Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance

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, including 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. Moreover, 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 multiple 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 Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.

Genome analysis and -omics approaches provide new insights into the biodegradation potential of Rhodococcus

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.

The Role of Yeasts as Biocontrol Agents for Pathogenic Fungi on Postharvest Grapes: A Review

In view of the growing concern about the impact of synthetic fungicides on human health and the environment, several government bodies have decided to ban them. As a result, a great number of studies have been carried out in recent decades with the aim of finding a biological alternative to inhibit the growth of fungal pathogens. In order to avoid the large losses of fruit and vegetables that these pathogens cause every year, the biological alternative's efficacy should be the same as that of a chemical pesticide. In this review, the main studies discussed concern Saccharomyces and non-Saccharomyces yeasts as potential antagonists against phytopathogenic fungi of the genera Penicillium and Aspergillus and the species Botrytis cinerea on table grapes, wine grapes, and raisins.

Genome-based analysis for the identification of genes involved in o-xylene degradation in Rhodococcus opacus R7

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.

Transcriptomic Analysis of Rhodococcus opacus R7 Grown on o-Xylene by RNA-Seq

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.

Flocculation Mechanisms in Brettanomyces bruxellensis: Influence of ethanol and sulfur dioxide on FLO gene expression

The mechanisms underlying flocculation in Brettanomyces bruxellensis, unlike the well-characterized FLO-family gene regulation in Saccharomyces cerevisiae, remain largely unexplored. This study investigates the flocculant phenotypes of 99 B. bruxellensis strains, revealing that only a minority exhibits this clumping behavior and confirms its strain-dependent attitude. Focusing on two strains, CBS2499 (flocculant) and UMY321 (non-flocculant), genetic analysis uncovered polymorphisms and distinct allelic heterozygosity in the FLO1 and FLO11 genes, potentially linked to the phenotypic differences. To further examine these traits, Response Surface Methodology (RSM) was used to simulate oenological conditions, testing the impact of pH, ethanol, and sulfur dioxide (SO₂) levels on flocculation and gene expression. The findings revealed that environmental stressors, especially ethanol and SO₂, significantly increase the expression of FLO1 and FLO11 in CBS2499, indicating a regulatory role in flocculation under stress. These insights broaden our understanding of stress adaptation in B. bruxellensis, especially its survival strategies in wine environments. By elucidating factors influencing flocculation, this study contributes valuable knowledge for managing B. bruxellensis spoilage, potentially aiding in the development of targeted approaches to reduce its impact on wine quality.

Endophytic Diversity in Vitis vinifera with Different Vineyard Managements and Vitis sylvestris Populations from Northern Italy: A Comparative Study of Culture-Dependent and Amplicon Sequencing Methods

This study aimed to investigate the endophytic microbial populations associated with wild and domesticated grapevines using both culture-based and culture-independent methods. Through culture-based methods, 148 endophytes were identified. The dominant fungal species included Aureobasidium pullulans, Alternaria alternata, and Cladosporium allicinum, while predominant bacterial species were Ralstonia pikettii, Nocardia niigatensis, and Sphingomonas echinoides. Culture-independent methods employed metagenomic techniques to explore microbial biodiversity, focusing on targeted amplification of bacterial 16S rRNA as well as fungal ITS and 26S rRNA gene regions. The main bacterial species identified included Halomonas sp., Sphingomonas sp. and Massilia sp., whereas the fungal population was dominated by Cladosporium sp., Malassezia sp. and Mucor sp. The findings revealed that vineyard management practices did not lead to statistically significant variations in microbial communities. The consistent presence of these genera across all samples suggests that they are stable components of the grapevine endophytic microbiota, remaining relatively unaffected by external environmental factors.

From Fruit to Beverage: Investigating Actinidia Species for Characteristics and Potential in Alcoholic Drink Production

There is a growing interest in various types of kiwifruits, such as the "yellow" kiwifruit (Actinidia chinensis var. chinensis) and the "baby" kiwifruit of Actinidia arguta. These fruits are rich in bioactive compounds, which contribute to their nutraceutical properties, but they nevertheless have a shorter shelf life, resulting in economic losses. This study aims to chemically characterize kiwifruit juices from SunGold and baby kiwifruit varieties (Hortgem Rua and Hortgem Tahi) to improve knowledge and explore the suitability of these products for producing low-alcohol beverages using non-Saccharomyces strains, with the purpose of reducing waste and generating value-added processing. Total soluble solids, acidity, hardness, dry matter, total phenolic content, and antioxidant capacity were used as indicators of fruit quality. Chemical characterization of fresh kiwifruit juices revealed distinct profiles among varieties, with SunGold juice exhibiting higher sugar content and acidity. Citric acid was the predominant organic acid, while, as expected, tartaric was not detected. Kiwifruit juice fermentations by T. delbrueckii UMY196 were always completed regardless of the type of juice used, producing beverages with ethanol content ranging from 6.46 to 8.85% (v/v). The analysis of volatile organic compounds highlighted the presence of several molecules, contributing to aroma profiles with relevant differences among the three kiwifruit-based drinks. In particular, the total concentration of esters in the beverages reached 8.2 mg/L, 9.2 mg/L, and 8.6 mg/L in the Tahi, Rua, and SunGold beverages, respectively. The qualitative and quantitative profiles of the kiwifruit drinks revealed a pronounced perception of acidity and fruity traits, with significant differences observed by Principal Component Analysis (PCA) in aroma descriptors among the proposed beverages. The possibility of using unsold, overripe, or waste fruits to prepare new products with an increase in the sustainability of this supply chain is set.

The Riboflavin Metabolism in Four Saccharomyces cerevisiae Wine Strains: Assessment in Oenological Condition and Potential Implications with the Light-Struck Taste

Riboflavin (RF), or vitamin B2, is an essential compound for yeast growth and a precursor of the flavin coenzymes, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), involved in redox and non-redox processes. RF is a photosensitive compound involved in the light-struck taste (LST), a fault causing the formation of off-flavors that can develop when the wine is exposed to light in the presence of methionine (Met), as well. As both RF and Met can be associated with detrimental changes in wines, a better comprehension of its yeast-mediated production is relevant to predict the maintenance of the desired character of the wine. This study aims at assessing the production of flavin derivatives (FDs) and Met by S. cerevisiae oenological starters under laboratory conditions. The results showed the presence of extra- and intracellular FDs, and Met is a strain-dependent characteristic being also affected by the initial content of RF in the medium. This finding was confirmed when the winemaking was carried out in a relevant environment. Our results evidenced the important impact of the yeast strain on the content of RF and its derivatives.