1
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Arenas S, Rivera N, Méndez Casallas FJ, Galvis B. Assessing Diesel Tolerance of Chromobacterium violaceum: Insights from Growth Kinetics, Substrate Utilization, and Implications for Microbial Adaptation. ACS OMEGA 2024; 9:23741-23752. [PMID: 38854507 PMCID: PMC11154896 DOI: 10.1021/acsomega.4c01698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024]
Abstract
This study aimed to determine the tolerance of Chromobacterium violaceum ATCC 12472 to diesel. The growth of the strain was evaluated through exposure to various diesel concentrations (1, 2.5, 5, 7.5, and 10% v/v), with continuous monitoring of growth via optical density measurements until the death phase was reached. Employing a logistic model, we analyzed the growth kinetics of C. violaceum and compared them with five other models to comprehend substrate utilization dynamics. Our results indicate that optimal bacterial growth occurred at 2.5% (v/v) or 18,125 mg/L diesel, while both higher and lower concentrations manifested inhibitory and increasingly stressful effects. The Aiba model emerged as the most fitting representation of substrate utilization by C. violaceum. In addition, our findings underscore the remarkable diesel tolerance of C. violaceum ATCC 12472, despite the inherently stressful nature of the medium. This study contributes to the understanding of microbial responses to environmental stressors and highlights the pivotal role of the substrate concentration in influencing microbial growth. These insights have implications for bioremediation strategies and enhance our understanding of bacterial ecological resilience in the presence of hydrocarbon pollutants.
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Affiliation(s)
- Sebastián Arenas
- Programa
de Ingeniería ambiental y Sanitaria, Universidad de La Salle, Bogotá 110231, Colombia
| | - Nathaly Rivera
- Programa
de Ingeniería ambiental y Sanitaria, Universidad de La Salle, Bogotá 110231, Colombia
| | | | - Boris Galvis
- Escuela
de Ingeniería de los Recursos Naturales y del Ambiente—EIDENAR, Universidad del Valle, Cali 760042, Colombia
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2
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Schultes FPJ, Welter L, Hufnagel D, Heghmanns M, Kasanmascheff M, Mügge C. An Active and Versatile Electron Transport System for Cytochrome P450 Monooxygenases from the Alkane Degrading Organism Acinetobacter sp. OC4. Chembiochem 2024:e202400098. [PMID: 38787654 DOI: 10.1002/cbic.202400098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/10/2024] [Accepted: 05/22/2024] [Indexed: 05/26/2024]
Abstract
Cytochrome P450 monooxygenases (CYPs) are valuable biocatalysts for the oxyfunctionalization of non-activated carbon-hydrogen bonds. Most CYPs rely on electron transport proteins as redox partners. In this study, the ferredoxin reductase (FdR) and ferredoxin (FD) for a cytochrome P450 monooxygenase from Acinetobacter sp. OC4 are investigated. Upon heterologous production of both proteins independently in Escherichia coli, spectral analysis showed their reduction capability towards reporter electron acceptors, e. g., cytochrome c. The individual proteins' specific activity towards cytochrome c reduction was 25 U mg-1. Furthermore, the possibility to enhance electron transfer by artificial fusion of the units was elucidated. FdR and FD were linked by helical linkers [EAAAK]n, flexible glycine linkers [GGGGS]n or rigid proline linkers [EPPPP]n of n=1-4 sequence repetitions. The system with a glycine linker (n=4) reached an appreciable specific activity of 19 U mg-1 towards cytochrome c. Moreover, their ability to drive different members of the CYP153A subfamily is demonstrated. By creating artificial self-sufficient P450s with FdR, FD, and a panel of four CYP153A representatives, effective hydroxylation of n-hexane in a whole-cell system was achieved. The results indicate this protein combination to constitute a functional and versatile surrogate electron transport system for this subfamily.
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Affiliation(s)
- Fabian Peter Josef Schultes
- Ruhr-University Bochum, Faculty of Biology and Biotechnology, Microbial Biotechnology, Universitätsstraße 150, 44780, Bochum, Germany
| | - Leon Welter
- Ruhr-University Bochum, Faculty of Biology and Biotechnology, Microbial Biotechnology, Universitätsstraße 150, 44780, Bochum, Germany
| | - Doreen Hufnagel
- Ruhr-University Bochum, Faculty of Biology and Biotechnology, Microbial Biotechnology, Universitätsstraße 150, 44780, Bochum, Germany
| | - Melanie Heghmanns
- Technical University Dortmund, Faculty for Chemistry and Chemical Biology, Otto-Hahn Straße 6, 44227, Dortmund, Germany
| | - Müge Kasanmascheff
- Technical University Dortmund, Faculty for Chemistry and Chemical Biology, Otto-Hahn Straße 6, 44227, Dortmund, Germany
| | - Carolin Mügge
- Ruhr-University Bochum, Faculty of Biology and Biotechnology, Microbial Biotechnology, Universitätsstraße 150, 44780, Bochum, Germany
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3
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Grechishnikova EG, Shemyakina AO, Novikov AD, Lavrov KV, Yanenko AS. Rhodococcus: sequences of genetic parts, analysis of their functionality, and development prospects as a molecular biology platform. Crit Rev Biotechnol 2023; 43:835-850. [PMID: 35786136 DOI: 10.1080/07388551.2022.2091976] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/19/2022] [Accepted: 05/12/2022] [Indexed: 12/19/2022]
Abstract
Rhodococcus bacteria are a fast-growing platform for biocatalysis, biodegradation, and biosynthesis, but not a platform for molecular biology. That is, Rhodococcus are not convenient for genetic engineering. One major issue for the engineering of Rhodococcus is the absence of a publicly available, curated, and commented collection of sequences of genetic parts that are functional in biotechnologically relevant species of Rhodococcus (R. erythropolis, R. rhodochrous, R. ruber, and R. jostii). Here, we present a collection of genetic parts for Rhodococcus (vector replicons, promoter regions, regulators, markers, and reporters) supported by a thorough analysis of their functionality. We also highlight and discuss the gaps in Rhodococcus-related genetic parts and techniques, which should be filled in order to make these bacteria a full-fledged molecular biology platform independent of Escherichia coli. We conclude that all major types of required genetic parts for Rhodococcus are available now, except multicopy replicons. As for model Rhodococcus strains, there is a particular shortage of strains with high electrocompetence levels and strains designed for solving specific genetic engineering tasks. We suggest that these obstacles are surmountable in the near future due to an intensification of research work in the field of genetic techniques for non-conventional bacteria.
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Affiliation(s)
- Elena G Grechishnikova
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Anna O Shemyakina
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Andrey D Novikov
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Konstantin V Lavrov
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
| | - Alexander S Yanenko
- NRC "Kurchatov Institute" - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- NRC "Kurchatov Institute", Moscow, Russia
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4
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Fenibo EO, Selvarajan R, Abia ALK, Matambo T. Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162951. [PMID: 36948313 DOI: 10.1016/j.scitotenv.2023.162951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 05/06/2023]
Abstract
Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Akebe Luther King Abia
- Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa; Environmental Research Foundation, Westville 3630, South Africa
| | - Tonderayi Matambo
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort 1709, South Africa.
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Xiang W, Hong S, Xue Y, Ma Y. Functional Analysis of Novel alkB Genes Encoding Long-Chain n-Alkane Hydroxylases in Rhodococcus sp. Strain CH91. Microorganisms 2023; 11:1537. [PMID: 37375039 DOI: 10.3390/microorganisms11061537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Rhodococcus sp. strain CH91 is capable of utilizing long-chain n-alkanes as the sole carbon source. Two new genes (alkB1 and alkB2) encoding AlkB-type alkane hydroxylase were predicted by its whole-genome sequence analysis. The purpose of this study was to elucidate the functional role of alkB1 and alkB2 genes in the n-alkane degradation of strain CH91. RT-qPCR analyses revealed that the two genes were induced by n-alkanes ranging from C16 to C36 and the expression of the alkB2 gene was up-regulated much higher than that of alkB1. The knockout of the alkB1 or alkB2 gene in strain CH91 resulted in the obvious reduction of growth and degradation rates on C16-C36 n-alkanes and the alkB2 knockout mutant exhibited lower growth and degradation rate than the alkB1 knockout mutant. When gene alkB1 or alkB2 was heterologously expressed in Pseudomonas fluorescens KOB2Δ1, the two genes could restore its alkane degradation activity. These results demonstrated that both alkB1 and alkB2 genes were responsible for C16-C36 n-alkanes' degradation of strain CH91, and alkB2 plays a more important role than alkB1. The functional characteristics of the two alkB genes in the degradation of a broad range of n-alkanes make them potential gene candidates for engineering the bacteria used for bioremediation of petroleum hydrocarbon contaminations.
