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Keywords = alkane hydroxylase

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18 pages, 1445 KiB  
Article
Antibiotic Resistance and Virulence Determinants of Pseudomonas aeruginosa Isolates Cultured from Hydrocarbon-Contaminated Environmental Samples
by Chioma Lilian Ozoaduche, Balázs Libisch, Daniel Itoro, Iyore Blessing Idemudia, Katalin Posta and Ferenc Olasz
Microorganisms 2025, 13(3), 688; https://doi.org/10.3390/microorganisms13030688 - 19 Mar 2025
Cited by 2 | Viewed by 931
Abstract
Crude oil and its derivates are among the most important environmental pollutants, where P. aeruginosa strains producing AlkB1 and AlkB2 alkane hydroxylases are often involved in their biodegradation. The aim of this study was to analyze antibiotic resistance and virulence determinants of a [...] Read more.
Crude oil and its derivates are among the most important environmental pollutants, where P. aeruginosa strains producing AlkB1 and AlkB2 alkane hydroxylases are often involved in their biodegradation. The aim of this study was to analyze antibiotic resistance and virulence determinants of a P. aeruginosa isolate cultured from a hydrocarbon-contaminated soil sample from Ogoniland, Nigeria, and to compare its characteristics with P. aeruginosa isolates cultured worldwide from hydrocarbon-contaminated environments or from clinical samples. Using the ResFinder reference database, a catB7 chloramphenicol acetyltransferase gene, an ampC-type PDC β-lactamase gene, and an OXA-50 type β-lactamase gene were identified in all P. aeruginosa strains analyzed in this study. In some of these P. aeruginosa strains, loss-of-function mutations were detected in the regulatory genes mexR, nalC, or nalD, predicting an efflux-mediated acquired antibiotic-resistance mechanism. Several P. aeruginosa sequence types that were associated with oil-contaminated environments have also been cultured from human clinical samples worldwide, including sequence types ST532, ST267, ST244, and ST1503. Our findings also indicate that environmental P. aeruginosa may serve as the source of human infections, warranting further studies from a One Health perspective about the application of P. aeruginosa for the in situ bioremediation of hydrocarbon-contaminated sites. Full article
(This article belongs to the Special Issue Bacterial Antibiotic Resistance, Second Edition)
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18 pages, 4084 KiB  
Article
Investigating the Potential of Native Soil Bacteria for Diesel Biodegradation
by Mihaela Marilena Stancu
Microorganisms 2025, 13(3), 564; https://doi.org/10.3390/microorganisms13030564 - 2 Mar 2025
Cited by 1 | Viewed by 1106
Abstract
In countries with a long petroleum extraction and processing history, such as Romania, extensive soil areas are often polluted with petroleum and its derivatives, posing significant environmental and human health risks. This study explores the diesel biodegradation potential of two native bacterial consortia [...] Read more.
In countries with a long petroleum extraction and processing history, such as Romania, extensive soil areas are often polluted with petroleum and its derivatives, posing significant environmental and human health risks. This study explores the diesel biodegradation potential of two native bacterial consortia isolated from hydrocarbon-polluted soils, focusing on their phenotypic and molecular characteristics, growth kinetics, alkane hydroxylase activity, hydrolase production, and biosurfactant synthesis capabilities. The bacterial consortia, CoP1 and CoP2, were successfully obtained using the standard successive enrichment culture method from two soil samples collected from a region affected by petroleum pollution. The CoP1 and CoP2 consortia demonstrated efficient diesel-degrading capabilities, achieving 50.81−84.32% degradation when cultured in a minimal medium containing 1–10% (v/v) diesel as the sole carbon and energy source. This biodegradation potential was corroborated by their significant alkane hydroxylase activity and the detection of multiple catabolic genes in their genomes. The CoP1 consortium contains at least four catabolic genes (alkB, alkM, todM, ndoM) as well as rhamnosyltransferase 1 genes (rhlAB), while the CoP2 consortium contains only two catabolic genes (ndoM, C23DO). The RND transporter gene (HAE1) was present in both consortia. Secondary metabolites, such as glycolipid-type biosurfactants, as well as extracellular hydrolases (protease, amylase, cellulase, and lipase), were produced by both consortia. The CoP1 and CoP2 consortia demonstrate exceptional efficiency in diesel degradation and biosurfactant production, making them well suited for the bioremediation of soils contaminated with petroleum and its derivatives. Full article
(This article belongs to the Section Microbial Biotechnology)
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22 pages, 7605 KiB  
Article
Generalization of Classification of AlkB Family Alkane Monooxygenases from Rhodococcus (sensu lato) Group Based on Phylogenetic Analysis and Genomic Context Comparison
by Kirill V. Petrikov, Anna A. Vetrova, Anastasia A. Ivanova, Olesya I. Sazonova and Irina Yu. Pozdnyakova-Filatova
Int. J. Mol. Sci. 2025, 26(4), 1713; https://doi.org/10.3390/ijms26041713 - 17 Feb 2025
Viewed by 1092
Abstract
Alkane-oxidizing bacteria play a crucial role in the global carbon cycle. Rhodococcus species are well-known hydrocarbon degraders, distinguished by the harboring of multiple homologs of AlkB family alkane monooxygenases. Although different types of rhodococcal AlkBs have been described, the overall picture of their [...] Read more.
