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Zhang H, Wu J, Li R, Kim DH, Bi X, Zhang G, Jiang B, Yong Ng H, Shi X. Novel intertidal wetland sediment-inoculated moving bed biofilm reactor treating high-salinity wastewater: Metagenomic sequencing revealing key functional microorganisms. BIORESOURCE TECHNOLOGY 2022; 348:126817. [PMID: 35134521 DOI: 10.1016/j.biortech.2022.126817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
In this study, two lab-scale moving bed biofilm reactors (MBBR), seeded with intertidal wetland sediment (IWS) and activated sludge (AS), were constructed to compare their performances in treating high-salinity (3%) wastewater. Under a wide range of influent TOC (178-620 mg/L) and NH4+-N (25-100 mg/L), both the MBBRs (Riws and Ras) exhibited excellent TOC removal efficiencies of >95%. Regarding nitrogen reduction, Riws exhibited a significantly superior TN removal efficiency of 90.2 ± 1.8% than that of Ras (76.8 ± 2.9%). A correlation analysis was innovatively conducted comparing the results between metagenomic sequencing and DNA pyrosequencing, and positive linear relationships were found with R2 values of 0.763-0.945. Meanwhile, for illustration of different TN removal performance, nitrogen metabolic pathways were also assessed. Moreover, a list of functional oxidases (EC: 1.13.11.1, EC: 1.13.11.2, EC: 1.13.11.24, EC: 1.13.12.16, EC: 1.4.3.4, EC: 1.16.3.3, EC: 1.14.14.28) was found in IWS, revealing its potential in degradation of recalcitrant organics.
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Affiliation(s)
- Haifeng Zhang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - Jiahua Wu
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - Ruifeng Li
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - Dong-Hoon Kim
- Department of Smart City Engineering, Inha University, 100 Inharo, Michuhol-gu, Incheon 22212, South Korea
| | - Xuejun Bi
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - Guoli Zhang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - Bo Jiang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China
| | - How Yong Ng
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Dr. 2, 117576, Singapore
| | - Xueqing Shi
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, PR China.
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Mapelli F, Barbato M, Chouaia B, Riva V, Daffonchio D, Borin S. Bacterial community structure and diversity along the halocline of Tyro deep-sea hypersaline anoxic basin. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01667-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Tyro is a deep hypersaline anoxic basin (DHAB) located at the seafloor of the Eastern Mediterranean sea. Tyro hosts a stratified eukaryotic microbiome moving from seawater to the brine, but no reports are available on its prokaryotic community. We provide the first snapshot of the bacterial community structure in Tyro brine, seawater-brine interface, and the overlaying deep seawater.
Methods
In this study, we combined the use of molecular analyses, i.e., DNA fingerprinting and 16S rRNA pyrosequencing for the description of the bacterial community structure and taxonomy. PiCRUST2 was used to infer information on the prokaryotes functional diversity. A culture-dependent approach was applied to enrich bacteria of interest for marine biotechnology.
Results
Bacterial communities sharply clustered moving from the seawater to the Tyro brine, in agreement with the abrupt increase of salinity values. Moreover, specific taxonomic groups inhabited the seawater-brine interface compared to the overlaying seawater and their identification revealed converging taxonomy with other DHABs in the Eastern Mediterranean sea. Functional traits inferred from the prokaryote taxonomy in the upper interface and the overlaying seawater indicated metabolic pathways for the synthesis of osmoprotectants, likely involved in bacterial adaptation to the steep increasing salinity. Metabolic traits related to methane and methylated compounds and to hydrocarbon degradation were also revealed in the upper interface of Tyro. The overall capability of the Tyro microbiome for hydrocarbon metabolism was confirmed by the isolation of hydrocarbonoclastic bacteria in the sediments.
Conclusions
Our results suggest that Tyro seawater-brine interface hosts a specific microbiome adapted to the polyextreme condition typical of DHABs with potential metabolic features that could be further explored for the characterization of the metabolic network connecting the brine with the deep seawater through the chemocline. Moreover, Tyro could be a reservoir of culturable microbes endowed with functionalities of interest for biotechnological applications like hydrocarbon bioremediation.