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Affiliation(s)
- Wei Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shan Hong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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6
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Masyagina OV, Matvienko AI, Ponomareva TV, Grodnitskaya ID, Sideleva EV, Kadutskiy VK, Prudnikova SV, Bezbido VS, Kudryavtseva KA, Evgrafova SY. Soil contamination by diesel fuel destabilizes the soil microbial pools: Insights from permafrost soil incubations. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121269. [PMID: 36780979 DOI: 10.1016/j.envpol.2023.121269] [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: 08/22/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Arctic contamination by diesel fuel (DF) is of great concern because of the uncertain feedback of permafrost carbon (C) and soil microbiota to DF in the context of climate change in high latitudes. We conducted a laboratory incubation experiment with a gradient of DF addition ratios to examine the responses of the soil microbiota of the typical permafrost soils in the tundra ecosystems of the Norilsk region (Siberia). The study revealed initial heterogeneity in the microbial activity of the studied soils (Histic Gleyic Cryosols (CR-hi,gl), Turbic Cryosols (CR-tu), Turbic Spodic Folic Cryosols (CR-tu,sd,fo), Gleyic Fluvisols (FL-gl)). We applied the two-pool model for evaluation of the effect of DF on the proportions of C pools and revealed significant differences between soil types in the fast and slow C pools in response to DF addition. The results showed that DF addition treatments had varying effects on the fast and slow C pools, microbial activity, and microbial community structure in the studied soils. For minor exceptions, DF dramatically accelerated C loss from the slow C pool in all soil types. We assume that differences in C pool and microbiota responses to DF addition were caused by soil texture and changes in microbial community structure. We isolated Serratia proteamaculans, S. liquefaciens, S. plymuthica, Rhodococcus erythropolis, Pseudomonas antarctica, P. libanensis, P. brassicacearum, and P. chlororaphis from the DF-polluted soils. These species are recommended for bioremediation to mitigate the DF contamination of permafrost soils, especially regarding climate change and the sustainable well-being of Arctic ecosystems.
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Affiliation(s)
- Oxana V Masyagina
- Sukachev Institute of Forest SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", 50/28 Akademgorodok St., 660036, Krasnoyarsk, Russian Federation.
| | - Anastasia I Matvienko
- Sukachev Institute of Forest SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", 50/28 Akademgorodok St., 660036, Krasnoyarsk, Russian Federation
| | - Tatiana V Ponomareva
- Sukachev Institute of Forest SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", 50/28 Akademgorodok St., 660036, Krasnoyarsk, Russian Federation
| | - Irina D Grodnitskaya
- Sukachev Institute of Forest SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", 50/28 Akademgorodok St., 660036, Krasnoyarsk, Russian Federation; Siberian Federal University, 660041, Krasnoyarsk, Russian Federation
| | | | - Valeriy K Kadutskiy
- Sukachev Institute of Forest SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", 50/28 Akademgorodok St., 660036, Krasnoyarsk, Russian Federation
| | | | - Viktoria S Bezbido
- Krasnoyarsk Regional Clinical Сentre of Motherhood and Сhildhood Care, 660074, Krasnoyarsk, Russian Federation
| | - Kristina A Kudryavtseva
- Krasnoyarsk Regional Clinical Сentre of Motherhood and Сhildhood Care, 660074, Krasnoyarsk, Russian Federation
| | - Svetlana Y Evgrafova
- Sukachev Institute of Forest SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", 50/28 Akademgorodok St., 660036, Krasnoyarsk, Russian Federation; Siberian Federal University, 660041, Krasnoyarsk, Russian Federation; Melnikov Permafrost Institute of the Siberian Branch of the Russian Academy of Science, 677010, Yakutsk, Russian Federation
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7
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Zhang N, Gao F, Cheng S, Xie H, Hu Z, Zhang J, Liang S. Mn oxides enhanced pyrene removal with both rhizosphere and non-rhizosphere microorganisms in subsurface flow constructed wetlands. CHEMOSPHERE 2022; 307:135821. [PMID: 35944687 DOI: 10.1016/j.chemosphere.2022.135821] [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: 03/29/2022] [Revised: 06/07/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
The polycyclic aromatic hydrocarbons (PAHs) are substantial wastewater pollutants emitted mostly by petroleum refineries and petrochemical industries, and their environmental fate has been of increasing concern among the public. Consequently, subsurface flow constructed wetlands (SFCWs) filled with Mn oxides (W-CW) or without Mn oxides (K-CW) were established to investigate the performance and mechanisms of pyrene (PYR) removal. The average removal rates of PYR in W-CW and K-CW were 96.00% and 92.33%, respectively. The PYR removal via other pathways (microbial degradation, photolysis, volatilisation, etc.) occupied a sizeable proportion, while the total PYR content in K-CW plant roots was significantly higher than that of W-CW. The microorganisms on the root surface and rhizosphere played an important role in PYR degradation in W-CW and K-CW and were higher in W-CW than that in K-CW in all matrix zones. The microorganisms between the 10-16 cm zone from the bottom of W-CW filled with Mn oxides (W-16) were positively correlated with PYR-degrading microorganisms, aerobic bacteria and facultative anaerobes, whereas K-16 without birnessite-coated sand was negatively correlated with these microorganisms.
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Affiliation(s)
- Ning Zhang
- Environment Research Institute, Shandong University, Jinan, 250100, China
| | - Fuwei Gao
- Zhongke Hualu Soil Remediation Engineering Co., Ltd, Dezhou, 253000, China
| | - Shiyi Cheng
- Jiangsu Ecological Environmental Monitoring Co., Ltd, Nanjing, 320100, China
| | - Huijun Xie
- Environment Research Institute, Shandong University, Jinan, 250100, China.
| | - Zhen Hu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Jian Zhang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, Shandong, 250100, China; College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong, 266590, China
| | - Shuang Liang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, Shandong, 250100, China
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8
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Zampolli J, Orro A, Vezzini D, Di Gennaro P. Genome-Based Exploration of Rhodococcus Species for Plastic-Degrading Genetic Determinants Using Bioinformatic Analysis. Microorganisms 2022; 10:microorganisms10091846. [PMID: 36144448 PMCID: PMC9506104 DOI: 10.3390/microorganisms10091846] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 11/24/2022] Open
Abstract
Plastic polymer waste management is an increasingly prevalent issue. In this paper, Rhodococcus genomes were explored to predict new plastic-degrading enzymes based on recently discovered biodegrading enzymes for diverse plastic polymers. Bioinformatics prediction analyses were conducted using 124 gene products deriving from diverse microorganisms retrieved from databases, literature data, omic-approaches, and functional analyses. The whole results showed the plastic-degrading potential of Rhodococcus genus. Among the species with high plastic-degrading potential, R. erythropolis, R. equi, R. opacus, R. qingshengii, R. fascians, and R. rhodochrous appeared to be the most promising for possible plastic removal. A high number of genetic determinants related to polyester biodegradation were obtained from different Rhodococcus species. However, score calculation demonstrated that Rhodococcus species (especially R. pyridinivorans, R. qingshengii, and R. hoagii) likely possess PE-degrading enzymes. The results identified diverse oxidative systems, including multicopper oxidases, alkane monooxygenases, cytochrome P450 hydroxylases, para-nitrobenzylesterase, and carboxylesterase, and they could be promising reference sequences for the biodegradation of plastics with C−C backbone, plastics with heteroatoms in the main chain, and polyesters, respectively. Notably, the results of this study could be further exploited for biotechnological applications in biodegradative processes using diverse Rhodococcus strains and through catalytic reactions.
