Search

In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, includ- ing BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. More- over, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multi- ple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodo- coccus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes. more...

19 páginas.- 9 figuras.- 6 tablas.- 102 referencias.- The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fbioe.2023.1158177/full#supplementary-material, Phenanthrene (PHE) is a highly toxic compound, widely present in soils. For this reason, it is essential to remove PHE from the environment. Stenotrophomonas indicatrix CPHE1 was isolated from an industrial soil contaminated by polycyclic aromatic hydrocarbons (PAHs) and was sequenced to identify the PHE degrading genes. Dioxygenase, monooxygenase, and dehydrogenase gene products annotated in S. indicatrix CPHE1 genome were clustered into different trees with reference proteins. Moreover, S. indicatrix CPHE1 whole-genome sequences were compared to genes of PAHs-degrading bacteria retrieved from databases and literature. On these basis, reverse transcriptase-polymerase chain reaction (RT-PCR) analysis pointed out that cysteine dioxygenase (cysDO), biphenyl-2,3-diol 1,2-dioxygenase (bphC), and aldolase hydratase (phdG) were expressed only in the presence of PHE. Therefore, different techniques have been designed to improve the PHE mineralization process in five PHE artificially contaminated soils (50 mg kg−1), including biostimulation, adding a nutrient solution (NS), bioaugmentation, inoculating S. indicatrix CPHE1 which was selected for its PHE-degrading genes, and the use of 2-hydroxypropyl-β-cyclodextrin (HPBCD) as a bioavailability enhancer. High percentages of PHE mineralization were achieved for the studied soils. Depending on the soil, different treatments resulted to be successful; in the case of a clay loam soil, the best strategy was the inoculation of S. indicatrix CPHE1 and NS (59.9% mineralized after 120 days). In sandy soils (CR and R soils) the highest percentage of mineralization was achieved in presence of HPBCD and NS (87.3% and 61.3%, respectively). However, the combination of CPHE1 strain, HPBCD, and NS showed to be the most efficient strategy for sandy and sandy loam soils (LL and ALC soils showed 35% and 74.6%, respectively). The results indicated a high degree of correlation between gene expression and the rates of mineralization. Copyright © 2023 Autors, This work was supported by the Spanish Ministry of Economy and Competitiveness under the research project CTM2017-82472-C2-1-R (AEI/FEDER, UE) and by Junta de Andalucía (Council of Economic Transformation, Industry, Knowledge, and University) under the research project PY20_01069 (FEDER Andalucía PO 2014–2020). more...

The gut microbiota is implicated in diverse interactions affecting human health. The present study reports a randomized, double-blind, placebo-controlled clinical study conducted by administering a new synbiotic formulation composed of two Lactobacillus strains (L. plantarum and L. acidophilus) and one Bifidobacterium strain (B. animalis subsp. lactis) and two types of fructans (fructo-oligosaccharides with a degree of polymerization of 3–5 and inulin-type fructans with 10 DP). The effects of this synbiotic were evaluated on healthy subjects for 28 days and the maintenance of its efficacy was evaluated at the end of a follow-up period of 28 days. The synbiotic treatment contributes to higher biodiversity of the gut microbiota, increasing the community richness with respect to the group with the prebiotics alone and the placebo group. Its positive effect is also reflected in the variation of microbial community structure favoring the beneficial short-chain fatty acids bacterial producers. The amelioration of the health status of the subjects was also established by the reduction of common infectious disease symptom incidence, the stimulation of the gut immune system showing a noteworthy variation of fecal β-defensin2 and calprotectin levels, and the modulation of the response of the respiratory tract’s immune system by salivary IgA as well as total antioxidant capacity biomarkers. more...