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Suárez-Moo P, Lamelas A, Garcia-Bautista I, Barahona-Pérez LF, Sandoval-Flores G, Valdes-Lozano D, Toledano-Thompson T, Polanco-Lugo E, Valdez-Ojeda R. Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico. PeerJ 2020; 8:e10339. [PMID: 33354414 PMCID: PMC7731659 DOI: 10.7717/peerj.10339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
Background Coastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites. Methods The potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation. Results We found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution.
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Affiliation(s)
- Pablo Suárez-Moo
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, Xalapa, Veracruz, Mexico
| | - Araceli Lamelas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, Xalapa, Veracruz, Mexico
| | - Itza Garcia-Bautista
- Unidad de Energia Renovable, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
| | | | - Gloria Sandoval-Flores
- Unidad Académica Multidisciplinaria Reynosa-Aztlán, Universidad Autonoma de Tamaulipas, Merida, Yucatan, Mexico
| | - David Valdes-Lozano
- Centro de Investigación y de Estudios Avanzados, Insituto Politecnico Nacional, Merida, Yucatan, Mexico
| | - Tanit Toledano-Thompson
- Unidad de Energia Renovable, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
| | - Erik Polanco-Lugo
- Campus de Ciencias Biológicas y Agropecuarias,, Universidad Autonoma de Yucatan, Merida, Yucatan, Mexico
| | - Ruby Valdez-Ojeda
- Unidad de Energia Renovable, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
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Hocinat A, Boudemagh A, Ali-Khodja H, Medjemadj M. Aerobic degradation of BTEX compounds by Streptomyces species isolated from activated sludge and agricultural soils. Arch Microbiol 2020; 202:2481-2492. [PMID: 32617605 DOI: 10.1007/s00203-020-01970-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/28/2020] [Accepted: 06/24/2020] [Indexed: 10/23/2022]
Abstract
In this study, we tested the ability of Streptomyces to use for their growth benzene, toluene, ethylbenzene, and o-, m-, p-xylenes as sole source of carbon and energy. These bacteria were isolated from agricultural soils and activated sludge samples from a wastewater treatment plant. The results show that Streptomyces are capable of degrading at least one of the BTEX compounds. Among them, 3 isolates from activated sludge called (U, F and V) and a single isolate (SA13) isolated from an agricultural soil, can use as the sole source of carbon and energy, all of these BTEX compounds at concentrations of 1500 mg/L. Based on the analysis of the 16S rRNA gene sequence, two active strains were identified as Streptomyces fimicarius, Streptomyces cavourensis, Streptomyces flavogriseus and Streptomyces pratensis. These strains can be excellent candidates for the bioremediation of the telluric and aquatic sites polluted by these xenobiotics.
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Affiliation(s)
- Amira Hocinat
- Faculté Des Sciences de La Nature Et de La Vie, Département de Microbiologie, Université Frères Mentouri-Constantine 1, 25017, Constantine, Algeria
| | - Allaoueddine Boudemagh
- Faculté Des Sciences de La Nature Et de La Vie, Département de Microbiologie, Université Frères Mentouri-Constantine 1, 25017, Constantine, Algeria
| | - Hocine Ali-Khodja
- Laboratoire de Pollution Et de Traitement Des Eaux, Faculté Des Sciences Exactes, Département de Chimie, Université Frères Mentouri-Constantine 1, Constantine, Algeria.
| | - Meissa Medjemadj
- Faculté Des Sciences de La Nature Et de La Vie, Département de Microbiologie, Université Frères Mentouri-Constantine 1, 25017, Constantine, Algeria
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Ganesh Kumar A, Mathew NC, Sujitha K, Kirubagaran R, Dharani G. Genome analysis of deep sea piezotolerant Nesiotobacter exalbescens COD22 and toluene degradation studies under high pressure condition. Sci Rep 2019; 9:18724. [PMID: 31822790 PMCID: PMC6904484 DOI: 10.1038/s41598-019-55115-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 10/03/2019] [Indexed: 11/09/2022] Open
Abstract
A marine isolate, Nesiotobacter exalbescens COD22, isolated from deep sea sediment (2100 m depth) was capable of degrading aromatic hydrocarbons. The Nesiotobacter sp. grew well in the presence of toluene at 0.1 MPa and 10 MPa at a rate of 0.24 h-1 and 0.12 h-1, respectively, in custom designed high pressure reactors. Percentage of hydrocarbon degradation was found to be 87.5% at ambient pressure and it reached 92% under high pressure condition within a short retention period of 72 h. The biodegradation of hydrocarbon was confirmed by the accumulation of dicarboxylic acid, benzoic acid, benzyl alcohol and benzaldehyde which are key intermediates in toluene catabolism. The complete genome sequence consists of 4,285,402 bp with 53% GC content and contained 3969 total coding genes. The complete genome analysis revealed unique adaptation and degradation capabilities for complex aromatic compounds, biosurfactant synthesis to facilitate hydrocarbon emulsification, advanced mechanisms for chemotaxis and presence of well developed flagellar assembly. The genomic data corroborated with the results of hydrocarbon biodegradation at high pressure growth conditions and confirmed the biotechnological potential of Nesiotobacter sp. towards bioremediation of hydrocarbon polluted deep sea environments.