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Affiliation(s)
- Jessica Zampolli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Alessandro Orro
- Institute of Biomedical Technologies, National Research Council, CNR, Via Fratelli Cervi 19, 20133 Segrate, Italy
| | - Daniele Vezzini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
- Correspondence: ; Tel.: +39 02 64482949
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9
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Delegan Y, Petrikov K, Frantsuzova E, Rudenko N, Solomentsev V, Suzina N, Travkin V, Solyanikova IP. Complete Genome Analysis of Rhodococcus opacus S8 Capable of Degrading Alkanes and Producing Biosurfactant Reveals Its Genetic Adaptation for Crude Oil Decomposition. Microorganisms 2022; 10:microorganisms10061172. [PMID: 35744693 PMCID: PMC9229178 DOI: 10.3390/microorganisms10061172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 02/05/2023] Open
Abstract
Microorganisms capable of decomposing hydrophobic substrates in cold climates are of considerable interest both in terms of studying adaptive reactions to low temperatures and in terms of their application in biotechnologies for cleaning up oil spills in a crude-oil polluted soil. The aim of this work was to investigate the genome of Rhodococcus opacus S8 and explore behavior traits of this strain grown in the presence of hexadecane. The genome size of strain S8 is 8.78 Mb, of which the chromosome size is 7.75 Mb. The S8 strain contains 2 circular plasmids of 135 kb and 105 kb and a linear plasmid with a size of 788 kb. The analysis of the genome revealed the presence of genes responsible for the degradation of alkanes and synthesis of biosurfactants. The peculiarities of morphology of microbial cells when interacting with a hydrophobic substrate were revealed. An adaptive mechanism responsible in the absence of oxygen for maintaining the process of degradation of hexadecane is discussed. The data obtained show that the strain S8 has great potential to be used in biotechnologies.
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Affiliation(s)
- Yanina Delegan
- Laboratory of Physiology of Microorganisms, Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (Y.D.); (E.F.)
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia;
| | - Kirill Petrikov
- Laboratory of Plasmid Biology, Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia;
| | - Ekaterina Frantsuzova
- Laboratory of Physiology of Microorganisms, Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (Y.D.); (E.F.)
- The Federal State Budget Educational Institution of Higher Education Pushchino State Institute of Natural Science, 142290 Pushchino, Moscow Region, Russia
| | - Natalia Rudenko
- Institute of Basic Biological Problems of Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia;
| | - Viktor Solomentsev
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia;
| | - Nataliya Suzina
- Laboratory of Cytology of Microorganisms, Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia;
| | - Vasili Travkin
- Regional Microbiological Center, Belgorod National Research University, 308015 Belgorod, Belgorod Region, Russia;
| | - Inna P. Solyanikova
- The Federal State Budget Educational Institution of Higher Education Pushchino State Institute of Natural Science, 142290 Pushchino, Moscow Region, Russia
- Regional Microbiological Center, Belgorod National Research University, 308015 Belgorod, Belgorod Region, Russia;
- Laboratory of Microbial Enzymology, Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- Correspondence:
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10
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Ma X, Duan D, Wang X, Cao J, Qiu J, Xie B. Degradation of Rhodococcus erythropolis SY095 modified with functional magnetic Fe 3O 4 nanoparticles. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211172. [PMID: 34950489 PMCID: PMC8692970 DOI: 10.1098/rsos.211172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
Alkali-surfactant-polymer flooding technology is widely employed to extract crude oil to enhance its production. The bacterial strain Rhodococcus erythropolis SY095 has shown high degradation activity of alkane of crude oil. In the past, many treatment strategies have been implemented to reduce oil concentration in wastewater. Previous studies mainly focused on the extracellular products of Erythrococcus rather than its degradation properties. In the current study, we designed an immobilization method to modify the surface of R. erythropolis SY095 with functional Fe3O4 nanoparticles (NPs) for biodegradation of crude oil and separation of the immobilized bacteria after degradation. We characterize the synthesized NPs through various methods, including scanning electron microscope energy-dispersive spectrometer, Fourier transform infrared spectroscopy, X-ray diffraction (XRD) and a vibrating sample magnetometer. We found that the size of the synthesized NPs was approximately 100 nm. Our results showed that R. erythropolis SY095 was successfully coated with functional magnetic NPs (MNPs) that could be easily separated from the solution via the application of an external magnetic field. The coated cells had a high tolerance for heavy metals. Our findings demonstrated that the immobilization of MNPs to bacterial surfaces is a promising approach for the degradation of crude oil.
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Affiliation(s)
- Xiaolei Ma
- Microbiology and Biotechnology Research Laboratory, The Institute of Seawater Desalination and Multi-Purpose Utilization, Ministry of Natural Resources of the People's Republic of China (MNR), Tianjin 300192, People's Republic of China
| | - Duomo Duan
- Tianjin Rehabilitation Center, The PLA Joint Logistic Support Force, Tianjin, 300191, People's Republic of China
| | - Xunliang Wang
- Microbiology and Biotechnology Research Laboratory, The Institute of Seawater Desalination and Multi-Purpose Utilization, Ministry of Natural Resources of the People's Republic of China (MNR), Tianjin 300192, People's Republic of China
| | - Junrui Cao
- Microbiology and Biotechnology Research Laboratory, The Institute of Seawater Desalination and Multi-Purpose Utilization, Ministry of Natural Resources of the People's Republic of China (MNR), Tianjin 300192, People's Republic of China
| | - Jinquan Qiu
- Microbiology and Biotechnology Research Laboratory, The Institute of Seawater Desalination and Multi-Purpose Utilization, Ministry of Natural Resources of the People's Republic of China (MNR), Tianjin 300192, People's Republic of China
| | - Baolong Xie
- Microbiology and Biotechnology Research Laboratory, The Institute of Seawater Desalination and Multi-Purpose Utilization, Ministry of Natural Resources of the People's Republic of China (MNR), Tianjin 300192, People's Republic of China
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11
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Zampolli J, Orro A, Manconi A, Ami D, Natalello A, Di Gennaro P. Transcriptomic analysis of Rhodococcus opacus R7 grown on polyethylene by RNA-seq. Sci Rep 2021; 11:21311. [PMID: 34716360 PMCID: PMC8556283 DOI: 10.1038/s41598-021-00525-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
Plastic waste management has become a global issue. Polyethylene (PE) is the most abundant synthetic plastic worldwide, and one of the most resistant to biodegradation. Indeed, few bacteria can degrade polyethylene. In this paper, the transcriptomic analysis unveiled for the first time Rhodococcus opacus R7 complex genetic system based on diverse oxidoreductases for polyethylene biodegradation. The RNA-seq allowed uncovering genes putatively involved in the first step of oxidation. In-depth investigations through preliminary bioinformatic analyses and enzymatic assays on the supernatant of R7 grown in the presence of PE confirmed the activation of genes encoding laccase-like enzymes. Moreover, the transcriptomic data allowed identifying candidate genes for the further steps of short aliphatic chain oxidation including alkB gene encoding an alkane monooxygenase, cyp450 gene encoding cytochrome P450 hydroxylase, and genes encoding membrane transporters. The PE biodegradative system was also validated by FTIR analysis on R7 cells grown on polyethylene.
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Affiliation(s)
- Jessica Zampolli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Alessandro Orro
- Institute of Biomedical Technologies, National Research Council, CNR, via Fratelli Cervi 19, Segrate, 20133, Milan, Italy
| | - Andrea Manconi
- Institute of Biomedical Technologies, National Research Council, CNR, via Fratelli Cervi 19, Segrate, 20133, Milan, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
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12
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Grüner‐Lempart S, Eckert J, Gredmaier L. Reinigung von lösemittelhaltiger Prozessabluft in Biorieselbettreaktoren. CHEM-ING-TECH 2021. [DOI: 10.1002/cite.202100058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sabine Grüner‐Lempart
- Hochschule Weihenstephan-Triesdorf Fakultät Bioingenieurwissenschaften, Fachbereich Verfahrenstechnik Am Hofgarten 10 85354 Freising Deutschland
| | - Julian Eckert
- Hochschule Weihenstephan-Triesdorf Fakultät Bioingenieurwissenschaften, Fachbereich Verfahrenstechnik Am Hofgarten 10 85354 Freising Deutschland
| | - Ludwig Gredmaier
- Technische Universität München Fakultät für Maschinenwesen, Lehrstuhl für Bioverfahrenstechnik Boltzmannstraße 15 85748 Garching Deutschland
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13
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Bodor A, Bounedjoum N, Feigl G, Duzs Á, Laczi K, Szilágyi Á, Rákhely G, Perei K. Exploitation of extracellular organic matter from Micrococcus luteus to enhance ex situ bioremediation of soils polluted with used lubricants. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:125996. [PMID: 33992922 DOI: 10.1016/j.jhazmat.2021.125996] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Chronic pollution by used lubricant oils (ULOs) poses a serious challenge to the environment. Under stress conditions, microorganisms, including potential degraders, can enter a viable but non-culturable (VBNC) state, complicating the bioremediation of ULO-polluted areas. Resuscitation-promoting factors (Rpfs) can reverse this transition and/or enhance the biodegradation performance of both native and augmented strains. Here, Rpf-containing extracellular organic matter (EOM) from Micrococcus luteus was used to enhance the ex situ ULO removal in biostimulated and bioaugmented (with Rhodococcus qingshengii KAG C, R. erythropolis PR4) soils. ULO bioconversion, microbial activity, and CFUs were significantly higher in EOM-treated soils compared to corresponding control soils. After 60 days, the initial ULO concentration (52,500 mg kg-1) was reduced by 37% and 45% with EOM-supplemented biostimulation and bioaugmentation, respectively. Based on high-throughput 16S rRNA analysis, the enhancement was attributable both to the reactivation of EOM-responsive hydrocarbonoclastic bacterial genera (e.g., Pseudomonas, Comamonas, Stenotrophomonas, Gordonia) and to the long-term positive effect of EOM on the degradative efficacy of the introduced rhodococci. Ecotoxicological responses revealed that reduced ULO concentration did not correlate with decreased soil toxicity. Our findings provide an insight into the applicability of EOM in bioremediation and its effects on the soil microbial activity and community composition.