The decline of the immune system with aging leads elderly people to be more susceptible to infections, posing high risk for their health. Vaccination is thus important to cope with this risk, even though not always effective. As a strategy to improve protection, adjuvants are used in concomitance with vaccines, however, occasionally producing important side effects. The use of probiotics has been proposed as an alternative to adjuvants due to their efficacy in reducing the risk of common infections through the interactions with the immune system and the gut microbiota. A placebo-controlled, randomized, double-blind, clinical trial was carried out on fifty elderly subjects, vaccinated for influenza, to determine the efficacy of a probiotic mixture in reducing common infection symptoms. The incidence of symptoms was evaluated after 28 days of probiotic intake (namely, T28) and after further 28 days of follow-up (namely, T56). The number of subjects, as well as the number of days with symptoms, was remarkably reduced at T28, and even more at T56 in the probiotic group. Furthermore, the influence of probiotics on immunological parameters was investigated, showing a significant positive improvement of total antioxidant capacity and β-defensin2 levels. Finally, faecal samples collected from participants were used to assess variations in the gut microbiota composition during the study, showing that probiotic intake enhanced the presence of genera related to a healthy status. Therefore, the collected results suggested that the treatment with the selected probiotic mixture could help in reducing common infectious disease symptom incidence through the stimulation of the immune system, improving vaccine efficacy, and modulating the composition of the resident gut microbiota by enhancing beneficial genera. more...

Cinnamon polyphenols are known as health-promoting agents. However, their positive impact depends on the extraction method and their bioaccessibility after digestion. In this work, cinnamon bark polyphenols were extracted in hot water and subjected to an in vitro enzymatic digestion. After a preliminary characterization of total polyphenols and flavonoids (respectively 520.05 ± 17.43 µgGAeq/mg and 294.77 ± 19.83 µgCATeq/mg powder extract), the extract antimicrobial activity was evidenced only against Staphylococcus aureus and Bacillus subtilis displaying a minimum inhibition growth concentration value of 2 and 1.3 mg/mL, respectively, although it was lost after in vitro extract digestion. The prebiotic potential was evaluated on probiotic Lactobacillus and Bifidobacterium strains highlighting a high growth on the in vitro digested cinnamon bark extract (up to 4 × 108 CFU/mL). Thus, the produced SCFAs and other secondary metabolites were extracted from the broth cultures and determined via GC-MSD analyses. The viability of healthy and tumor colorectal cell lines (CCD841 and SW480) was assayed after the exposition at two different concentrations (23 and 46 µgGAeq/mL) of the cinnamon extract, its digested, and the secondary metabolites produced in presence of cinnamon extract or its digested, showing positive protective effects against a tumorigenic condition. more...

Plastic pollution is a global concern due to the long half-life and high resistance of many synthetic plastics to natural biodegradation. Therefore, great effort is required to avoid littering. However, the challenge of managing the ever-increasing quantities of plastic waste is daunting. The biodegradation of synthetic plastics, such as polyethylene (PE), polyethylene terephthalate (PET), polypropylene (PP), polyvinyl chloride (PVC), polystyrene (PS), and polyurethane (PUR) by microorganisms is either slow or under investigation as to whether it occurs at all in different environmental niches (e.g., soil, aquatic systems). There is an urgent need to complement the existing knowledge on the biodegradation and biotransformation of synthetic plastics to enable effective bioremediation strategies to mitigate the effects of environmental plastic contamination. Therefore, the aim of this review is to highlight current fundamental and applied research regarding the most promising biodegradation processes for synthetic plastics, the synthesis and applications of the most effective plastic-degrading enzymes, successful biotechnological strategies to improve degradation, such as enzyme engineering and novel reactor designs, and plastic waste bioconversion into value-added products. In addition, this review is intended to depict indications for techno-economic analyses toward the valorization of plastic biodegradation processes and the environmental impacts of synthetic plastic biodegradation. Combining strategies, such as enzymatic plastic degradation followed by microbial biotransformation with the broad array of available pretreatment methods and abiotic factors, can contribute, under confined conditions, to the end-of-life utilization of plastics, consequently leading to more efficient biorecycling processes, and hence, to a circular plastic economy. more...