Alkane-oxidizing bacteria play a crucial role in the global carbon cycle. Rhodococcus species are well-known hydrocarbon degraders, distinguished by the harboring of multiple homologs of AlkB family alkane monooxygenases. Although different types of rhodococcal AlkBs have been described, the overall picture of their diversity remains unclear, leaving gaps in the current classification. We conducted a phylogenetic analysis of all AlkBs identified in Rhodococcus (sensu lato) and examined the genomic context of the corresponding genes. The sequence clustering was well aligned with genomic neighborhoods, allowing both features to be used as criteria for proposing AlkB types that form distinct phylogenetic groups and have characteristic genomic contexts. Our approach allowed us to revise the classification of previously described AlkBs, identifying eight types on their basis, and to propose three new ones. Alkane monooxygenases whose genes are co-localized with rubredoxin genes can be considered a generalized AlkBR type, the most common among all Rhodococcus. In the AlkB0 type, which is a paralog of AlkBR, violations of conservativity in known alkane monooxygenase signature motifs were found. Our findings provide a more consistent classification framework for rhodococcal AlkB that prevents the over-reporting of “novel” types and contributes to a deeper understanding of alkane monooxygenase diversity. Full article
(This article belongs to the Section Biochemistry)
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18 pages, 1663 KiB  
Review
N-Alkane Assimilation by Pseudomonas aeruginosa and Its Interactions with Virulence and Antibiotic Resistance
by Balázs Libisch
Antibiotics 2024, 13(11), 1028; https://doi.org/10.3390/antibiotics13111028 - 31 Oct 2024
Cited by 3 | Viewed by 1834
Abstract
Pseudomonas aeruginosa strains with potential for degrading n-alkanes are frequently cultured from hydrocarbon-contaminated sites. The initial hydroxylation step of long-chain n-alkanes is mediated by the chromosomally encoded AlkB1 and AlkB2 alkane hydroxylases. The acquisition of an additional P. putida GPo1-like alkane [...] Read more.
Pseudomonas aeruginosa strains with potential for degrading n-alkanes are frequently cultured from hydrocarbon-contaminated sites. The initial hydroxylation step of long-chain n-alkanes is mediated by the chromosomally encoded AlkB1 and AlkB2 alkane hydroxylases. The acquisition of an additional P. putida GPo1-like alkane hydroxylase gene cluster can extend the substrate range assimilated by P. aeruginosa to <C12 n-alkanes. Efficient niche colonization of hydrocarbon-contaminated sites is facilitated by avid iron-uptake systems, such as pyoverdine, and the production of several compounds with antimicrobial activities. A GPo1-like gene cluster can facilitate detoxification and solvent tolerance in P. aeruginosa. The overproduction of various multidrug efflux pumps, in particular, the MexAB-OprM system, can also contribute to solvent tolerance, which is often associated with reduced susceptibility or full resistance to certain clinically relevant antibiotics. These characteristics, together with the remarkable conservation of P. aeruginosa virulence determinants among human, animal, and environmental isolates, necessitate further studies from a One Health perspective into the acquired antibiotic resistance mechanisms of environmental P. aeruginosa strains and possible ways for their dissemination into the human population. Full article
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27 pages, 2689 KiB  
Review
Novel Approach of Tackling Wax Deposition Problems in Pipeline Using Enzymatic Degradation Process: Challenges and Potential Solutions
by Shazleen Saadon, Raja Noor Zaliha Raja Abd Rahman, Nor Hafizah Ahmad Kamarudin, Sara Shahruddin, Siti Rohaida Mohd Shafian, Norhidayah Ahmad Wazir and Mohd Shukuri Mohamad Ali
Processes 2024, 12(10), 2074; https://doi.org/10.3390/pr12102074 - 25 Sep 2024
Cited by 2 | Viewed by 1915
Abstract
Anthropogenic activities have led to hydrocarbon spills, and while traditional bioremediation methods are costly and time-consuming, recent research has focused on engineered enzymes for managing pollutant. The potential of enzymes for resolving wax flow problems in the petroleum industry remains unexplored. This paper [...] Read more.