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Affiliation(s)
- Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Feigl
- Department of Plant Biology, University of Szeged, Szeged, Hungary
| | - Ágnes Duzs
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary
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14
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Ivshina IB, Kuyukina MS, Krivoruchko AV, Tyumina EA. Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species. Pathogens 2021; 10:974. [PMID: 34451438 PMCID: PMC8398200 DOI: 10.3390/pathogens10080974] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022] Open
Abstract
Under conditions of increasing environmental pollution, true saprophytes are capable of changing their survival strategies and demonstrating certain pathogenicity factors. Actinobacteria of the genus Rhodococcus, typical soil and aquatic biotope inhabitants, are characterized by high ecological plasticity and a wide range of oxidized organic substrates, including hydrocarbons and their derivatives. Their cell adaptations, such as the ability of adhering and colonizing surfaces, a complex life cycle, formation of resting cells and capsule-like structures, diauxotrophy, and a rigid cell wall, developed against the negative effects of anthropogenic pollutants are discussed and the risks of possible pathogenization of free-living saprotrophic Rhodococcus species are proposed. Due to universal adaptation features, Rhodococcus species are among the candidates, if further anthropogenic pressure increases, to move into the group of potentially pathogenic organisms with "unprofessional" parasitism, and to join an expanding list of infectious agents as facultative or occasional parasites.
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Affiliation(s)
- Irina B. Ivshina
- Perm Federal Research Center UB RAS, Institute of Ecology and Genetics of Microorganisms UB RAS, 13 Golev Str., 614081 Perm, Russia; (M.S.K.); (A.V.K.); (E.A.T.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Maria S. Kuyukina
- Perm Federal Research Center UB RAS, Institute of Ecology and Genetics of Microorganisms UB RAS, 13 Golev Str., 614081 Perm, Russia; (M.S.K.); (A.V.K.); (E.A.T.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Anastasiia V. Krivoruchko
- Perm Federal Research Center UB RAS, Institute of Ecology and Genetics of Microorganisms UB RAS, 13 Golev Str., 614081 Perm, Russia; (M.S.K.); (A.V.K.); (E.A.T.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Elena A. Tyumina
- Perm Federal Research Center UB RAS, Institute of Ecology and Genetics of Microorganisms UB RAS, 13 Golev Str., 614081 Perm, Russia; (M.S.K.); (A.V.K.); (E.A.T.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
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15
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Draft Genome Sequence of Rhodococcus erythropolis VKPM Ac-1659, a Putative Oil-Degrading Strain Isolated from Polluted Soil in Siberia. Microbiol Resour Announc 2021; 10:e0053521. [PMID: 34292073 PMCID: PMC8297445 DOI: 10.1128/mra.00535-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The draft genome sequence of Rhodococcus erythropolis VKPM Ac-1659, a putative oil-degrading strain, is reported. This genome sequence may provide better insights into the diversity and evolution of the genes responsible for hydrocarbon degradation in soil microorganisms.
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16
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Donini E, Firrincieli A, Cappelletti M. Systems biology and metabolic engineering of Rhodococcus for bioconversion and biosynthesis processes. Folia Microbiol (Praha) 2021; 66:701-713. [PMID: 34215934 PMCID: PMC8449775 DOI: 10.1007/s12223-021-00892-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/12/2021] [Indexed: 11/04/2022]
Abstract
Rhodococcus spp. strains are widespread in diverse natural and anthropized environments thanks to their high metabolic versatility, biodegradation activities, and unique adaptation capacities to several stress conditions such as the presence of toxic compounds and environmental fluctuations. Additionally, the capability of Rhodococcus spp. strains to produce high value-added products has received considerable attention, mostly in relation to lipid accumulation. In relation with this, several works carried out omic studies and genome comparative analyses to investigate the genetic and genomic basis of these anabolic capacities, frequently in association with the bioconversion of renewable resources and low-cost substrates into triacylglycerols. This review is focused on these omic analyses and the genetic and metabolic approaches used to improve the biosynthetic and bioconversion performance of Rhodococcus. In particular, this review summarizes the works that applied heterologous expression of specific genes and adaptive laboratory evolution approaches to manipulate anabolic performance. Furthermore, recent molecular toolkits for targeted genome editing as well as genome-based metabolic models are described here as novel and promising strategies for genome-scaled rational design of Rhodococcus cells for efficient biosynthetic processes application.
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Affiliation(s)
- Eva Donini
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
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17
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Laddha H, Pawar PR, Prakash G. Bioconversion of waste acid oil to docosahexaenoic acid by integration of "ex novo'' and "de novo'' fermentation in Aurantiochytrium limacinum. BIORESOURCE TECHNOLOGY 2021; 332:125062. [PMID: 33839510 DOI: 10.1016/j.biortech.2021.125062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Thraustochytrids have predominantly been grown on hydrophilic substrates i.e. by "de novo" fermentation. The fatty acid composition of thraustochytrids oil in "de novo" mode is enriched in saturated palmitic acid and polyunsaturated docosahexaenoic acid. The "ex novo" fermentation of a novel Aurantiochytrium limacinum ICTSG-17 with waste acid oil altered the fatty acid composition of produced oil. This led to increased total unsaturated fatty acids (TUFA) and concomitant decrease in the total saturated fatty acids (TSFA) resulting in higher TUFA/TSFA ratio. However, cell growth and DHA content in "ex novo" were lower than that of "de novo" fermentation. Integration of "de novo" and "ex novo" fermentation modes were devised to attain high biomass and lipids enriched in DHA. Sequential "de novo"-"ex novo" fermentation resulted in ~20 g/L biomass and ~40% DHA content and higher TUFA/TSFA ratio as compared to that of "de novo" mode.
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Affiliation(s)
- Hrishikesh Laddha
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India
| | - Pratik R Pawar
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India
| | - Gunjan Prakash
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India.
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18
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Diallo MM, Vural C, Şahar U, Ozdemir G. Kurstakin molecules facilitate diesel oil assimilation by Acinetobacter haemolyticus strain 2SA through overexpression of alkane hydroxylase genes. ENVIRONMENTAL TECHNOLOGY 2021; 42:2031-2045. [PMID: 31752596 DOI: 10.1080/09593330.2019.1689301] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
Biodegradation is a cost-effective process commonly used to eliminate many xenobiotic hydrocarbons such as diesel oils. However, their hydrophobic character reduces the biodegradation efficiency. In order to overcome this hurdle, kurstakins isolated from Bacillus thuringiensis strain 7SA were used as emulsifying agents. The influence of kurstakin molecules on diesel oil degradation by Acinetobacter haemolyticus strain 2SA was evaluated in the presence and absence of the aforementioned lipopeptide. The degradation rates and gene expressions of alkane hydroxylases were evaluated at days 4, 10, 14 and 21. Results showed that kurstakin molecules increased the hydrophobicity of 2SA. Moreover, diesel oil degradation activities were higher in the presence of kurstakin with 29%, 35%, 29% and 23% improvement at 4th, 10th, 14th and 21st day respectively. Statistical analysis indicated that the difference between the degradation rates in the presence and absence of kurstakin was significant with p = 0.03. The detection of three different hydroxylase genes namely alkB, almA and cyp153 in 2SA genome, might have allowed more efficient degradability of alkanes. According to the real-time PCR results, cyp153 was the most induced gene during diesel oil degradation in the presence and absence of kurstakin. Yet, the three genes demonstrated higher levels of expression in the presence of kurstakin when compared to its absence. This study showed that kurstakins enhance the diesel oil biodegradation rate by increasing the hydrophobicity of 2SA. In addition to their anti-fungal activities, kurstakins can be used as biosurfactant to increase biodegradation of diesel oil.