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Affiliation(s)
- A Ganesh Kumar
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India.
| | - Noelin Chinnu Mathew
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - K Sujitha
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - R Kirubagaran
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
| | - G Dharani
- Marine Biotechnology Division, Earth System Science Organization - National Institute of Ocean Technology (ESSO - NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India
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6
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El-Sayed WS, Elbahloul Y, Saad ME, Hanafy AM, Hegazi AH, ElShafei GMS, Elbadry M. Impact of nanoparticles on transcriptional regulation of catabolic genes of petroleum hydrocarbon-degrading bacteria in contaminated soil microcosms. J Basic Microbiol 2018; 59:166-180. [PMID: 30468270 DOI: 10.1002/jobm.201800186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 09/29/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022]
Abstract
This study was conducted to determine what effects nanoparticles (NPs) like TiO2 , ZnO, and Ag may pose on natural attenuation processes of petroleum hydrocarbons in contaminated soils. The solid NPs used were identified using x-ray diffraction technique and their average size was certified as 18.2, 16.9, and 18.3 nm for Ag-NPs, ZnO-NPs, and TiO2 -NPs, respectively. NPs in soil microcosms behave differently where it was dissolved as in case of Ag-NPs, partially dissolved as in ZnO-NPs or changed into other crystalline phase as in TiO2 -NPs. In this investigation, catabolic gene encoding catechol 2,3 dioxygenase (C23DO) was selected specifically as biomarker for monitoring hydrocarbon biodegradation potential by measuring its transcripts by RT-qPCR. TiO2 -NPs amended microcosms showed almost no change in C23DO expression profile or bacterial community which were dominated by Bacillus sp., Mycobacterium sp., Microbacterium sp., Clostridium sp., beside uncultured bacteria, including uncultured proteobacteria, Thauera sp. and Clostridia. XRD pattern suggested that TiO2 -NPs in microcosms were changed into other non-inhibitory crystalline phase, consequently, showing the maximum degradation profile for most low molecular weight oil fractions and partially for the high molecular weight ones. Increasing ZnO-NPs concentration in microcosms resulted in a reduction in the expression of C23DO with a concomitant slight deteriorative effect on bacterial populations ending up with elimination of Clostridium sp., Thauera sp., and uncultured proteobacteria. The oil-degradation efficiency was reduced compared to TiO2 -NPs amended microcosms. In microcosms, Ag-NPs were not detected in the crystalline form but were available in the ionic form that inhibited most bacterial populations and resulted in a limited degradation profile of oil, specifically the low molecular weight fractions. Ag-NPs amended microcosms showed a significant reduction (80%) in C23DO gene expression and a detrimental effect on bacterial populations including key players like Mycobacterium sp., Microbacterium sp., and Thauera sp. involved in the biodegradation of petroleum hydrocarbons.
