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Background The light-dependent reactions involving riboflavin (RF) and methionine (Met) as substrates are responsible for the light-struck taste (LST). This fault is associated to cabbage-like odours due to the formation of methanethiol and dimethyl disulfide impacting negatively on the sensory properties of white wine. The reaction can occur for a relatively short period of time in white wine bottled in clear glass under both natural and artificial lights. Scope and approach This review aimed to point out the aspects related to the mechanisms of light-dependent reactions and the oenological strategies applicable to counteract the appearance of this detrimental fault. Key findings and conclusions LST can be prevented through the proper choice of the fermenting yeast, the addition of certain adjuvants being able to remove RF, and additives with a protective effect, such as hydrolysable tannins. As the use of these oenological tools plays an important role in limiting the detrimental change, they represent the strategies applicable in productive approaches. In this context, the more recent findings are summarized also to update the knowledge about the complex reaction mechanisms allowing to overcome the formation of this fault and supporting the wine industry.

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.

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.

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.

The Brettanomyces bruxellensis species plays various roles in both the industrial and food sectors. At the biotechnological level, B. bruxellensis is considered to be a promising species for biofuel production. Its presence in alcoholic beverages can be detrimental or beneficial to the final product; B. bruxellensis can contribute to spoilage of wine and beer, but can also produce good aromas. However, little is known about its genetic characteristics and, despite the complete sequencing of several B. bruxellensis genomes and knowledge of its metabolic pathways, the toolkits for its efficient and easy genetic modification are still underdeveloped. Moreover, the different ploidy states and the high level of genotype diversity within this species makes the development of effective genetic manipulation tools challenging. This review summarizes the available tools for the genetic manipulation of B. bruxellensis and how they may be employed to improve the quality of wine and beer.

The consumption of traditional wine has decreased in Europe during the last fifteen years. In parallel, new wine alternatives obtained by blending wines and fruit juices or by flavoring wines with artificial or natural flavors have appeared on the market. Recently, an innovative fruit wine obtained by co-fermentation of grape must and kiwi juice has been proposed and its potential of attraction for consumers should be exploited. To assess the potential consumer acceptability and expectations towards this new product, an online choice experiment has been conducted involving a consumer group of young adults (18–35 years old, n = 373). After the data collection, participants were divided into two groups according to whether they had already tasted a fruit wine (neophiles) or had never tasted it (new entries). For each group, the individual’s responses (on wine consumption habits, expectations and willingness to consume and pay a fruit wine) were analyzed through Principal Component Analysis. Different consumption styles and expectation patterns were defined in the two groups. However, in general, neophiles showed consumption patterns based on the evaluation of fruit quality, sales format, alcoholic content and the presence or not of bubbles, not giving importance to the brand. In contrast, new entries’ responses identified consumption patterns driven by the willingness to pay for a new product, the product value for money and packaging features. Differences between the two groups in expectations about the product sensory characteristics also emerged. These findings should contribute to this area of study by integrating environmental, economic and social dimensions and addressing food innovation and sustainability in the fruit and wine chains.