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Affiliation(s)
- Mamadou Malick Diallo
- Department of Biology, Basic and Industrial Microbiology Section, Ege University, Izmir, Turkey
| | - Caner Vural
- Department of Biology, Basic and Industrial Microbiology Section, Ege University, Izmir, Turkey
| | - Umut Şahar
- Department of Biology, Molecular Biology Section, Ege University, Izmir, Turkey
| | - Guven Ozdemir
- Department of Biology, Basic and Industrial Microbiology Section, Ege University, Izmir, Turkey
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19
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Long Z, Wang X, Wang Y, Dai H, Li C, Xue Y, Deng Y, Zhang H, Yu Y, Fang H. Characterization of a novel carbendazim-degrading strain Rhodococcus sp. CX-1 revealed by genome and transcriptome analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142137. [PMID: 32916495 DOI: 10.1016/j.scitotenv.2020.142137] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 05/21/2023]
Abstract
The persistence and ecotoxicity of carbendazim residues pose a potential risk to environmental ecology and human health. Here, a novel and highly efficient carbendazim-degrading bacterium Rhodococcus sp. CX-1, capable of utilizing carbendazim as its sole source of carbon and energy, was isolated from contaminated soil. The biodegradation characteristics and metabolic pathways were studied by mass spectrometry, genomic annotation, and transcriptome analysis. The degradation rate of carbendazim by strain CX-1 was 3.98-9.90 mg/L/h under different conditions, and the optimum degradation conditions were 40 °C and pH 7.0. The addition of carbon sources (glucose, fructose, and sucrose, 100 mg/L) could accelerate carbendazim degradation. HPLC-MS/MS identification suggested that carbendazim is first hydrolyzed into 2-aminobenzimidazole and then to 2-hydroxybenzimidazole, and is ultimately mineralized to carbon dioxide. The genome of strain CX-1 contained 6,511,628 bp nucleotides, 2 linear plasmids, 2 circular plasmids, and 6437 protein coding genes. Genome annotation and transcriptome analysis indicated that carbendazim degradation may be regulated by the degradation genes harbored in the chromosome and in plasmid 2, and two different degradation pathways of carbendazim by imidazole ring cleavage or benzene ring cleavage were predicted. This study provided new insight to reveal the biodegradation mechanism of carbendazim; furthermore, strain CX-1 is a promising bioresource for carbendazim bioremediation.
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Affiliation(s)
- Zhengnan Long
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiuguo Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao 266101, China
| | - Yingjun Wang
- Zibo Tobacco Limited Liability Company, Shandong, China
| | - Huawei Dai
- Zibo Tobacco Limited Liability Company, Shandong, China
| | - Changhao Li
- Zibo Tobacco Limited Liability Company, Shandong, China
| | - Yongfei Xue
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yanfei Deng
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Houpu Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
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20
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Novoa A, Keet JH, Lechuga-Lago Y, Pyšek P, Roux JJL. Urbanization and Carpobrotus edulis invasion alter the diversity and composition of soil bacterial communities in coastal areas. FEMS Microbiol Ecol 2020; 96:5848193. [PMID: 32463431 DOI: 10.1093/femsec/fiaa106] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/27/2020] [Indexed: 11/13/2022] Open
Abstract
Coastal dunes are ecosystems of high conservation value that are strongly impacted by human disturbances and biological invasions in many parts of the world. Here, we assessed how urbanization and Carpobrotus edulis invasion affect soil bacterial communities on the north-western coast of Spain, by comparing the diversity, structure and composition of soil bacterial communities in invaded and uninvaded soils from urban and natural coastal dune areas. Our results suggest that coastal dune bacterial communities contain large numbers of rare taxa, mainly belonging to the phyla Actinobacteria and Proteobacteria. We found that the presence of the invasive C. edulis increased the diversity of soil bacteria and changed community composition, while urbanization only influenced bacterial community composition. Furthermore, the effects of invasion on community composition were conditional on urbanization. These results were contrary to predictions, as both C. edulis invasion and urbanization have been shown to affect soil abiotic conditions of the studied coastal dunes in a similar manner, and therefore were expected to have similar effects on soil bacterial communities. Our results suggest that other factors (e.g. pollution) might be influencing the impact of urbanization on soil bacterial communities, preventing an increase in the diversity of soil bacteria in urban areas.
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Affiliation(s)
- Ana Novoa
- Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences, CZ-252 43 Průhonice, Czech Republic.,Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, 7602 Matieland, South Africa.,Invasive Species Programme, South African National Biodiversity Institute, Kirstenbosch Research Centre, 7735 Claremont, South Africa
| | - Jan-Hendrik Keet
- Department of Botany and Zoology, Stellenbosch University, 7602 Matieland, South Africa
| | - Yaiza Lechuga-Lago
- Laboratorio de investigación n21, Ecofisioloxía, Departamento de Bioloxía Vexetal e Ciencias do Solo, Edificio de Ciencias Experimentais, University of Vigo, Campus Universitario, As Lagoas Marcosende, 36310 Vigo, Pontevedra, Spain
| | - Petr Pyšek
- Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences, CZ-252 43 Průhonice, Czech Republic.,Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, 7602 Matieland, South Africa.,Department of Ecology, Faculty of Science, Charles University, Viničná 7, CZ-128 44 Prague, Czech Republic
| | - Johannes J Le Roux
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, 7602 Matieland, South Africa.,Department of Botany and Zoology, Stellenbosch University, 7602 Matieland, South Africa.,Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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21
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Laczi K, Erdeiné Kis Á, Szilágyi Á, Bounedjoum N, Bodor A, Vincze GE, Kovács T, Rákhely G, Perei K. New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era. Front Microbiol 2020; 11:590049. [PMID: 33304336 PMCID: PMC7701123 DOI: 10.3389/fmicb.2020.590049] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.
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Affiliation(s)
- Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Ágnes Erdeiné Kis
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | | | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
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22
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Ho MT, Li MSM, McDowell T, MacDonald J, Yuan ZC. Characterization and genomic analysis of a diesel-degrading bacterium, Acinetobacter calcoaceticus CA16, isolated from Canadian soil. BMC Biotechnol 2020; 20:39. [PMID: 32711499 PMCID: PMC7477861 DOI: 10.1186/s12896-020-00632-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 07/16/2020] [Indexed: 12/18/2022] Open
Abstract
Background With the high demand for diesel across the world, environmental decontamination from its improper usage, storage and accidental spills becomes necessary. One highly environmentally friendly and cost-effective decontamination method is to utilize diesel-degrading microbes as a means for bioremediation. Here, we present a newly isolated and identified strain of Acinetobacter calcoaceticus (‘CA16’) as a candidate for the bioremediation of diesel-contaminated areas. Results Acinetobacter calcoaceticus CA16 was able to survive and grow in minimal medium with diesel as the only source of carbon. We determined through metabolomics that A. calcoaceticus CA16 appears to be efficient at diesel degradation. Specifically, CA16 is able to degrade 82 to 92% of aliphatic alkane hydrocarbons (CnHn + 2; where n = 12–18) in 28 days. Several diesel-degrading genes (such as alkM and xcpR) that are present in other microbes were also found to be activated in CA16. Conclusions The results presented here suggest that Acinetobacter strain CA16 has good potential in the bioremediation of diesel-polluted environments.
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Affiliation(s)
- Margaret T Ho
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Michelle S M Li
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada
| | - Tim McDowell
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, N5V 4T3, Canada
| | - Jacqueline MacDonald
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada
| | - Ze-Chun Yuan
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada. .,London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, N5V 4T3, Canada.
