 10.1016/s1001-0742(08)62253-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A novel biphenyl-degrading bacterial strain LA-4 was isolated from activated sludge. It was identified as Dyella ginsengisoli according to phylogenetic similarity of 16S rRNA gene sequence. This isolate could utilize biphenyl as sole source of carbon and energy, which degraded over 95 mg/L biphenyl within 36 h. The major metabolites formed from biphenyl, such as 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) and benzoic acid, were identified by LC-MS. The crude cell extract of strain LA-4 exhibited the activity of 2,3-dihydroxybiphenyl 1,2-dioxygenase (2,3-DHBD) and the kinetic parameters K(m) was 26.48 micromol/L and V(max) was 8.12 U/mg protein. A conserved region of the biphenyl dioxygenase gene bphA1 of strain LA-4 was amplified by PCR and confirmed by DNA sequencing.
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Affiliation(s)
- Ang Li
- School of Environmental and Biological Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), Dalian University of Technology, Dalian 116024, China.
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Miyauchi K, Sukda P, Nishida T, Ito E, Matsumoto Y, Masai E, Fukuda M. Isolation of dibenzofuran-degrading bacterium, Nocardioides sp. DF412, and characterization of its dibenzofuran degradation genes. J Biosci Bioeng 2008; 105:628-35. [DOI: 10.1263/jbb.105.628] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Accepted: 03/05/2008] [Indexed: 11/17/2022]
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Two angular dioxygenases contribute to the metabolic versatility of dibenzofuran-degrading Rhodococcus sp. strain HA01. Appl Environ Microbiol 2008; 74:3812-22. [PMID: 18441103 DOI: 10.1128/aem.00226-08] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodococcus sp. strain HA01, isolated through its ability to utilize dibenzofuran (DBF) as the sole carbon and energy source, was also capable, albeit with low activity, of transforming dibenzo-p-dioxin (DD). This strain could also transform 3-chlorodibenzofuran (3CDBF), mainly by angular oxygenation at the ether bond-carrying carbon (the angular position) and an adjacent carbon atom, to 4-chlorosalicylate as the end product. Similarly, 2-chlorodibenzofuran (2CDBF) was transformed to 5-chlorosalicylate. However, lateral oxygenation at the 3,4-positions was also observed and yielded the novel product 2-chloro-3,4-dihydro-3,4-dihydroxydibenzofuran. Two gene clusters encoding enzymes for angular oxygenation (dfdA1A2A3A4 and dbfA1A2) were isolated, and expression of both was observed during growth on DBF. Heterologous expression revealed that both oxygenase systems catalyze angular oxygenation of DBF and DD but exhibited complementary substrate specificity with respect to CDBF transformation. While DfdA1A2A3A4 oxygenase, with high similarity to DfdA1A2A3A4 oxygenase from Terrabacter sp. strain YK3, transforms 3CDBF by angular dioxygenation at a rate of 29% +/- 4% that of DBF, 2CDBF was not transformed. In contrast, DbfA1A2 oxygenase, with high similarity to the DbfA1A2 oxygenase from Terrabacter sp. strain DBF63, exhibited complementary activity with angular oxygenase activity against 2CDBF but negligible activity against 3CDBF. Thus, Rhodococcus sp. strain HA01 constitutes the first described example of a bacterial strain where coexpression of two angular dioxygenases was observed. Such complementary activity allows for the efficient transformation of chlorinated DBFs.
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Gai Z, Yu B, Li L, Wang Y, Ma C, Feng J, Deng Z, Xu P. Cometabolic degradation of dibenzofuran and dibenzothiophene by a newly isolated carbazole-degrading Sphingomonas sp. strain. Appl Environ Microbiol 2007; 73:2832-8. [PMID: 17337542 PMCID: PMC1892858 DOI: 10.1128/aem.02704-06] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 02/20/2007] [Indexed: 11/20/2022] Open
Abstract
A carbazole-utilizing bacterium was isolated by enrichment from petroleum-contaminated soil. The isolate, designated Sphingomonas sp. strain XLDN2-5, could utilize carbazole (CA) as the sole source of carbon, nitrogen, and energy. Washed cells of strain XLDN2-5 were shown to be capable of degrading dibenzofuran (DBF) and dibenzothiophene (DBT). Examination of metabolites suggested that XLDN2-5 degraded DBF to 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienic acid and subsequently to salicylic acid through the angular dioxygenation pathway. In contrast to DBF, strain XLDN2-5 could transform DBT through the ring cleavage and sulfoxidation pathways. Sphingomonas sp. strain XLDN2-5 could cometabolically degrade DBF and DBT in the growing system using CA as a substrate. After 40 h of incubation, 90% of DBT was transformed, and CA and DBF were completely removed. These results suggested that strain XLDN2-5 might be useful in the bioremediation of environments contaminated by these compounds.