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Affiliation(s)
- Wael S El-Sayed
- Biology Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Yasser Elbahloul
- Biology Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Mohamed E Saad
- Biology Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Ahmed M Hanafy
- Biology Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Abdelrahman H Hegazi
- Chemistry Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Gamal M S ElShafei
- Chemistry Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Chemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Medhat Elbadry
- Biology Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Agricultural Microbiology Department, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
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Isolation and characterization of three novel catechol 2,3-dioxygenase from three novel haloalkaliphilic BTEX-degrading Pseudomonas strains. Int J Biol Macromol 2018; 106:1107-1114. [DOI: 10.1016/j.ijbiomac.2017.08.113] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 11/21/2022]
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8
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Röthig T, Ochsenkühn MA, Roik A, van der Merwe R, Voolstra CR. Long-term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome. Mol Ecol 2016; 25:1308-23. [PMID: 26840035 PMCID: PMC4804745 DOI: 10.1111/mec.13567] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/19/2016] [Accepted: 01/27/2016] [Indexed: 01/03/2023]
Abstract
Scleractinian corals are assumed to be stenohaline osmoconformers, although they are frequently subjected to variations in seawater salinity due to precipitation, freshwater run-off and other processes. Observed responses to altered salinity levels include differences in photosynthetic performance, respiration and increased bleaching and mortality of the coral host and its algal symbiont, but a study looking at bacterial community changes is lacking. Here, we exposed the coral Fungia granulosa to strongly increased salinity levels in short- and long-term experiments to disentangle temporal and compartment effects of the coral holobiont (i.e. coral host, symbiotic algae and associated bacteria). Our results show a significant reduction in calcification and photosynthesis, but a stable microbiome after short-term exposure to high-salinity levels. By comparison, long-term exposure yielded unchanged photosynthesis levels and visually healthy coral colonies indicating long-term acclimation to high-salinity levels that were accompanied by a major coral microbiome restructuring. Importantly, a bacterium in the family Rhodobacteraceae was succeeded by Pseudomonas veronii as the numerically most abundant taxon. Further, taxonomy-based functional profiling indicates a shift in the bacterial community towards increased osmolyte production, sulphur oxidation and nitrogen fixation. Our study highlights that bacterial community composition in corals can change within days to weeks under altered environmental conditions, where shifts in the microbiome may enable adjustment of the coral to a more advantageous holobiont composition.
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Affiliation(s)
- Till Röthig
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Michael A Ochsenkühn
- Biological and Organometallic Catalysis Laboratories, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Anna Roik
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Riaan van der Merwe
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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Guo G, Fang T, Wang C, Huang Y, Tian F, Cui Q, Wang H. Isolation and characterization of two novel halotolerant Catechol 2, 3-dioxygenases from a halophilic bacterial consortium. Sci Rep 2015; 5:17603. [PMID: 26621792 PMCID: PMC4664950 DOI: 10.1038/srep17603] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 11/03/2015] [Indexed: 02/08/2023] Open
Abstract
Study of enzymes in halophiles will help to understand the mechanism of aromatic hydrocarbons degradation in saline environment. In this study, two novel catechol 2,3-dioxygenases (C23O1 and C23O2) were cloned and overexpressed from a halophilic bacterial consortium enriched from an oil-contaminated saline soil. Phylogenetic analysis indicated that the novel C23Os and their relatives formed a new branch in subfamily I.2.A of extradiol dioxygenases and the sequence differences were further analyzed by amino acid sequence alignment. Two enzymes with the halotolerant feature were active over a range of 0–30% salinity and they performed more stable at high salinity than in the absence of salt. Surface electrostatic potential and amino acids composition calculation suggested high acidic residues content, accounting for their tolerance to high salinity. Moreover, two enzymes were further characterized. The enzymes activity both increased in the presence of Fe3+, Fe2+, Cu2+ and Al3+ and showed no significant inhibition by other tested metal ions. The optimal temperatures for the C23Os were 40 °C and 60 °C and their best substrates were catechol and 4-methylcatechol respectively. As the firstly isolated and characterized catechol dioxygenases from halophiles, the two halotolerant C23Os presented novel characteristics suggesting their potential application in aromatic hydrocarbons biodegradation.