Anthropogenic activities have led to hydrocarbon spills, and while traditional bioremediation methods are costly and time-consuming, recent research has focused on engineered enzymes for managing pollutant. The potential of enzymes for resolving wax flow problems in the petroleum industry remains unexplored. This paper offers a comprehensive review of the current state of research activities related to the bioremediation of petroleum-polluted sites and the biodegradation of specific petroleum hydrocarbons. The assayed enzymes that took part in the degradation were discussed in detail. Lipase, laccase, alkane hydroxylase, alcohol dehydrogenase, esterase, AlkB homologs and cytochrome P450 monooxygenase are among the enzymes responsible for the degradation of more than 50% of the hydrocarbons in contaminated soil and wastewater and found to be active on carbon C8 to C40. The possible biodegradation mechanism of petroleum hydrocarbons was also elucidated. The enzymes’ primary metabolic pathways include terminal, subterminal, and ω-oxidation. Next, given the successful evidence of the hydrocarbon treatment efficiency, the authors analyzed the opportunity for the enzymatic degradation approach if it were to be applied to a different scenario: managing wax deposition in petroleum-production lines. With properties such as high transformation efficiency and high specificity, enzymes can be utilized for the treatment of viscous heavy oil for transportability, evidenced by the 20 to 99% removal of hydrocarbons. The challenges associated with the new approach are also discussed. The production cost of enzymes, the characteristics of hydrocarbons and the operating conditions of the production line may affect the biocatalysis reaction to some extent. However, the challenges can be overcome by the usage of extremophilic enzymes. The combination of technological advancement and deployment strategies such as the immobilization of a consortium of highly thermophilic and halotolerant enzymes is suggested. Recovering and reusing enzymes offers an excellent strategy to improve the economics of the technology. This paper provides insights into the opportunity for the enzymatic degradation approach to be expanded for wax deposition problems in pipelines. Full article
(This article belongs to the Special Issue Application of Enzymes in Sustainable Biocatalysis)
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15 pages, 4937 KiB  
Article
Mechanism of Crude Oil Biodegradation in Bioreactors: A Model Approach
by Carlos Costa and Nicolás Millán
Water 2024, 16(12), 1653; https://doi.org/10.3390/w16121653 - 10 Jun 2024
Cited by 3 | Viewed by 2194
Abstract
Oil-degrading bacteria have the ability to degrade alkanes present in crude oil because of a special enzymatic system, the alkane hydroxylase complex (AlkH). The mechanism for the transport and degradation of alkanes present in crude oil remains unclear, especially related to the first [...] Read more.