La qualità del suolo è una delle principali problematiche ambientali degli ultimi decenni a causa dell’aumento dell’inquinamento antropico. In condizioni di stress, i microrganismi del suolo subiscono alterazioni che attraverso tecnologie molecolari possono essere usate come parametro per il monitoraggio dei siti contaminati. I batteri appartenenti al genere Rhodococcus hanno un ruolo importante nella degradazione dei composti più recalcitranti. Sono versatili ed ampiamente distribuiti in natura; essi degradano diversi composti organici, tra cui idrocarburi alifatici ed aromatici, eterociclici, nitrili, sulfuri ed erbicidi. Inoltre, essi possono sopravvivere in presenza di composti tossici, carenza di carbonio, irradiazione UV e stress osmotico. Questa versatilità è correlata alla complessità dei loro genomi, i quali contengono molteplici geni catabolici, ridondanza genica e un sofisticato network regolatorio. L’obiettivo di questo progetto è ottenere nuovi tools molecolari da ceppi di Rhodococcus da usare come marcatori per valutare la qualità dei suoli, mediante analisi dei pathway metabolici e dei cluster genici coinvolti nella degradazione dei contaminanti ambientali. In questo lavoro, l’attenzione è stata rivolta verso i genomi dei ceppi: R. opacus R7, R. aetherivorans BCP1 e R. erythropolis MI2. Un’analisi fenotipica ha permesso di valutare il potenziale metabolico e la risposta allo stress dei ceppi R7 e BCP1; sono stati testati diversi contaminanti (idrocarburi alifatici e cicloalcani, aromatici, policiclici aromatici, acidi naftenici ed altri acidi carbossilici) e varie condizioni di stress (alta osmolarità, differenti valori di pH, composti tossici, antibiotici). Un approccio genomico ha permesso di correlare le abilità metaboliche a determinanti genici, coinvolti nei diversi metabolismi (naftalene, o-xilene, n-alcani, acidi naftenici, fenoli, ftalato) e nella persistenza ambientale. In particolare, sono stati esaminati i pathway degradativi dell’o-xilene e degli acidi naftenici di R. opacus R7. Analisi bioinformatiche e molecolari hanno permesso di valutare il coinvolgimento di diversi geni nei pathway degradativi. R7 è in grado di degradare l’o-xilene inducendo la trascrizione dei geni akb (sistema diossigenasico) formando il diidrodiolo. Tuttavia, la ridondanza di monossigenasi e idrossilasi (prmA and pheA1A2A3), ha suggerito l’attivazione di altri sistemi convergenti, strategia utilizzata dai rhodococci per degradare composti recalcitranti e persistere in ambienti contaminati. I pathway degradativi degli acidi naftenici (NAs) non sono ancora noti ma sono state proposte due possibili vie: i) aromatizzazione dell’anello del cicloesano ii) attivazione come CoA tioestere. I risultati delle RT e RT-qPCR hanno mostrato che R7 degrada l’acido cicloesanocarbossilico (CHCA), attraverso una cicloesano carbossilato-CoA ligasi (aliA). L’applicazione di questo lavoro è stata dimostrata in esperimenti di microcosmo simulando condizioni reali con sabbia bioaugmentata con R7. Le capacità dei batteri autoctoni e di R7 di degradare il CHCA sono state comparate e i risultati mostrano che R7 degrada il contaminante più velocemente rispetto alla comunità microbica e che il suo contributo aumenta la velocità di degradazione del CHCA, seguita monitorando l’espressione del gene aliA mediante esperimenti di RT e RT-qPCR. Un’applicazione biotecnologica di questo lavoro è stata valutata in R. erythropolis MI2, studiando il pathway di degradazione del 4,4’- acido disolfuro ditiobutirrico (DTDB), un promettente substrato per la sintesi dei politioesteri poiché il suo intermedio metabolico, acido 4-mercaptobutirrico ne è un precursore. L’obiettivo di questo studio è stato perseguito generando mutanti di delezione del ceppo MI2 per i geni coinvolti nelle reazioni finali del pathway di degradazione. Soil quality has been one of the major issues of the last decades, because of the increase of anthropogenic pollution. Soil contains organisms involved in vital functions (nutrient/hydrological cycles and degradation of toxic compounds). Under stress conditions, soil microorganisms undergo several alterations so molecular technologies use microbial communities as an ecological parameter in monitoring polluted sites. Bacteria belonging to Rhodococcus genus have an important role in recalcitrant compound degradations. It is a metabolically versatile genus, widely distributed in nature. Rhodococcus spp. can degrade a wide range of organic compounds (aliphatic/aromatic hydrocarbons, heterocyclic, nitriles, sulfuric, herbicides) and to survive in presence of toxic compounds, carbon starvation, UV irradiation and osmotic stress. In line with their catabolic diversity, they possess large and complex genomes, containing a multiplicity of catabolic genes, high genetic redundancy and a sophisticated regulatory network. The aim of this project is to obtain molecular tools to use as "marker" sequences for soil assessment, through analysis of metabolic pathways and catabolic gene clusters involved in the degradation of the most diffused environmental contaminants. In particular, this work focused the attention on three Rhodococcus strain genomes: R. opacus R7, R. aetherivorans BCP1 and R. erythropolis MI2. A Phenotype Microarray approach was used to evaluate R7 and BCP1 strains metabolic potential and their stress response. Also, the capability to utilize various contaminants (aliphatic hydrocarbons and cycloalkanes, aromatic compounds, polycyclic aromatic compounds, naphthenic acids and other carboxylic acids) and to persist under stress conditions (high osmolarity, pH stress, toxic compounds, antibiotics) was tested. A genome-based approach was used to relate their abilities to genetic determinants involved in the analysed metabolisms (naphthalene, o-xylene, n-alkanes, naphthenic acids, phenols, phthalate) and in their environmental persistence. In particular, o-xylene and naphthenic acids degradations were investigated in R. opacus R7. Computational and molecular analyses revealed the putative involvement of several genes in these degradation pathways. R7 can degrade o-xylene by the induction of the akb genes (deoxygenation) producing the corresponding dihydrodiol. Likewise, the redundancy of sequences encoding for monooxygenases/hydroxylases (prmA and pheA1A2A3), supports the involvement of other genes that induce the formation of phenols, converging to the phenol oxidation path. The activation of converging oxygenase systems represents a strategy in Rhodococcus genus to degrade recalcitrant compounds and to persist in contaminated environments. NAs degradation pathway is not fully clear but two main routes have been proposed: i) aromatization of the cyclohexane ring ii) activation as CoA thioester. RT and RT-qPCR results showed that R. opacus R7 degrade cyclohexanecarboxylic acid (CHCA) molecule (used as a model) by a cyclohexane carboxylate CoA ligase (aliA). An application of this work was demonstrated by a microcosm approach, simulating a bioaugmentation process with R7 strain. Autochthone bacteria and R7 capabilities to degrade CHCA were evaluated and compared; results indicated that R7 can degrade the contaminant faster than the microbial community and that its contribute increased CHCA degradation rate. The degradation rate was followed by RT and RT-qPCR, monitoring the expression of the aliA gene. Moreover, a biotechnological application was investigated in R. erythropolis MI2, studying the disulfide 4,4-dithiodibutyric acid (DTDB) degradation pathway. DTDB is a promising substrate for polythioester (PTE) synthesis; indeed, its degradation produces the PTE building block 4-mercaptobutyric acid. The aim was pursued generating R. erythropolis MI2 marker-free deletion mutants for genes involved in the final steps of the pathway.