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Affiliation(s)
- Zhonghui Gai
- State Key Laboratory of Microbial Technology, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Yu B, Ma C, Zhou W, Zhu S, Wang Y, Qu J, Li F, Xu P. Simultaneous biodetoxification of S, N, and O pollutants by engineering of a carbazole-degrading gene cassette in a recombinant biocatalyst. Appl Environ Microbiol 2006; 72:7373-6. [PMID: 16936043 PMCID: PMC1636170 DOI: 10.1128/aem.01374-06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 08/14/2006] [Indexed: 11/20/2022] Open
Abstract
The gene cassette encoding enzymes responsible for degrading carbazole to anthranilic acid was introduced into a dibenzothiophene degrader. The resultant strain, Rhodococcus erythropolis XPDN, could simultaneously transform the model pollutants dibenzothiophene, carbazole, and dibenzofuran to nontoxic metabolites and may have an application potential for bioremediation.
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Affiliation(s)
- Bo Yu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
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Kleinsteuber S, Riis V, Fetzer I, Harms H, Müller S. Population dynamics within a microbial consortium during growth on diesel fuel in saline environments. Appl Environ Microbiol 2006; 72:3531-42. [PMID: 16672500 PMCID: PMC1472369 DOI: 10.1128/aem.72.5.3531-3542.2006] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity and dynamics of a bacterial community extracted from an exploited oil field with high natural soil salinity near Comodoro Rivadavia in Patagonia (Argentina) were investigated. Community shifts during long-term incubation with diesel fuel at four salinities between 0 and 20% NaCl were monitored by single-strand conformation polymorphism community fingerprinting of the PCR-amplified V4-V5 region of the 16S rRNA genes. Information obtained by this qualitative approach was extended by flow cytometric analysis to follow quantitatively the dynamics of community structures at different salinities. Dominant and newly developing clusters of individuals visualized via their DNA patterns versus cell sizes were used to identify the subcommunities primarily involved in the degradation process. To determine the most active species, subcommunities were separated physically by high-resolution cell sorting and subsequent phylogenetic identification by 16S rRNA gene sequencing. Reduced salinity favored the dominance of Sphingomonas spp., whereas at elevated salinities, Ralstonia spp. and a number of halophilic genera, including Halomonas, Dietzia, and Alcanivorax, were identified. The combination of cytometric sorting with molecular characterization allowed us to monitor community adaptation and to identify active and proliferating subcommunities.
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Affiliation(s)
- Sabine Kleinsteuber
- UFZ Centre for Environmental Research Leipzig-Halle, Department of Environmental Microbiology, Permoserstrasse 15, 04318 Leipzig, Germany
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Xu P, Yu B, Li FL, Cai XF, Ma CQ. Microbial degradation of sulfur, nitrogen and oxygen heterocycles. Trends Microbiol 2006; 14:398-405. [PMID: 16860985 DOI: 10.1016/j.tim.2006.07.002] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Revised: 06/12/2006] [Accepted: 07/07/2006] [Indexed: 10/24/2022]
Abstract
Sulfur (S), nitrogen (N) and oxygen (O) heterocycles are among the most potent environmental pollutants. Microbial degradation of these pollutants is attracting more and more attention because such bioprocesses are environmentally friendly. The biotechnological potential of these processes is being investigated, for example, to achieve better sulfur removal by immobilized biocatalysts with magnetite nanoparticles or by solvent-tolerant bacteria, and to obtain valuable intermediates from these heterocycles. Other recent advances have demonstrated the mechanisms of angular dioxygenation of nitrogen heterocycles by microbes. However, these technologies are not yet available for large-scale applications so future research must investigate proper modifications for industrial applications of these processes. This review focuses on recent progress in understanding how microbes degrade S, N and O heterocycles.