Oil-degrading bacteria have the ability to degrade alkanes present in crude oil because of a special enzymatic system, the alkane hydroxylase complex (AlkH). The mechanism for the transport and degradation of alkanes present in crude oil remains unclear, especially related to the first step in hydrocarbons oxidation. In this work, we present a novel model of the crude oil biodegradation mechanism by considering the contact between the oil drop and the cell and calculating the mass transfer coefficients in three oleophilic bacteria (B. licheniformis, P. putida and P. glucanolyticus). The mass transfer coefficients are evaluated under critical time conditions, when the kinetics and mass transport are in balance, and the difference in the values obtained (kL α = 1.60 × 10−3, 5.25 × 10−4 and 6.19 × 10−4 m/d, respectively) shows the higher value of the mass transfer coefficient and higher biodegradation potential for B. licheniformis. Because the morphology of the cells has been analyzed by optical and electron microscopy, in the proposed model, the increase in the size of the cells in P. glucanolyticus compared to P. putida exhibits higher values of the mass transfer coefficients and this is attributed, as a novel statement, to a bigger window for alkanes transport (contact area) when the external area of the cell is bigger. Full article
(This article belongs to the Special Issue Biological Treatment of Water Contaminants: A New Insight)
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12 pages, 3207 KiB  
Article
Functional Analysis of Novel alkB Genes Encoding Long-Chain n-Alkane Hydroxylases in Rhodococcus sp. Strain CH91
by Wei Xiang, Shan Hong, Yanfen Xue and Yanhe Ma
Microorganisms 2023, 11(6), 1537; https://doi.org/10.3390/microorganisms11061537 - 9 Jun 2023
Cited by 9 | Viewed by 2641
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 [...] Read more.
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. Full article
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17 pages, 4649 KiB  
Communication
Whole Genome Analysis and Assessment of the Metabolic Potential of Gordonia rubripertincta Strain 112, a Degrader of Aromatic and Aliphatic Compounds
by Ekaterina Frantsuzova, Alexander Bogun, Viktor Solomentsev, Anna Vetrova, Rostislav Streletskii, Inna Solyanikova and Yanina Delegan
Biology 2023, 12(5), 721; https://doi.org/10.3390/biology12050721 - 15 May 2023
Cited by 10 | Viewed by 2228
Abstract
The application of Gordonia strains in biotechnologies of environmental purification as degraders of pollutants of different chemical structures is an interesting research topic. The strain Gordonia rubripertincta 112 (IEGM112) is capable of utilizing diesel fuel, alkanes, and aromatic compounds. The aim of this [...] Read more.
The application of Gordonia strains in biotechnologies of environmental purification as degraders of pollutants of different chemical structures is an interesting research topic. The strain Gordonia rubripertincta 112 (IEGM112) is capable of utilizing diesel fuel, alkanes, and aromatic compounds. The aim of this work was to study the potential of G. rubripertincta 112 as a degrader of aromatic and aliphatic compounds and analyze its complete genome in comparison with other known G. rubripertincta strains. The genome had a total length of 5.28 Mb and contained 4861 genes in total, of which 4799 were coding sequences (CDS). The genome contained 62 RNA genes in total, of which 50 were tRNAs, three were ncRNAs, and nine were rRNAs. The strain bears plasmid elements with a total length of 189,570 nucleotides (plasmid p1517). The strain can utilize 10.79 ± 1.17% of hexadecane and 16.14 ± 0.16% of decane over 3 days of cultivation. In the genome of the strain, we have found metabolic pathways of alkane (cytochrome P450 hydroxylases) and catechol (ortho- and meta-pathways) degradation. These results will help us to further approach the fundamental study of the processes occurring in the strain cells and to enrich our knowledge of the catabolic capabilities of G. rubripertincta. Full article
(This article belongs to the Section Microbiology)
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22 pages, 4123 KiB  
Article
Potential of Indigenous Strains Isolated from the Wastewater Treatment Plant of a Crude Oil Refinery
by Signe Viggor, Merike Jõesaar, Celeste Peterson, Riho Teras and Maia Kivisaar
Microorganisms 2023, 11(3), 752; https://doi.org/10.3390/microorganisms11030752 - 15 Mar 2023
Cited by 1 | Viewed by 2148
Abstract
Contamination of the environment with crude oil or other fuels is an enormous disaster for all organisms. The microbial communities for bioremediation have been an effective tool for eliminating pollution. This study aimed to determine individual cultures’ and a strain mixture’s ability to [...] Read more.