The attention towards the bacteria associated with human health is growing more and more, above all regarding the bacteria that inhabit the niches offered by the human body, i.e., the gastrointestinal tract, skin, vaginal environment, and lungs. Among the secondary metabolites released by microorganisms associated with human health, little consideration is given to the biosurfactants, molecules with both hydrophobic and hydrophilic nature. Their role in the complex human environment is not only the mere biosurfactant function, but they could also control the microbiota through the quorum sensing system and the antimicrobial activity. These functions protect them and, accordingly, the human body principally from microbial and fungal pathogens. Consequently, nowadays, biosurfactants are emerging as promising bioactive molecules due to their very different structures, biological functions, low toxicity, higher biodegradability, and versatility. Therefore, this review provides a comprehensive perspective of biosurfactants with antimicrobial activity produced by bacteria associated with the human body and related to everything human beings are in contact with, e.g., food, beverages, and food-waste dumping sites. For the first time, the role of an “-omic” approach is highlighted to predict gene products for biosurfactant production, and an overview of the available gene sequences is reported. Besides, antimicrobial biosurfactants’ features, challenges, and potential applications in the biomedical, food, and nutraceutical industries are discussed. more...

Xylenes are considered one of the most common hazardous sources of environmental contamination. The biodegradation of these compounds has been often reported, rarer the ability to oxidize the ortho-isomer. Among few o-xylene-degrading bacteria, Rhodococcus opacus R7 is well known for its capability to degrade diverse aromatic hydrocarbons and toxic compounds, including o-xylene as only carbon and energy source. This work shows for the first time the RNA-seq approach to elucidate the genetic determinants involved in the o-xylene degradation pathway in R. opacus R7. Transcriptomic data showed 542 differentially expressed genes that are associated with the oxidation of aromatic hydrocarbons and stress response, osmotic regulation and central metabolism. Gene ontology (GO) enrichment and KEGG pathway analysis confirmed significant changes in aromatic compound catabolic processes, fatty acid metabolism, beta-oxidation, TCA cycle enzymes, and biosynthesis of metabolites when cells are cultured in the presence of o-xylene. Interestingly, the most up-regulated genes belong to the akb gene cluster encoding for the ethylbenzene (Akb) dioxygenase system. Moreover, the transcriptomic approach allowed identifying candidate enzymes involved in R7 o-xylene degradation for their likely participation in the formation of the metabolites that have been previously identified. Overall, this approach supports the identification of several oxidative systems likely involved in o-xylene metabolism confirming that R. opacus R7 possesses a redundancy of sequences that converge in o-xylene degradation through R7 peculiar degradation pathway. This work advances our understanding of o-xylene metabolism in bacteria belonging to Rhodococcus genus and provides a framework of useful enzymes (molecular tools) that can be fruitfully targeted for optimized o-xylene consumption. more...

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. more...

Background Bacteria belonging to the Rhodococcus genus play an important role in the degradation of many contaminants, including methylbenzenes. These bacteria, widely distributed in the environment, are known to be a powerhouse of numerous degradation functions, due to their ability to metabolize a wide range of organic molecules including aliphatic, aromatic, polycyclic aromatic compounds (PAHs), phenols, and nitriles. In accordance with their immense catabolic diversity, Rhodococcus spp. possess large and complex genomes, which contain a multiplicity of catabolic genes, a high genetic redundancy of biosynthetic pathways and a sophisticated regulatory network. The present study aimed to identify genes involved in the o-xylene degradation in R. opacus strain R7 through a genome-based approach. Results Using genome-based analysis we identified all the sequences in the R7 genome annotated as dioxygenases or monooxygenases/hydroxylases and clustered them into two different trees. The akb, phe and prm sequences were selected as genes encoding respectively for dioxygenases, phenol hydroxylases and monooxygenases and their putative involvement in o-xylene oxidation was evaluated. The involvement of the akb genes in o-xylene oxidation was demonstrated by RT-PCR/qPCR experiments after growth on o-xylene and by the selection of the R7–50 leaky mutant. Although the akb genes are specifically activated for o-xylene degradation, metabolic intermediates of the pathway suggested potential alternative oxidation steps, possibly through monooxygenation. This led us to further investigate the role of the prm and the phe genes. Results showed that these genes were transcribed in a constitutive manner, and that the activity of the Prm monooxygenase was able to transform o-xylene slowly in intermediates as 3,4-dimethylphenol and 2-methylbenzylalcohol. Moreover, the expression level of phe genes, homologous to the phe genes of Rhodococcus spp. 1CP and UPV-1 with a 90% identity, could explain their role in the further oxidation of o-xylene and R7 growth on dimethylphenols. Conclusions These results suggest that R7 strain is able to degrade o-xylene by the Akb dioxygenase system leading to the production of the corresponding dihydrodiol. Likewise, the redundancy of sequences encoding for several monooxygenases/phenol hydroxylases, supports the involvement of other oxygenases converging in the o-xylene degradation pathway in R7 strain. Electronic supplementary material The online version of this article (10.1186/s12864-018-4965-6) contains supplementary material, which is available to authorized users. more...