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Affiliation(s)
- Guang Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Tingting Fang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yong Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Fang Tian
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Qijia Cui
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
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Bargiela R, Gertler C, Magagnini M, Mapelli F, Chen J, Daffonchio D, Golyshin PN, Ferrer M. Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data. Front Microbiol 2015; 6:1270. [PMID: 26635742 PMCID: PMC4656828 DOI: 10.3389/fmicb.2015.01270] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/30/2015] [Indexed: 11/13/2022] Open
Abstract
Biostimulation with different nitrogen sources is often regarded as a strategy of choice in combating oil spills in marine environments. Such environments are typically depleted in nitrogen, therefore limiting the balanced microbial utilization of carbon-rich petroleum constituents. It is fundamental, yet only scarcely accounted for, to analyze the catabolic consequences of application of biostimulants. Here, we examined such alterations in enrichment microcosms using sediments from chronically crude oil-contaminated marine sediment at Ancona harbor (Italy) amended with natural fertilizer, uric acid (UA), or ammonium (AMM). We applied the web-based AromaDeg resource using as query Illumina HiSeq meta-sequences (UA: 27,893 open reading frames; AMM: 32,180) to identify potential catabolic differences. A total of 45 (for UA) and 65 (AMM) gene sequences encoding key catabolic enzymes matched AromaDeg, and their participation in aromatic degradation reactions could be unambiguously suggested. Genomic signatures for the degradation of aromatics such as 2-chlorobenzoate, indole-3-acetate, biphenyl, gentisate, quinoline and phenanthrene were common for both microcosms. However, those for the degradation of orcinol, ibuprofen, phenylpropionate, homoprotocatechuate and benzene (in UA) and 4-aminobenzene-sulfonate, p-cumate, dibenzofuran and phthalate (in AMM), were selectively enriched. Experimental validation was conducted and good agreement with predictions was observed. This suggests certain discrepancies in action of these biostimulants on the genomic content of the initial microbial community for the catabolism of petroleum constituents or aromatics pollutants. In both cases, the emerging microbial communities were phylogenetically highly similar and were composed by very same proteobacterial families. However, examination of taxonomic assignments further revealed different catabolic pathway organization at the organismal level, which should be considered for designing oil spill mitigation strategies in the sea.
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Affiliation(s)
- Rafael Bargiela
- Systems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | | | | | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy
| | | | - Daniele Daffonchio
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy ; Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | | | - Manuel Ferrer
- Systems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas Madrid, Spain
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Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea). BIOMED RESEARCH INTERNATIONAL 2015; 2015:981829. [PMID: 26273661 PMCID: PMC4530241 DOI: 10.1155/2015/981829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 02/01/2015] [Accepted: 02/01/2015] [Indexed: 11/17/2022]
Abstract
Coastal environments worldwide are threatened by the effects of pollution, a risk particularly high in semienclosed basins like the Mediterranean Sea that is poorly studied from bioremediation potential perspective especially in the Southern coast. Here, we investigated the physical, chemical, and microbiological features of hydrocarbon and heavy metals contaminated sediments collected at El-Max bay (Egypt). Molecular and statistical approaches assessing the structure of the sediment-dwelling bacterial communities showed correlations between the composition of bacterial assemblages and the associated environmental parameters. Fifty strains were isolated on mineral media supplemented by 1% crude oil and identified as a diverse range of hydrocarbon-degrading bacteria involved in different successional stages of biodegradation. We screened the collection for biotechnological potential studying biosurfactant production, biofilm formation, and the capability to utilize different hydrocarbons. Some strains were able to grow on multiple hydrocarbons as unique carbon source and presented biosurfactant-like activities and/or capacity to form biofilm and owned genes involved in different detoxification/degradation processes. El-Max sediments represent a promising reservoir of novel bacterial strains adapted to high hydrocarbon contamination loads. The potential of the strains for exploitation for in situ intervention to combat pollution in coastal areas is discussed.
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13
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Li H, Zhang Q, Wang XL, Ma XY, Lin KF, Liu YD, Gu JD, Lu SG, Shi L, Lu Q, Shen TT. Biodegradation of benzene homologues in contaminated sediment of the East China Sea. BIORESOURCE TECHNOLOGY 2012; 124:129-136. [PMID: 22989641 DOI: 10.1016/j.biortech.2012.08.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Revised: 08/08/2012] [Accepted: 08/10/2012] [Indexed: 06/01/2023]