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.

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.

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.

The Rhodococcus genus comprises of Gram-positive, non-motile, nonsporulating, aerobic bacteria, with a high G+C content and a mycolic acid-containing cell wall. Members of Rhodoccocus genus are widely distributed in soil, water and marine sediments; moreover, some of them are pathogens for humans and animals (R. equi) while others cause diseases of plants (R. fascians). Due to their metabolic flexibility and their tolerance to various stresses, they play an important role in nutrient cycling and have potential applications in bioremediation, biotransformations, and biocatalysis. Consistent with the wide catabolic diversity, they possess large and complex genomes, which contain a multiplicity of catabolic genes, a high genetic redundancy of biosynthetic pathways and a sophisticated regulatory network. Compared to the increasing number of Rhodococcus spp. genomes that have been sequenced, very limited studies are available on their wide metabolic abilities and on their potentials for biodegradation activities related to genomic features. The present work focuses on the analysis of metabolic capabilities and genomic features of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 that were isolated from an aerobic butane-utilizing consortium and from an aromatic hydrocarbon contaminated soil, respectively. Phylogenetic analyses and genomic comparison with correlated species were performed to characterize the unique regions present in the genome of R7 and BCP1 strains. Phenotype Microarray analysis was also conducted using the Biolog redox technology with commercially available Biolog microtiter plates (pre-loaded substrates) and with microtiter plates that were manually prepared with additional organic/ xenobiotic compounds to be tested. Compared to BCP1, R7 strain generally showed higher metabolic activities compared on the tested carbon sources and broader range of nitrogen and sulfur sources. BCP1 specifically utilized some carboxylic acids and amino fatty acids as carbon and nitrogen sources, respectively. The two strains were able to resist to various chemicals, pH values and osmolytic substances. Phenotype microarray results also highlighted new biodegradation capacities of BCP1 and R7 strains towards aliphatic and aromatic hydrocarbons as well as emergent contaminants like naphthenic acids. These metabolic data were combined with the genomic study to genetically interpret the metabolic features of these bacterial strains with potential application for bioremediation and industrial processes.