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Hu X, Li D, Qiao Y, Song Q, Guan Z, Qiu K, Cao J, Huang L. Salt tolerance mechanism of a hydrocarbon-degrading strain: Salt tolerance mediated by accumulated betaine in cells. JOURNAL OF HAZARDOUS MATERIALS 2020; 392:122326. [PMID: 32092654 DOI: 10.1016/j.jhazmat.2020.122326] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/15/2020] [Accepted: 02/15/2020] [Indexed: 06/10/2023]
Abstract
Rhodococcus sp. HX-2 could degrade diesel oil in the presence of 1%-10 % NaCl. The compatible solute betaine accumulated in cells with increasing NaCl concentration, and this was found to be the main mechanism of resistance of HX-2 to high salt concentration. Exogenously added betaine can be transported into cells, which improved cell growth and the percentage degradation of diesel oil in the presence of high [NaCl] in solution and in soil. Scanning electron microscopy data suggested that addition of exogenous betaine facilitated salt tolerance by stimulating exopolysaccharide production. Fourier-transform infrared analysis suggested that surface hydroxyl, amide and phosphate groups may be related to tolerance of high-salt environments. Four betaine transporter-encoding genes (H0, H1, H3, H5) and the betaine producer gene betB were induced in Rhodococcus sp. HX-2 by NaCl stress. The maximal induction of H0, H1, H3 and H5 transcription depended on high salinity plus the presence of betaine. These results demonstrate that salt tolerance is mediated by accumulated betaine in Rhodococcus sp. HX-2 cells, and the potential of this strain for application in bioremediation of hydrocarbon pollution in saline environments.
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Affiliation(s)
- Xin Hu
- College of Chemistry and Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin Key Laboratory of Drug Targeting and Bioimaging, Tianjin University of Technology, Tianjin, 300384, China
| | - Dahui Li
- College of Chemistry and Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin Key Laboratory of Drug Targeting and Bioimaging, Tianjin University of Technology, Tianjin, 300384, China
| | - Yue Qiao
- College of Chemistry and Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin Key Laboratory of Drug Targeting and Bioimaging, Tianjin University of Technology, Tianjin, 300384, China
| | - Qianqian Song
- College of Chemistry and Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin Key Laboratory of Drug Targeting and Bioimaging, Tianjin University of Technology, Tianjin, 300384, China
| | - Zhiguo Guan
- College of Chemistry and Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin Key Laboratory of Drug Targeting and Bioimaging, Tianjin University of Technology, Tianjin, 300384, China
| | - Kaixuan Qiu
- College of Chemistry and Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin Key Laboratory of Drug Targeting and Bioimaging, Tianjin University of Technology, Tianjin, 300384, China
| | - Jiachang Cao
- College of Chemistry and Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin Key Laboratory of Drug Targeting and Bioimaging, Tianjin University of Technology, Tianjin, 300384, China
| | - Lei Huang
- College of Chemistry and Chemical Engineering, Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, Tianjin Key Laboratory of Drug Targeting and Bioimaging, Tianjin University of Technology, Tianjin, 300384, China.
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Bodor A, Petrovszki P, Erdeiné Kis Á, Vincze GE, Laczi K, Bounedjoum N, Szilágyi Á, Szalontai B, Feigl G, Kovács KL, Rákhely G, Perei K. Intensification of Ex Situ Bioremediation of Soils Polluted with Used Lubricant Oils: A Comparison of Biostimulation and Bioaugmentation with a Special Focus on the Type and Size of the Inoculum. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E4106. [PMID: 32526873 PMCID: PMC7312492 DOI: 10.3390/ijerph17114106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 11/16/2022]
Abstract
Used lubricant oils (ULOs) strongly bind to soil particles and cause persistent pollution. In this study, soil microcosm experiments were conducted to model the ex situ bioremediation of a long term ULO-polluted area. Biostimulation and various inoculation levels of bioaugmentation were applied to determine the efficacy of total petrol hydrocarbon (TPH) removal. ULO-contaminated soil microcosms were monitored for microbial respiration, colony-forming units (CFUs) and TPH bioconversion. Biostimulation with inorganic nutrients was responsible for 22% of ULO removal after 40 days. Bioaugmentation using two hydrocarbon-degrader strains: Rhodococcus quingshengii KAG C and Rhodococcus erythropolis PR4 at a small inoculum size (107 CFUs g-1 soil), reduced initial TPH concentration by 24% and 29%, respectively; the application of a higher inoculum size (109 CFUs g-1 soil) led to 41% and 32% bioconversion, respectively. After 20 days, all augmented CFUs decreased to the same level as measured in the biostimulated cases, substantiating the challenge for the newly introduced hydrocarbon-degrading strains to cope with environmental stressors. Our results not only highlight that an increased number of degrader cells does not always correlate with enhanced TPH bioconversion, but they also indicate that biostimulation might be an economical solution to promote ULO biodegradation in long term contaminated soils.
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Affiliation(s)
- Attila Bodor
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary; (A.B.); (P.P.); (Á.E.K.); (G.E.V.); (K.L.); (N.B.); (Á.S.); (K.L.K.); (K.P.)
- Institute of Environmental and Technological Sciences, University of Szeged, H-6726 Szeged, Hungary
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary;
| | - Péter Petrovszki
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary; (A.B.); (P.P.); (Á.E.K.); (G.E.V.); (K.L.); (N.B.); (Á.S.); (K.L.K.); (K.P.)
| | - Ágnes Erdeiné Kis
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary; (A.B.); (P.P.); (Á.E.K.); (G.E.V.); (K.L.); (N.B.); (Á.S.); (K.L.K.); (K.P.)
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary;
| | - György Erik Vincze
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary; (A.B.); (P.P.); (Á.E.K.); (G.E.V.); (K.L.); (N.B.); (Á.S.); (K.L.K.); (K.P.)
- Doctoral School of Environmental Sciences, University of Szeged, H-6720 Szeged, Hungary
| | - Krisztián Laczi
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary; (A.B.); (P.P.); (Á.E.K.); (G.E.V.); (K.L.); (N.B.); (Á.S.); (K.L.K.); (K.P.)
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary; (A.B.); (P.P.); (Á.E.K.); (G.E.V.); (K.L.); (N.B.); (Á.S.); (K.L.K.); (K.P.)
- Institute of Environmental and Technological Sciences, University of Szeged, H-6726 Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary; (A.B.); (P.P.); (Á.E.K.); (G.E.V.); (K.L.); (N.B.); (Á.S.); (K.L.K.); (K.P.)
| | - Balázs Szalontai
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary;
| | - Gábor Feigl
- Department of Plant Biology, University of Szeged, H-6726 Szeged, Hungary;
| | - Kornél L. Kovács
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary; (A.B.); (P.P.); (Á.E.K.); (G.E.V.); (K.L.); (N.B.); (Á.S.); (K.L.K.); (K.P.)
- Department of Oral Biology and Experimental Dental Research, University of Szeged, H-6720 Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary; (A.B.); (P.P.); (Á.E.K.); (G.E.V.); (K.L.); (N.B.); (Á.S.); (K.L.K.); (K.P.)
- Institute of Environmental and Technological Sciences, University of Szeged, H-6726 Szeged, Hungary
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary;
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary; (A.B.); (P.P.); (Á.E.K.); (G.E.V.); (K.L.); (N.B.); (Á.S.); (K.L.K.); (K.P.)
- Institute of Environmental and Technological Sciences, University of Szeged, H-6726 Szeged, Hungary
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Solyanikova IP, Golovleva LA. Hexadecane and Hexadecane-Degrading Bacteria: Mechanisms of Interaction. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261718060152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Immobilization of P. stutzeri on Activated Carbons for Degradation of Hydrocarbons from Oil-in-Saltwater Emulsions. NANOMATERIALS 2019; 9:nano9040500. [PMID: 30939741 PMCID: PMC6523707 DOI: 10.3390/nano9040500] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/14/2019] [Accepted: 03/23/2019] [Indexed: 12/17/2022]
Abstract
Production water is the largest byproduct of the oil industry and must be treated before disposal, either by reinjection or shedding processes, with the purpose of eliminating emulsified crude oil and avoiding the operational and toxic problems associated with it. The objective of this work was to immobilize a hydrocarbon-degrading strain on activated carbons, to evaluate the biocomplex’s capacity for catalyzing hydrocarbons from Oil in Brine emulsions (O/W) simulating produced waters. Activated carbons were prepared and their chemical and porous properties were estimated by XPS, pHPZC and SEM, N2 adsorption, and mercury porosimetry. Biomaterials were synthesized and hydrocarbon removal tests were performed. The basic and neutral carbons immobilized Pseudomonas stutzeri by physisorption in the macroporous space and electrostatic interactions (108–109 UFC∙g−1), while acid materials inhibited bacterial growth. Removal of aromatic hydrocarbons was more efficient using materials (60%–93%) and biomaterials (16%–84%) than using free P. stutzeri (1%–47%), and the removal efficiencies of crude oil were 22%, 48% and 37% for P. stutzeri and two biomaterials, respectively. The presence of minor hydrocarbons only when P. stutzeri was present confirmed the biotransformation process.