Abstract
This study focused on acclimating a microbial enrichment to biodegrade benzene, toluene, ethylbenzene and xylenes (BTEX) in a wide range of salinity. The enrichment degraded 120 mg/L toluene within 5d in the presence of 2M NaCl or 150 mg/L toluene within 7d in the presence of 1-1.5M NaCl. PCR-DGGE (polymerase chain reaction-denatured gradient gel electrophoresis) profiles demonstrated the dominant species in the enrichments distributed between five main phyla: Gammaproteobacteria, Sphingobacteriia, Prolixibacter, Flavobacteriia and Firmicutes. The Marinobacter, Prolixibacter, Balneola, Zunongwangia, Halobacillus were the dominant genus. PCR detection of genotypes involved in bacterial BETX degradation revealed that the degradation pathways contained all the known initial oxidative attack of BTEX by monooxygenase and dioxygenase. And the subsequent ring fission was catalysed by catechol 1,2-dioxygenase and catechol 2,3-dioxygenase. Nuclear magnetic resonance (NMR) spectroscopy profiles showed that the bacterial consortium adjusted the osmotic pressure by ectoine and hydroxyectoine as compatible solutes to acclimate the different salinity conditions.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Functional Materials Chemistry, School of Bioengineering, East China University of Science and Technology, Shanghai 200237, PR China
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Antunes A, Ngugi DK, Stingl U. Microbiology of the Red Sea (and other) deep-sea anoxic brine lakes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:416-433. [PMID: 23761304 DOI: 10.1111/j.1758-2229.2011.00264.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The Red Sea harbours approximately 25 deep-sea anoxic brine pools. They constitute extremely unique and complex habitats with the conjugation of several extreme physicochemical parameters rendering them some of the most inhospitable environments on Earth. After 50 years of research mostly driven by chemists, geophysicists and geologists, the microbiology of the brines has been receiving increased interest in the last decade. Recent molecular and cultivation-based studies have provided us with a first glimpse on the enormous biodiversity of the local microbial communities, the identification of several new taxonomic groups, and the isolation of novel extremophiles that thrive in these environments. This review presents a general overview of these unusual biotopes and compares them with other similar environments in the Mediterranean Sea and the Gulf of Mexico, with a focus on their microbial ecology.
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Affiliation(s)
- André Antunes
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Moreno MDL, Sánchez-Porro C, Piubeli F, Frias L, García MT, Mellado E. Cloning, characterization and analysis of cat and ben genes from the phenol degrading halophilic bacterium Halomonas organivorans. PLoS One 2011; 6:e21049. [PMID: 21695219 PMCID: PMC3112211 DOI: 10.1371/journal.pone.0021049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 05/18/2011] [Indexed: 11/28/2022] Open
Abstract
Background Extensive use of phenolic compounds in industry has resulted in the generation of saline wastewaters that produce significant environmental contamination; however, little information is available on the degradation of phenolic compounds in saline conditions. Halomonas organivorans G-16.1 (CECT 5995T) is a moderately halophilic bacterium that we isolated in a previous work from saline environments of South Spain by enrichment for growth in different pollutants, including phenolic compounds. PCR amplification with degenerate primers revealed the presence of genes encoding ring-cleaving enzymes of the β-ketoadipate pathway for aromatic catabolism in H. organivorans. Findings The gene cluster catRBCA, involved in catechol degradation, was isolated from H. organivorans. The genes catA, catB, catC and the divergently transcribed catR code for catechol 1,2-dioxygenase (1,2-CTD), cis,cis-muconate cycloisomerase, muconolactone delta-isomerase and a LysR-type transcriptional regulator, respectively. The benzoate catabolic genes (benA and benB) are located flanking the cat genes. The expression of cat and ben genes by phenol and benzoic acid was shown by RT-PCR analysis. The induction of catA gene by phenol and benzoic acid was also probed by the measurement of 1,2-CTD activity in H. organivorans growth in presence of these inducers. 16S rRNA and catA gene-based phylogenies were established among different degrading bacteria showing no phylogenetic correlation between both genes. Conclusions/Significance In this work, we isolated and determined the sequence of a gene cluster from a moderately halophilic bacterium encoding ortho-pathway genes involved in the catabolic metabolism of phenol and analyzed the gene organization, constituting the first report characterizing catabolic genes involved in the degradation of phenol in moderate halophiles, providing an ideal model system to investigate the potential use of this group of extremophiles in the decontamination of saline environments.