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Affiliation(s)
- Ping Xu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China.
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Jin S, Zhu T, Xu X, Xu Y. Biodegradation of Dibenzofuran by Janibacter terrae Strain XJ-1. Curr Microbiol 2006; 53:30-6. [PMID: 16775784 DOI: 10.1007/s00284-005-0180-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Accepted: 12/02/2005] [Indexed: 10/24/2022]
Abstract
The dibenzofuran (DF)-degrading bacterium, Janibacter terrae strain XJ-1, was isolated from sediment from East Lake in Wuhan, China. This strain grows aerobically on DF as the sole source of carbon and energy; it has a doubling time of 12 hours at 30 degrees C; and it almost completely degraded 100 mg/L(-1) DF in 5 days, producing 2,2',3-trihydroxybiphenyl, salicylic acid, gentisic acid, and other metabolites. The dbdA (DF dioxygenase) gene cluster in the strain is almost identical to that on a large plasmid in Terrabacter sp. YK3. Unlike Janibacter sp. strain YY-1, XJ-1 accumulates gentisic acid rather than catechol as a final product of DF degradation.
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Affiliation(s)
- Shiwei Jin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
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Iida T, Nakamura K, Izumi A, Mukouzaka Y, Kudo T. Isolation and characterization of a gene cluster for dibenzofuran degradation in a new dibenzofuran-utilizing bacterium, Paenibacillus sp. strain YK5. Arch Microbiol 2005; 184:305-15. [PMID: 16284749 DOI: 10.1007/s00203-005-0045-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Revised: 08/15/2005] [Accepted: 09/19/2005] [Indexed: 10/25/2022]
Abstract
Spore-forming bacterial strains capable of utilizing dibenzofuran (DF) as a sole source of carbon and energy were isolated. Characteristics of the isolates justified their classification into the genus Paenibacillus, and their closest relative was P. naphthalenovorans. Degenerate primers for aromatic hydrocarbon dioxygenase alpha subunit (AhDOa) genes and genomic DNA of the strain YK5 were used for gene isolation. The nucleotide sequences of clones of the PCR products revealed that the strain YK5 carries at least five different AhDOa genes. Northern hybridization analysis showed that one of the AhDOa genes was transcribed under DF-containing culture conditions. A gene cluster encoding the AhDOa was isolated. The genes predicted to encode extradiol dioxygenase (dbfB) and hydrolase (dbfC) were found to be an upstream of genes encoding the alpha and beta subunit of the AhDO (dbfA1 and dbfA2, respectively); the latter two gene products showed 60 and 53% identity to the amino acid sequences of DbfA1 and DbfA2 of Terrabacter sp. DBF63, respectively. Two Paenibacillus validus JCM 9077 strains transformed with the dbf gene clusters acquired the ability to convert DF to 2,2',3-trihydroxybiphenyl (THBP) and salicylic acid (SAL). These results suggest that the enzymes encoded by the gene cluster isolated in this study are involved in DF metabolism in YK5.
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Affiliation(s)
- Toshiya Iida
- Environmental Molecular Biology Laboratory, RIKEN, Wako, Saitama 351-0198, Japan.
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Futamata H, Uchida T, Yoshida N, Yonemitsu Y, Hiraishi A. Distribution of Dibenzofuran-Degrading Bacteria in Soils Polluted with Different Levels of Polychlorinated Dioxins. Microbes Environ 2004. [DOI: 10.1264/jsme2.19.172] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Hiroyuki Futamata
- Department of Ecological Engineering, Toyohashi University of Technology
| | - Tetsuya Uchida
- Department of Ecological Engineering, Toyohashi University of Technology
| | - Naoko Yoshida
- Department of Ecological Engineering, Toyohashi University of Technology
| | | | - Akira Hiraishi
- Department of Ecological Engineering, Toyohashi University of Technology
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