Contamination of the environment with crude oil or other fuels is an enormous disaster for all organisms. The microbial communities for bioremediation have been an effective tool for eliminating pollution. This study aimed to determine individual cultures’ and a strain mixture’s ability to utilize alkanes (single alkanes and crude oil). The proper study of pure cultures is necessary to design synergistically working consortia. The Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13 strains isolated from a wastewater treatment plant of a crude oil refinery can grow in media containing various aromatic and aliphatic hydrocarbons. The genome of the strain ICP1 contains four genes encoding alkane hydroxylases, whose transcription depended on the length of the alkane in the media. We observed that the hydrophobic cells of the strain ICP1 adhered to hydrophobic substrates, and their biofilm formation increased the bioavailability and biodegradation of the hydrocarbons. Although strain ICTN13 also has one alkane hydroxylase-encoding gene, the growth of the strain in a minimal medium containing alkanes was weak. Importantly, the growth of the mixture of strains in the crude oil-containing medium was enhanced compared with that of the single strains, probably due to the specialization in the degradation of different hydrocarbon classes and co-production of biosurfactants. Full article
(This article belongs to the Section Environmental Microbiology)
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19 pages, 1304 KiB  
Review
Bioengineering for the Microbial Degradation of Petroleum Hydrocarbon Contaminants
by Minzhen Wang, Mingzhu Ding and Yingjin Yuan
Bioengineering 2023, 10(3), 347; https://doi.org/10.3390/bioengineering10030347 - 10 Mar 2023
Cited by 27 | Viewed by 6480
Abstract
Petroleum hydrocarbons are relatively recalcitrant compounds, and as contaminants, they are one of the most serious environmental problems. n-Alkanes are important constituents of petroleum hydrocarbons. Advances in synthetic biology and metabolic engineering strategies have made n-alkane biodegradation more designable and maneuverable for solving [...] Read more.
Petroleum hydrocarbons are relatively recalcitrant compounds, and as contaminants, they are one of the most serious environmental problems. n-Alkanes are important constituents of petroleum hydrocarbons. Advances in synthetic biology and metabolic engineering strategies have made n-alkane biodegradation more designable and maneuverable for solving environmental pollution problems. In the microbial degradation of n-alkanes, more and more degradation pathways, related genes, microbes, and alkane hydroxylases have been discovered, which provide a theoretical basis for the further construction of degrading strains and microbial communities. In this review, the current advances in the microbial degradation of n-alkanes under aerobic condition are summarized in four aspects, including the biodegradation pathways and related genes, alkane hydroxylases, engineered microbial chassis, and microbial community. Especially, the microbial communities of “Alkane-degrader and Alkane-degrader” and “Alkane-degrader and Helper” provide new ideas for the degradation of petroleum hydrocarbons. Surfactant producers and nitrogen providers as a “Helper” are discussed in depth. This review will be helpful to further achieve bioremediation of oil-polluted environments rapidly. Full article
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13 pages, 2982 KiB  
Article
Kinetics of Arab Light Crude Oil Degradation by Pseudomonas and Bacillus Strains
by Carlos Costa, Anais Santos and Milena A. Vega
Water 2022, 14(23), 3802; https://doi.org/10.3390/w14233802 - 22 Nov 2022
Cited by 6 | Viewed by 3706
Abstract
The biodegradation of crude oil is a consequence of the presence of a specific enzymatic system in the microorganisms selected: the alkane hydroxylase (AlkH). The enzymatic biodegradation has been described since 1994, when the enzyme was first isolated from P. putida (formerly P. [...] Read more.