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Affiliation(s)
| | | | - Francine Piubeli
- Department of Food Science, University of Campinas, Sao Paulo, Brazil
| | - Luciana Frias
- Department of Food Science, University of Campinas, Sao Paulo, Brazil
| | - María Teresa García
- Department of Microbiology and Parasitology, University of Sevilla, Sevilla, Spain
| | - Encarnación Mellado
- Department of Microbiology and Parasitology, University of Sevilla, Sevilla, Spain
- * E-mail:
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Tkavc R, Gostinčar C, Turk M, Visscher PT, Oren A, Gunde-Cimerman N. Bacterial communities in the 'petola' microbial mat from the Sečovlje salterns (Slovenia). FEMS Microbiol Ecol 2010; 75:48-62. [PMID: 21062327 DOI: 10.1111/j.1574-6941.2010.00985.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The Sečovlje saltern is one of the few remaining solar salterns for traditional, seasonal salt production. The bottom of the crystallizer ponds is covered with a microbial mat, known as the 'petola', that has continuously been cultivated from medieval times. Outside the salt production season, the petola is fertilized with anoxic marine mud and covered with saline water; during the season, it is covered by brine. Here, we have applied culture-independent techniques and microelectrode-based activity measurements to study the bacterial communities in three different layers of the petola during the peak of the harvesting season. For reference, we used nonactive petola that had been abandoned for several years. The upper 2 mm of the petola were dominated by the cyanobacterial species Coleofasciculus chthonoplastes and the Phormidium/Lyngbya group, and Gammaproteobacteria (Acinetobacter sp.), while the third anoxic layer was dominated by as yet uncultured phyla. The nonactive petola showed a higher biodiversity. Oxygen and sulfide concentrations differed between the mats studied, in terms of the depth of oxygen penetration and diel changes. This study provides the first molecular insight into the microbiology of the petola, and it represents an important contribution towards understanding the geomicrobiological cycles of the traditional Sečovlje saltern.
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Affiliation(s)
- Rok Tkavc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Sei A, Fathepure B. Biodegradation of BTEX at high salinity by an enrichment culture from hypersaline sediments of Rozel Point at Great Salt Lake. J Appl Microbiol 2009; 107:2001-8. [DOI: 10.1111/j.1365-2672.2009.04385.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sass AM, McKew BA, Sass H, Fichtel J, Timmis KN, McGenity TJ. Diversity of Bacillus-like organisms isolated from deep-sea hypersaline anoxic sediments. SALINE SYSTEMS 2008; 4:8. [PMID: 18541011 PMCID: PMC2464584 DOI: 10.1186/1746-1448-4-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Accepted: 06/09/2008] [Indexed: 11/23/2022]
Abstract
Background The deep-sea, hypersaline anoxic brine lakes in the Mediterranean are among the most extreme environments on earth, and in one of them, the MgCl2-rich Discovery basin, the presence of active microbes is equivocal. However, thriving microbial communities have been detected especially in the chemocline between deep seawater and three NaCl-rich brine lakes, l'Atalante, Bannock and Urania. By contrast, the microbiota of these brine-lake sediments remains largely unexplored. Results Eighty nine isolates were obtained from the sediments of four deep-sea, hypersaline anoxic brine lakes in the Eastern Mediterranean Sea: l'Atalante, Bannock, Discovery and Urania basins. This culture collection was dominated by representatives of the genus Bacillus and close relatives (90% of all isolates) that were investigated further. Physiological characterization of representative strains revealed large versatility with respect to enzyme activities or substrate utilization. Two third of the isolates did not grow at in-situ salinities and were presumably present as endospores. This is supported by high numbers of endospores in Bannock, Discovery and Urania basins ranging from 3.8 × 105 to 1.2 × 106 g-1 dw sediment. However, the remaining isolates were highly halotolerant growing at salinities of up to 30% NaCl. Some of the novel isolates affiliating with the genus Pontibacillus grew well under anoxic conditions in sulfidic medium by fermentation or anaerobic respiration using dimethylsulfoxide or trimethylamine N-oxide as electron acceptor. Conclusion Some of the halophilic, facultatively anaerobic relatives of Bacillus appear well adapted to life in this hostile environment and suggest the presence of actively growing microbial communities in the NaCl-rich, deep-sea brine-lake sediments.
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Affiliation(s)
- Andrea M Sass
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK.