Rhodococcus members excrete secondary metabolites, especially compounds which act as biosurfactants. In this work, we demonstrated the ability of Rhodococcus opacus R7 to produce a novel bioactive compound belonging to the class of biosurfactants with antimicrobial properties during the growth on naphthalene. Chemical and biochemical analyses of the isolated compound demonstrated that the biosurfactant could be classified as a hydrophobic peptide. The ESI-full mass spectrometry revealed that the isolated biosurfactant showed a molecular weight of 1292 Da and NMR spectra evidenced the composition of the following amino acid residues: Ala, Thr, Asp, Gly, Ser. Surfactant activity of the R. opacus R7 compound was quantified by the critical micelle dilution (CMD) method and the critical micelle concentration (CMC) was estimated around 20 mg L−1 with a corresponding surface tension of 48 mN m−1. Moreover, biological assays demonstrated that R. opacus R7 biosurfactant peptide exhibited antimicrobial activity against Escherichia coli ATCC 29522 and Staphylococcus aureus ATCC 6538 with the minimum inhibition growth concentration (MIC) values of 2.6 mg mL−1 and 1.7 mg mL−1, respectively. In this study for the first time, a hydrophobic peptide with both biosurfactant and antimicrobial activity was isolated from a bacterium belonging to Rhodococcus genus. more...

Nowadays, the increase of the unconventional oil deposit exploitation and the amount of oil sands process-affected waters (OSPW) in tailing ponds emerges the importance of developing bio-monitoring strategies for the restoration of these habitats. The major constituents of such deposits are naphthenic acids (NAs), emerging contaminant mixtures with toxic and recalcitrant properties. With the aim of developing bio-monitoring strategies based on culture-independent approach, we identified genes coding for enzymes involved in NA degradation from Rhodococcus opacus R7 genome, after the evaluation of its ability to mineralize model NAs. R. opacus R7 whole-genome analysis unveiled the presence of pobA and chcpca gene clusters putatively involved in NAs degradation. Gene expression analysis demonstrated the specific induction of R7 aliA1 gene, encoding for a long-chain-fatty-acid-CoA ligase, in the presence of cyclohexanecarboxylic acid (CHCA) and hexanoic acid (HA), selected as representative compounds for alicyclic and linear NAs, respectively. Therefore, aliA1 gene was selected as a molecular marker to monitor the biodegradative potential of slurry-phase sand microcosms in different conditions: spiked with CHCA, in the presence of R. opacus R7, the autochthonous microbial community, and combining these factors. Results revealed that the aliA1-targeting culture-independent approach could be a useful method for bio-monitoring of NA degradation in a model laboratory system. more...

The paper investigates the use of poly(1-vinylpyrrolidone-co-2-dimethylaminoethylmetacrilate) (PVP-co-DMAEMA) as a novel coating agent in the preparation of alginate-based microcapsule for the supplement delivery of probiotics. Probiotic Lactobacillus plantarum is used to study the viability of the encapsulated bacterium when exposed to conditions simulating the gastrointestinal tract and industrial process. Results demonstrate that the PVP-co-DMAEMA polymer constitutes a pH-responsive coating suitable for probiotic supplement delivery. more...