The biodegradation of crude oil is a consequence of the presence of a specific enzymatic system in the microorganisms selected: the alkane hydroxylase (AlkH). The enzymatic biodegradation has been described since 1994, when the enzyme was first isolated from P. putida (formerly P. oleovorans), but the kinetics of microbial degradation has been weakly considered. We studied and described in this work the kinetics of Arab Light biodegradation, a light crude oil used for gasoline production (46.4% C7–C12 n-alkanes), using two oleophilic strains (Bacillus licheniformis and Pseudomonas putida). Alkanes were extracted from aqueous solutions in the bioreactors by dichloromethane, with a high ratio aqueous:organic volumes (1:0.2 mL) for the amplification of the GC n-alkane signals, and GC spectra were monitored in time over 40 days. Petroleum emulsions were visualized using optical microscopy as a result of biosurfactant segregation, which is necessary for the enzymatic biodegradation of oil by microorganisms. Kinetic analysis in biodegradation of Arab Light (total petroleum hydrocarbons, TPH) exhibits first-order kinetics with 0.098 d−1 and 0.082 d−1 as kinetic coefficients for 8.6 g/L initial crude oil concentration (30 °C), which results in degradation rates of 843 mg/Ld and 705 mg/Ld in B. licheniformis and P. putida, respectively. These results can be applied for oil spill bioremediation, using these microorganisms with the objective of removing contamination by petroleum alkanes. Full article
(This article belongs to the Special Issue Advances in Management of Solid Waste and Wastewater Treatment)
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15 pages, 3571 KiB  
Article
CYP153A71 from Alcanivorax dieselolei: Oxidation beyond Monoterminal Hydroxylation of n-Alkanes
by Cheri Louise Jacobs, Rodolpho do Aido-Machado, Carmien Tolmie, Martha Sophia Smit and Diederik Johannes Opperman
Catalysts 2022, 12(10), 1213; https://doi.org/10.3390/catal12101213 - 11 Oct 2022
Cited by 4 | Viewed by 3417
Abstract
Selective oxyfunctionalization of non-activated C–H bonds remains a major challenge in synthetic chemistry. The biocatalytic hydroxylation of non-activated C–H bonds by cytochrome P450 monooxygenases (CYPs), however, offers catalysis with high regio- and stereoselectivity using molecular oxygen. CYP153s are a class of CYPs known [...] Read more.
Selective oxyfunctionalization of non-activated C–H bonds remains a major challenge in synthetic chemistry. The biocatalytic hydroxylation of non-activated C–H bonds by cytochrome P450 monooxygenases (CYPs), however, offers catalysis with high regio- and stereoselectivity using molecular oxygen. CYP153s are a class of CYPs known for their selective terminal hydroxylation of n-alkanes and microorganisms, such as the bacterium Alcanivorax dieselolei, have evolved extensive enzymatic pathways for the oxyfunctionalization of various lengths of n-alkanes, including a CYP153 to yield medium-chain 1-alkanols. In this study, we report the characterization of the terminal alkane hydroxylase from A. dieselolei (CYP153A71) for the oxyfunctionalization of medium-chain n-alkanes in comparison to the well-known CYP153A6 and CYP153A13. Although the expected 1-alkanols are produced, CYP153A71 readily converts the 1-alkanols to the corresponding aldehydes, fatty acids, as well as α,ω-diols. CYP153A71 is also shown to readily hydroxylate medium-chain fatty acids. The X-ray crystal structure of CYP153A71 bound to octanoic acid is solved, yielding an insight into not only the regioselectivity, but also the binding orientation of the substrate, which can be used in future studies to evolve CYP153A71 for improved oxidations beyond terminal n-alkane hydroxylation. Full article
(This article belongs to the Special Issue Biocatalysis in Organic Chemistry and Enzyme Engineering)
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21 pages, 10760 KiB  
Article
Genome-Based Exploration of Rhodococcus Species for Plastic-Degrading Genetic Determinants Using Bioinformatic Analysis
by Jessica Zampolli, Alessandro Orro, Daniele Vezzini and Patrizia Di Gennaro
Microorganisms 2022, 10(9), 1846; https://doi.org/10.3390/microorganisms10091846 - 15 Sep 2022
Cited by 27 | Viewed by 4830
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 [...] Read more.
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. Full article
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14 pages, 2115 KiB  
Article
Bioaugmentation-Enhanced Remediation of Crude Oil Polluted Water in Pilot-Scale Floating Treatment Wetlands
by Khadeeja Rehman, Muhammad Arslan, Jochen A. Müller, Muhammad Saeed, Asma Imran, Imran Amin, Tanveer Mustafa, Samina Iqbal and Muhammad Afzal
Water 2021, 13(20), 2882; https://doi.org/10.3390/w13202882 - 14 Oct 2021
Cited by 17 | Viewed by 3772
Abstract
Floating treatment wetlands (FTWs) are cost-effective systems for the remediation of polluted water. In FTWs, the metabolic activity of microorganisms associated with plants is fundamental to treatment efficiency. Bioaugmentation, the addition of microorganisms with pollutant-degrading capabilities, appears to be a promising means to [...] Read more.