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Kim D, Kim SW, Choi KY, Lee JS, Kim E. Molecular cloning and functional characterization of the genes encoding benzoate and p-hydroxybenzoate degradation by the halophilic Chromohalobacter sp. strain HS-2. FEMS Microbiol Lett 2008; 280:235-41. [PMID: 18248426 DOI: 10.1111/j.1574-6968.2008.01067.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Chromohalobacter sp. strain HS-2 was isolated from salted fermented clams and analyzed for the ability to grow on benzoate and p-hydroxybenzoate as the sole carbon and energy source. HS-2 was characterized as moderately halophilic, with an optimal NaCl concentration of 10%. The genes encoding the benzoate metabolism were cloned into a cosmid vector, sequenced, and then analyzed to reveal the benzoate (benABCD) and catechol (catBCA) catabolic genes, both of which are flanked on either side by LysR-type transcriptional regulator (catR) and membrane transport protein for benzoate (benE) in the gene order catRBCAbenABCDE. Near the large cat-ben cluster, a p-hydroxybenzoate hydroxylase gene (pobA) and two putative regulatory genes (pcaQ and pobR) were additionally detected. The HS-2 genes involved in benzoate and p-hydroxybenzoate degradation are tightly clustered within a c. 19 kb region, and show quite a different genetic organization from those of other benzoate catabolic genes. Reverse transcriptase-PCR experiments show that benzoate induces the expression of benzoate 1,2-dioxygenase, catechol 1,2-dioxygenase, and protocatechuate 3,4-dioxygenase while p-hydroxybenzoate only induced the expression of p-hydroxybenzoate hydroxylase. When expressed in Escherichia coli, benzoate 1,2-dioxygenase (BenABC) and p-hydroxybenzoate hydroxylase (PobA) transformed benzoate and p-hydroxybenzoate into cis-benzoate dihydrodiol and protocatechuate, respectively.
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Affiliation(s)
- Dockyu Kim
- Department of Environmental Engineering, BK21 Team for Biohydrogen Production, Chosun University, Gwangju, Korea
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van der Wielen PWJJ, Bolhuis H, Borin S, Daffonchio D, Corselli C, Giuliano L, D'Auria G, de Lange GJ, Huebner A, Varnavas SP, Thomson J, Tamburini C, Marty D, McGenity TJ, Timmis KN. The Enigma of Prokaryotic Life in Deep Hypersaline Anoxic Basins. Science 2005; 307:121-3. [PMID: 15637281 DOI: 10.1126/science.1103569] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Deep hypersaline anoxic basins in the Mediterranean Sea are a legacy of dissolution of ancient subterranean salt deposits from the Miocene period. Our study revealed that these hypersaline basins are not biogeochemical dead ends, but support in situ sulfate reduction, methanogenesis, and heterotrophic activity. A wide diversity of prokaryotes was observed, including a new, abundant, deeply branching order within the Euryarchaeota. Furthermore, we demonstrated the presence of a unique, metabolically active microbial community in the Discovery basin, which is one of the most extreme terrestrial saline environments known, as it is almost saturated with MgCl2 (5 M).
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Zucchi M, Angiolini L, Borin S, Brusetti L, Dietrich N, Gigliotti C, Barbieri P, Sorlini C, Daffonchio D. Response of bacterial community during bioremediation of an oil-polluted soil. J Appl Microbiol 2003; 94:248-57. [PMID: 12534816 DOI: 10.1046/j.1365-2672.2003.01826.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIM To study the response of the bacterial community to bioremediation of a soil with an aged contamination of crude oil. METHODS AND RESULTS The bacterial community in laboratory soil columns during a 72-day biostimulation treatment was followed by analysing the number of total cultivable hydrocarbon-degrading bacteria, soil respiratory activity and the 16S-23S rDNA internal transcribed spacer homoduplex heteroduplex polymorphisms (ITS-HHP) of total soil bacterial DNA. ITS-HHP permits an estimate of both length and sequence polymorphism in a 16S-23S rDNA spacer population, using to advantage the homoduplex and heteroduplex fragments that are generated during PCR. The treatment, made by air sparging and biostimulation with a mineral nutrient and surfactant solution, resulted in a 39.5% decrease of the total hydrocarbon content. Within 4 days of treatment onset the bacterial community underwent a first phase of activation that led to a substantial increase in the observable diversity. Subsequently, after a 12-day period of stability, another activation phase was observed with further shifts of the community structure and an increase in the abundance and diversity of catechol-2,3-dioxygenase (C23O) genes. CONCLUSIONS The overall data suggest an important contribution of uncultivable bacteria to the soil bioremediation, since, during the second activation phase, the increases of the respiratory activity, bacterial diversity and C23O gene abundance and diversity were not accompanied by a corresponding increase of the cultivable bacteria number. SIGNIFICANCE AND IMPACT OF THE STUDY This study shows that successive phases of activation of bacterial populations occur during a bioremediation treatment of oil-polluted soil.
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Affiliation(s)
- M Zucchi
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, DISTAM, Università degli Studi, Milano, Italy
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