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27
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Ji N, Wang X, Yin C, Peng W, Liang R. CrgA Protein Represses AlkB2 Monooxygenase and Regulates the Degradation of Medium-to-Long-Chain n-Alkanes in Pseudomonas aeruginosa SJTD-1. Front Microbiol 2019; 10:400. [PMID: 30915046 PMCID: PMC6422896 DOI: 10.3389/fmicb.2019.00400] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/15/2019] [Indexed: 11/13/2022] Open
Abstract
AlkB monooxygenases in bacteria are responsible for the hydroxylation of medium- and long-chain n-alkanes. In this study, one CrgA protein of Pseudomonas aeruginosa SJTD-1, a member of LysR family, was proved to regulate AlkB2 monooxygenase and the degradation of medium-to-long-chain n-alkanes (C14-C20) by directly binding to the upstream of alkB2 gene. Two specific sites for CrgA binding were found in the promoter region of alkB2 gene, and the imperfect mirror repeat (IIR) structure was proved critical for CrgA recognition and binding. Hexadecyl CoA and octadecyl CoA could effectively release the CrgA binding and start the transcription of alkB2 gene, implying a positive regulation of metabolic intermediate. In the presence of medium-to-long-chain n-alkanes (C14-C20), deletion of crgA gene could enhance the transcription and expression of AlkB2 monooxygenase significantly; and in n-octadecane culture, strain S1ΔalkB1&crgA grew more vigorously than strain S1 ΔalkB1 &crgA . Almost no regulation of CrgA protein was observed to alkB1 gene in vitro and in vivo. Therefore, CrgA acted as a negative regulator for the medium-to-long-chain n-alkane utilization in P. aeruginosa SJTD-1. The work will promote the regulation mechanism study of n-alkane degradation in bacteria and help the bioremediation method development for petroleum pollution.
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Affiliation(s)
- Nannan Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuli Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chong Yin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanli Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Zampolli J, Zeaiter Z, Di Canito A, Di Gennaro P. Genome analysis and -omics approaches provide new insights into the biodegradation potential of Rhodococcus. Appl Microbiol Biotechnol 2018; 103:1069-1080. [PMID: 30554387 DOI: 10.1007/s00253-018-9539-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 01/05/2023]
Abstract
The past few years observed a breakthrough of genome sequences of bacteria of Rhodococcus genus with significant biodegradation abilities. Invaluable knowledge from genome data and their functional analysis can be applied to develop and design strategies for attenuating damages caused by hydrocarbon contamination. With the advent of high-throughput -omic technologies, it is currently possible to utilize the functional properties of diverse catabolic genes, analyze an entire system at the level of molecule (DNA, RNA, protein, and metabolite), simultaneously predict and construct catabolic degradation pathways. In this review, the genes involved in the biodegradation of hydrocarbons and several emerging plasticizer compounds in Rhodococcus strains are described in detail (aliphatic, aromatics, PAH, phthalate, polyethylene, and polyisoprene). The metabolic biodegradation networks predicted from omics-derived data along with the catabolic enzymes exploited in diverse biotechnological and bioremediation applications are characterized.
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Affiliation(s)
- Jessica Zampolli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Zahraa Zeaiter
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Alessandra Di Canito
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
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Chen Z, Zheng Z, Wang FL, Niu YP, Miao JL, Li H. Intracellular Metabolic Changes of Rhodococcus sp. LH During the Biodegradation of Diesel Oil. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:803-812. [PMID: 30218327 DOI: 10.1007/s10126-018-9850-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
Abstract
In recent years, some marine microbes have been used to degrade diesel oil. However, the exact mechanisms underlying the biodegradation are still poorly understood. In this study, a hypothermophilous marine strain, which can degrade diesel oil in cold seawater was isolated from Antarctic floe-ice and identified and named as Rhodococcus sp. LH. To clarify the biodegradation mechanisms, a gas chromatography-mass spectrometry (GC-MS)-based metabolomics strategy was performed to determine the diesel biodegradation process-associated intracellular biochemical changes in Rhodococcus sp. LH cells. With the aid of partial least squares-discriminant analysis (PLS-DA), 17 differential metabolites with variable importance in the projection (VIP) value greater than 1 were identified. Results indicated that the biodegradation of diesel oil by Rhodococcus sp. LH was affected by many different factors. Rhodococcus sp. LH could degrade diesel oil through terminal or sub-terminal oxidation reactions, and might also possess the ability to degrade aromatic hydrocarbons. In addition, some surfactants, especially fatty acids, which were secreted by Rhodococcus into medium could also assist the strain in dispersing and absorbing diesel oil. Lack of nitrogen in the seawater would lead to nitrogen starvation, thereby restraining the amino acid circulation in Rhodococcus sp. LH. Moreover, nitrogen starvation could also promote the conversation of relative excess carbon source to storage materials, such as 1-monolinoleoylglycerol. These results would provide a comprehensive understanding about the complex mechanisms of diesel oil biodegradation by Rhodococcus sp. LH at the systematic level.
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Affiliation(s)
- Ze Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhou Zheng
- The First Institute of Oceanography, State Oceanic Administration, Qingdao, 266061, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
| | - Feng-Lian Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yuan-Pu Niu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jin-Lai Miao
- The First Institute of Oceanography, State Oceanic Administration, Qingdao, 266061, China.
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
| | - Hao Li
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Mutafova B, Momchilova S, Pomakova D, Avramova T, Mutafov S. Enhanced cell surface hydrophobicity favors the 9α-hydroxylation of androstenedione by resting Rhodococcus sp. cells. Eng Life Sci 2018; 18:949-954. [PMID: 32624889 DOI: 10.1002/elsc.201800089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/02/2018] [Accepted: 07/18/2018] [Indexed: 11/07/2022] Open
Abstract
The achievement of an effective process of 9α-hydroxylation of 4-androstene-3,17-dione is of significant importance as it leads to the formation of the key intermediate 9α-hydroxy-4-androstene-3,17-dione which is not possible by chemical means. In this study, the 9α-hydroxylation of 4-androstene-3,17-dione was carried out by resting Rhodococcus sp. cells. The ability of the naturally hydrophobic Rhodococcus to assimilate n-alkanes was employed to obtain a cell depot with an intentionally increased cell surface hydrophobicity. The control Rhodococcus sp. cells were cultivated on medium containing glucose instead of n-alkanes as a source of carbon and energy. Cells were harvested, washed from the cultivation media, and subjected to transformation of crystal androstenedione in buffer medium. The hydrophobicity of the n-alkanes- and glucose-grown cells, their total lipid content, and fatty acid composition were determined. The ultrastructure of the n-alkanes- and glucose-grown cells and their steroid hydroxylating activities were examined and compared. The results obtained in the present study showed that the intentionally achieved growth-driven enhancement of the already hydrophobic Rhodococcus sp. cells made them even more compatible with the hydrophobic steroid substrate and enhanced its accessibility, which provided an increased steroid hydroxylating activity and lack of the accompanying product destruction.