Floating treatment wetlands (FTWs) are cost-effective systems for the remediation of polluted water. In FTWs, the metabolic activity of microorganisms associated with plants is fundamental to treatment efficiency. Bioaugmentation, the addition of microorganisms with pollutant-degrading capabilities, appears to be a promising means to enhance the treatment efficiency of FTWs. Here, we quantified the effect of bioaugmentation with a four-membered bacterial consortium on the remediation of water contaminated with crude oil in pilot-scale FTWs planted with Phragmites australis or Typha domingensis. The bacteria had been isolated from the endosphere and rhizosphere of various plants and carry the alkane hydroxylase gene, alkB, involved in aerobic hydrocarbon degradation. During a treatment period of 36 days, FTWs planted with P. australis achieved a reduction in hydrocarbon concentration from 300 mg/L to 16 mg/L with and 56 mg/L without bioaugmentation. In the FTWs planted with T. domingensis, respective hydrocarbon concentrations were 46 mg/L and 84 mg/L. The inoculated bacteria proliferated in the rhizoplane and in the plant interior. Copy numbers of the alkB gene and its mRNA increased over time in plant-associated samples, suggesting increased bacterial hydrocarbon degradation. The results show that bioaugmentation improved the treatment of oil-contaminated water in FTWs by at least a factor of two, indicating that the performance of full-scale systems can be improved at only small costs. Full article
(This article belongs to the Special Issue Pollutants Removal from Wastewater Using Constructed Wetlands)
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15 pages, 25733 KiB  
Article
Characterization and Transcriptome Analysis of a Long-Chain n-Alkane-Degrading Strain Acinetobacter pittii SW-1
by Weina Kong, Cheng Zhao, Xingwang Gao, Liping Wang, Qianqian Tian, Yu Liu, Shuwen Xue, Zhuang Han, Fulin Chen and Shiwei Wang
Int. J. Environ. Res. Public Health 2021, 18(12), 6365; https://doi.org/10.3390/ijerph18126365 - 11 Jun 2021
Cited by 27 | Viewed by 4169
Abstract
Strain sw-1, isolated from 7619-m seawater of the Mariana Trench, was identified as Acinetobacter pittii by 16S rRNA gene and whole-genome sequencing. A. pittii sw-1 was able to efficiently utilize long-chain n-alkanes (C18–C36), but not short- and medium-chain [...] Read more.
Strain sw-1, isolated from 7619-m seawater of the Mariana Trench, was identified as Acinetobacter pittii by 16S rRNA gene and whole-genome sequencing. A. pittii sw-1 was able to efficiently utilize long-chain n-alkanes (C18–C36), but not short- and medium-chain n-alkanes (C8–C16). The degradation rate of C20 was 91.25%, followed by C18, C22, C24, C32, and C36 with the degradation rates of 89.30%, 84.03%, 80.29%, 30.29%, and 13.37%, respectively. To investigate the degradation mechanisms of n-alkanes for this strain, the genome and the transcriptome analyses were performed. Four key alkane hydroxylase genes (alkB, almA, ladA1, and ladA2) were identified in the genome. Transcriptomes of strain sw-1 grown in C20 or CH3COONa (NaAc) as the sole carbon source were compared. The transcriptional levels of alkB and almA, respectively, increased 78.28- and 3.51-fold in C20 compared with NaAc, while ladA1 and ladA2 did not show obvious change. The expression levels of other genes involved in the synthesis of unsaturated fatty acids, permeases, membrane proteins, and sulfur metabolism were also upregulated, and they might be involved in n-alkane uptake. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) confirmed that alkB expression was significantly induced by C20, C24, and C32, and almA induction extent by C24 and C32 was higher than that with C20. Furthermore, ladA2 expression was only induced by C32, and ladA1 expression was not induced by any of n-alkanes. In addition, A. pittii sw-1 could grow with 0%–3% NaCl or 8 out of 10 kinds of the tested heavy metals and degrade n-alkanes at 15 °C. Taken together, these results provide comprehensive insights into the degradation of long-chain n-alkanes by Acinetobacter isolated from the deep ocean environment. Full article
(This article belongs to the Section Environmental Microbiology)
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