La contaminazione dei suoli è uno dei fenomeni più preoccupanti degli ultimi decenni a causa del moltiplicarsi di situazioni di forte inquinamento ambientale da parte di attività antropiche. I parametri microbiologici dovrebbero essere considerati nella valutazione della qualità del suolo. Per aggirare alcune difficoltà nell’isolamento dei microrganismi, sono stati sviluppati approcci molecolari di coltivazione indipendente. In questa prospettiva, lo scopo è quello di ottenere “tools” molecolari dallo studio di vie metaboliche microbiche coinvolte nella degradazione dei contaminanti più diffusi nell'ambiente al fine di identificare sequenze marker per valutare la funzionalità di diversi suoli contaminati da idrocarburi. Questo progetto può essere declinato in tre fasi principali: 1. isolamento di microrganismi con potenziali capacità degradative e il sequenziamento dei loro genomi; 2. analisi dei genomi e caratterizzazione dei pathway metabolici e dei geni catabolici coinvolti nella degradazione di composti idrocarburici al fine di individuare sequenze marker; 3. analisi di suoli utilizzando le funzioni metaboliche individuate per valutare la loro capacità autodepurativa. Tra i batteri che occupano un ruolo principale nella degradazione dei contaminanti del suolo si ritrovano i microrganismi appartenenti al genere Rhodococcus. I rhodococci sono batteri aerobi Gram-positivi, metabolicamente versatili e frequentemente presenti nell'ambiente. Da studi precedenti il ceppo di R. opacus R7 è stato isolato da un suolo contaminato da idrocarburi policiclici aromatici e caratterizzato per la sua capacità di crescere in presenza di naftalene, o-xilene e diversi n-alcani. Al fine di investigare ulteriormente le sue potenzialità metaboliche è stato condotto uno screening fenotipico mediante test di crescita con la tecnologia del Phenotype Microarray basata sull’utilizzo di un colorante (tetrazolium violet) come marcatore di metabolismo attivo: in presenza di metabolismo attivo il colorante diventa viola con una reazione irreversibile. Gli esperimenti di screening fenotipico sono stati condotti su 41 diversi composti idrocarburici. Al fine di individuare le sequenze coinvolte in questi metabolismi, le sequenze genomiche del ceppo di R7 sono state comparate con quelle di ceppi di riferimento, come Rhodococcus sp. BCP1 e R. jostii RHA1 mediante tools bioinformatici e informazioni derivanti dalla letteratura. Sono stati identificati diversi cluster genici coinvolti nel metabolismo di composti idrocarburici: alk, prm, akb, dsz, nar, gen bph, acidi naftenici e cat, pca, paa, hmg, cluster genici coinvolti nel metabolismo periferico. Al fine di analizzare campioni di suolo contaminato utilizzando le funzioni metaboliche individuate, sono stati allestiti esperimenti in microcosmo. È stato utilizzato un suolo proveniente da una zona agricola che è stato caratterizzato valutando parametri pedologici, chimici e microbiologici. Le analisi chimiche hanno evidenziato l’assenza di o-xilene. Per questo, mediante un nuovo metodo di contaminazione, il suolo è stato contaminato con o-xilene e secondo un piano sperimentale, sono stati allestiti diversi microcosmi in fase solida. Sono state condotte cinetiche di biodegradazione in diverse condizioni e sono state monitorate le funzioni metaboliche presenti attraverso l’utilizzo di sequenze geniche coinvolte. I risultati hanno mostrato che la degradazione osservata nei microcosmi addizionati del ceppo R7 era pari a quella nei microcosmi dove era presente solo la flora batterica autoctona. Inoltre il potenziale autodepurativo del suolo è stato valutato mediante l’utilizzo di sequenze marker appartenenti ai cluster prm e akb che si sono rivelati coinvolti nel metabolismo di composti appartenenti al gruppo dei BTEX, in particolare dell’o-xilene. The project deals with the problem of soil contamination due to human activities. Under stress conditions caused by contamination, the development and biochemical activities of soil microorganisms undergo several alterations. Therefore, microbiologically-related parameters should be involved in the assessment of soil quality. As there are some difficulties in enriching and isolating microorganisms from soil, cultivation-independent molecular approaches have been developed. The aim of this project was to obtain molecular tools to use as "marker" sequences for the evaluation of the environmental quality of contaminated soils. The identified degradative capabilities were used to evaluate the potential of the depuration of an hydrocarbon contaminated soil using a culture-independent approach. The project can be divided into three main steps: 1. the isolation of interesting bacteria belonging to Rhodococcus genus and sequencing of the whole-genome. Characterization of novel metabolic potentials of hydrocarbon-degradative bacteria belonging to Rhodococcus genus using Phenotype Microarray analysis; 2. genome analysis to identify different genes and metabolic pathways involved in the degradation of different hydrocarbons to use as "marker" sequences; 3. assessment of contaminated soil based on the catabolic functions identified in microcosms experiments. R. opacus R7 is a Gram-positive bacterium isolated from a polycyclic aromatic hydrocarbon contaminated soil for its ability to grow on naphthalene and o-xylene. The metabolic abilities of this strain were investigated more widely in presence of different carbon sources and different xenobiotic compounds using the Phenotype Microarray (Biolog) analysis. To thoroughly investigate the sequences involved in hydrocarbons degradation, the whole-genome sequence of R7 was compared to reference strains, such as Rhodococcus sp. BCP1 and R. jostii RHA1, using different bioinformatics tools and literature retrievals. Several gene clusters involved in hydrocarbon metabolism were identified: alk, prm, akb, dsz, nar, gen bph, naphthenic acids clusters and cat, pca, paa, hmg clusters involved in peripheral metabolisms. Solid-phase microcosm experiments were performed to assess the potential of depuration of an hydrocarbon contaminated soil. The soil was characterized considering agronomic, chemical and microbiological parameters. The chemical analyses showed the absence of o-xylene. Therefore, it was contaminated with an o-xylene solution using a newly developed spiking method. According to the experimental plan, different solid-phase microcosms were set up. The biodegradation kinetics and the marker sequences involved in this metabolism were monitored. The results showed that the o-xylene biodegradation activity derived from both autochthonous bacteria and R7 strain. The depuration potential of the soil was assessed using marker sequences such as prm and akb genes. more...