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Affiliation(s)
- Blaga Mutafova
- Bulgarian Academy of Sciences The Stephan Angeloff Institute of Microbiology Sofia Bulgaria
| | - Svetlana Momchilova
- Bulgarian Academy of Sciences Institute of Organic Chemistry with Centre of Phytochemistry Sofia Bulgaria
| | - Dimitrina Pomakova
- Bulgarian Academy of Sciences The Stephan Angeloff Institute of Microbiology Sofia Bulgaria
| | - Tatyana Avramova
- Bulgarian Academy of Sciences The Stephan Angeloff Institute of Microbiology Sofia Bulgaria
| | - Sava Mutafov
- Bulgarian Academy of Sciences The Stephan Angeloff Institute of Microbiology Sofia Bulgaria
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Habib S, Ahmad SA, Johari WLW, Shukor MYA, Alias SA, Khalil KA, Yasid NA. Evaluation of conventional and response surface level optimisation of n-dodecane (n-C12) mineralisation by psychrotolerant strains isolated from pristine soil at Southern Victoria Island, Antarctica. Microb Cell Fact 2018; 17:44. [PMID: 29549881 PMCID: PMC5857080 DOI: 10.1186/s12934-018-0889-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/08/2018] [Indexed: 11/23/2022] Open
Abstract
Background Biodegradation of hydrocarbons in Antarctic soil has been reported to be achieved through the utilisation of indigenous cold-adapted microorganisms. Although numerous bacteria isolated from hydrocarbon-contaminated sites in Antarctica were able to demonstrate promising outcomes in utilising hydrocarbon components as their energy source, reports on the utilisation of hydrocarbons by strains isolated from pristine Antarctic soil are scarce. In the present work, two psychrotolerant strains isolated from Antarctic pristine soil with the competency to utilise diesel fuel as the sole carbon source were identified and optimised through conventional and response surface method. Results Two potent hydrocarbon-degraders (ADL15 and ADL36) were identified via partial 16S rRNA gene sequence analysis, and revealed to be closely related to the genus Pseudomonas and Rhodococcus sp., respectively. Factors affecting diesel degradation such as temperature, hydrocarbon concentration, pH and salt tolerance were studied. Although strain ADL36 was able to withstand a higher concentration of diesel than strain ADL15, both strains showed similar optimal condition for the cell’s growth at pH 7.0 and 1.0% (w/v) NaCl at the conventional ‘one-factor-at-a-time’ level. Both strains were observed to be psychrotrophs with optimal temperatures of 20 °C. Qualitative and quantitative analysis were performed with a gas chromatograph equipped with a flame ionisation detector to measure the reduction of n-alkane components in diesel. In the pre-screening medium, strain ADL36 showed 83.75% of n-dodecane mineralisation while the reduction of n-dodecane by strain ADL15 was merely at 22.39%. The optimised condition for n-dodecane mineralisation predicted through response surface methodology enhanced the reduction of n-dodecane to 99.89 and 38.32% for strain ADL36 and strain ADL15, respectively. Conclusions Strain ADL36 proves to be a better candidate for bioaugmentation operations on sites contaminated with aliphatic hydrocarbons especially in the Antarctic and other cold regions. The results obtained throughout strongly supports the use of RSM for medium optimisation.
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Affiliation(s)
- Syahir Habib
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Wan Lutfi Wan Johari
- Department of Environmental Sciences, Faculty of Environmental Studies, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Yunus Abd Shukor
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Siti Aisyah Alias
- Institute of Ocean and Earth Sciences, C308 Institute of Postgraduate Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Khalilah Abdul Khalil
- Department of Biomolecular Sciences, Faculty of Applied Sciences, Universiti Teknologi MARA, 40450, Shah Alam, Selangor, Malaysia
| | - Nur Adeela Yasid
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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Dos Santos JJ, Maranho LT. Rhizospheric microorganisms as a solution for the recovery of soils contaminated by petroleum: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 210:104-113. [PMID: 29331851 DOI: 10.1016/j.jenvman.2018.01.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 12/27/2017] [Accepted: 01/04/2018] [Indexed: 06/07/2023]
Abstract
Petroleum is currently the world's main energy source, and its demand is expected to increase in coming years. Its intense exploitation can lead to an increase in the number of environmental accidents, such as spills and leaks, and an increase in the generation of environmental liabilities resulting from refining. Due to its hydrophobic characteristics and slow process of biodegradation, petroleum can remain in the environment for a long time and its toxicity can cause a negative impact on both terrestrial and aquatic ecosystems, with the main negative effects related to its carcinogenic potential for both animals and humans. The objective of the present review is to discuss environmental contamination by oil, conventional treatment techniques and bioremediation an alternative tool for recovery petroleum-contaminated soils, focusing on the rhizodegradation process, plant growth-promoting rhizobacteria (PGPR), a phytoremediation strategy in which the microorganisms that colonize the roots of phytoremediatior plants are responsible for the biodegradation of petroleum. These microorganisms can be selected and tested individually or in the form of consortia to evaluate their potential for oil degradation, or even to measure the use of biosurfactants produced by them to constitute tools for the development of environmental recovery strategies and biotechnological application.
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Affiliation(s)
- Jéssica Janzen Dos Santos
- Master Program in Industrial Biotechnology, Universidade Positivo (UP), R. Prof. Pedro Viriato Parigot de Souza, 5300, Curitiba, PR 81.280-330, Brazil
| | - Leila Teresinha Maranho
- Master Program in Industrial Biotechnology, Universidade Positivo (UP), R. Prof. Pedro Viriato Parigot de Souza, 5300, Curitiba, PR 81.280-330, Brazil.
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Biodegradation of 7-Ketocholesterol by Rhodococcus erythropolis MTCC 3951: Process optimization and enzymatic insights. Chem Phys Lipids 2017; 207:253-259. [DOI: 10.1016/j.chemphyslip.2017.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/18/2017] [Accepted: 05/23/2017] [Indexed: 01/22/2023]
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Park C, Shin B, Jung J, Lee Y, Park W. Metabolic and stress responses of Acinetobacter oleivorans DR1 during long-chain alkane degradation. Microb Biotechnol 2017; 10:1809-1823. [PMID: 28857443 PMCID: PMC5658608 DOI: 10.1111/1751-7915.12852] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 11/28/2022] Open
Abstract
Acinetobacter oleivorans DR1 can utilize C12–C30 alkanes as a sole carbon source but not short‐chain alkanes (C6, C10). Two copies of each alkB‐, almA‐ and ladA‐type alkane hydroxylase (AH) are present in the genome of DR1 cells. Expression and mutational analyses of AHs showed that alkB1 and alkB2 are the major AH‐encoding genes under C12–C30, and the roles of other almA‐ and ladA genes are negligible. Our data suggested that AlkB1 is responsible for long‐chain alkane utilization (C24–C26), and AlkB2 is important for medium‐chain alkane (C12–C16) metabolism. Phylogenetic analyses revealed large incongruities between phylogenies of 16S rRNA and each AH gene, which implies that A. oleivorans DR1 has acquired multiple alkane hydroxylases through horizontal gene transfer. Transcriptomic and qRT‐PCR analyses suggested that genes participating in the synthesis of siderophore, trehalose and poly 3‐hydroxybutyrate (PHB) were expressed at much higher levels when cells used C30 than when used succinate as a carbon source. The following biochemical assays supported our gene expression analyses: (i) quantification of siderophore, (ii) measurement of trehalose and (iii) observation of PHB storage. Interestingly, highly induced both ackA gene encoding an acetate kinase A and pta gene encoding a phosphotransacetylase suggested unusual ATP synthesis during C30 alkane degradation, which was demonstrated by ATP measurement using the ΔackA mutant. Impaired growth of the ΔaceA mutant indicated that the glyoxylate shunt pathway is important when C30 alkane is utilized. Our data provide insight into long‐chain alkane degradation in soil microorganisms.
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Affiliation(s)
- Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Korea
| | - Bora Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Korea
| | - Jaejoon Jung
- National Marine Biodiversity Institute of Korea, Chungcheongnam-Do, 33662, Korea
| | - Yunho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Korea
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Draft Genome Sequence of Rhodococcus erythropolis VSD3, a Diesel Fuel-Degrading and Plant Growth-Promoting Bacterium Isolated from Hedera helix Leaves. GENOME ANNOUNCEMENTS 2017; 5:5/8/e01680-16. [PMID: 28232452 PMCID: PMC5323631 DOI: 10.1128/genomea.01680-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We report here the 6.55-Mb draft genome sequence of Rhodococcus erythropolis VSD3, a Gram-positive bacterium of the Nocardiaceae family, isolated from leaves of Hedera helix growing at a high-traffic city center in Belgium. The exploration of its genome will contribute to the assessment of its application as an inoculant in phylloremediation approaches.
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Kundu D, Hazra C, Chaudhari A. Biodegradation of 2,6-dinitrotoluene and plant growth promoting traits by Rhodococcus pyridinivorans NT2: Identification and toxicological analysis of metabolites and proteomic insights. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2016. [DOI: 10.1016/j.bcab.2016.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Sousa SF, Sousa JFM, Barbosa ACC, Ferreira CE, Neves RPP, Ribeiro AJM, Fernandes PA, Ramos MJ. Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD). J Phys Chem A 2016; 120:5300-6. [DOI: 10.1021/acs.jpca.6b01536] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sérgio F. Sousa
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Joana F. M. Sousa
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Ana C. C. Barbosa
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Cleide E. Ferreira
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P. P. Neves
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - António J. M. Ribeiro
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria João Ramos
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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