The use of cellulose nanocrystals (CNCs) as a biomaterial able to inhibit host cell bacterial adhesion is described. Pre-incubation of E. coli ATCC 25922 with a suspension of 0.1% CNCs afforded a significant 2 log reduction of bacterial adhesion to the intestinal cell monolayer HT29. This effect could be attributed to the interaction between the CNCs and the bacterial cell surface as confirmed using fluorescence microscopy experiments. more...

In the present study, the response of Rhodococcus aetherivorans BCP1 and Rhodococcus opacus R7 to various stress conditions and several antimicrobials was examined by PM in relation with genetic determinants, as revealed by annotation analysis of the two genomes. Comparison between metabolic activities and genetic features of BCP1 and R7 provided new insight into the environmental persistence of these two members of the genus Rhodococcus. (C) 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved. more...

Rhodococcus opacus strain R7 (CIP107348) degrades several mono- and polycyclic aromatic hydrocarbons. Here, we present the high-quality draft genome sequence of strain R7, consisting of 10,118,052 bp, with a G+C content of 67.0%, 9,602 protein-coding genes, and 62 RNAs genes. more...

Rhodococcus opacus R7 is a Gram-positive bacterium isolated from a polycyclic aromatic hydrocarbon contaminated soil for its versatile metabolism; indeed the strain is able to grow on naphthalene, o-xylene, and several long- and medium-chain n-alkanes. In this work we determined the degradation of n-alkanes in Rhodococcus opacus R7 in presence of n- dodecane (C12), n- hexadecane (C16), n- eicosane (C20), n- tetracosane (C24) and the metabolic pathway in presence of C12. The consumption rate of C12 was 88%, of C16 was 69%, of C20 was 51% and of C24 it was 78%. The decrement of the degradation rate seems to be correlated to the length of the aliphatic chain of these hydrocarbons. On the basis of the metabolic intermediates determined by the R7 growth on C12, our data indicated that R. opacus R7 metabolizes medium-chain n-alkanes by the primary alcohol formation. This represents a difference in comparison with other Rhodococcus strains, in which a mixture of the two alcohols was observed. By GC-MSD analysis we also identified the monocarboxylic acid, confirming the terminal oxidation. Moreover, the alkB gene cluster from R. opacus R7 was isolated and its involvement in the n-alkane degradation system was investigated by the cloning of this genomic region into a shuttle-vector E. coli-Rhodococcus to evaluate the alkane hydroxylase activity. Our results showed an increased biodegradation of C12 in the recombinant strain R. erythropolis AP (pTipQT1-alk R7) in comparison with the wild type strain R. erythropolis AP. These data supported the involvement of the alkB gene cluster in the n-alkane degradation in the R7 strain. more...