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A Gram-positive, aerobic, non-motile bacterium with a rod-coccus shape, designated DK17T, was isolated from a crude oil-contaminated soil and identified as a member of the genus Rhodococcus based on 16S rRNA gene analysis, showing highest similarity (99.93%) to Rhodococcus jostii DSM 44719T. However, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain DK17T and type strains within the genus Rhodococcus were below the species delineation thresholds of 95% and 70%, respectively. In contrast, DK17ᵀ exhibited ANI and dDDH values over 99% and 92%, respectively, with R. jostii RHA1. Comparative genomic analysis revealed that DK17T and RHA1 shared 93.5% of genes, while RHA1 and R. jostii NBRC 16295T shared only 78.6%, indicating a closer relationship between DK17T and RHA1. Both strains possess large genomes (~9.5-9.7 Mb) comprising a linear chromosome and multiple plasmids, and encode multiple dioxygenases and secondary metabolite biosynthetic gene clusters. In vitro assays confirmed o-xylene degradation by both DK17T and R. jostii RHA1, consistent with the presence of the akb gene cluster. Both strains shared C16:0 as a major fatty acid and menaquinone-8 (H2) as the dominant quinone. Based on genomic, phenotypic, and chemotaxonomic data, DK17T (=KCCM 90599T = InaCC B1662T) is proposed as a novel species, Rhodococcus aromaticivorans sp. nov., and R. jostii RHA1 is reclassified as a member of the same species.

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.

Poly-β-hydroxybutyrate (PHB) is a biodegradable polymer, synthesized as carbon and energy reserve by bacteria and archaea. To the best of our knowledge, this is the first report on PHB production by a rare actinomycete species, Rhodococcus pyridinivorans BSRT1-1. Response surface methodology (RSM) employing central composite design, was applied to enhance PHB production in a flask scale. A maximum yield of 3.6 ± 0.5 g/L in biomass and 43.1 ± 0.5 wt% of dry cell weight (DCW) of PHB were obtained when using RSM optimized medium, which was improved the production of biomass and PHB content by 2.5 and 2.3-fold, respectively. The optimized medium was applied to upscale PHB production in a 10 L stirred-tank bioreactor, maximum biomass of 5.2 ± 0.5 g/L, and PHB content of 46.8 ± 2 wt% DCW were achieved. Furthermore, the FTIR and 1 H NMR results confirmed the polymer as PHB. DSC and TGA analysis results revealed the melting, glass transition, and thermal decomposition temperature of 171.8, 4.03, and 288 °C, respectively. In conclusion, RSM can be a promising technique to improve PHB production by a newly isolated strain of R. pyridinivorans BSRT1-1 and the properties of produced PHB possessed similar properties compared to commercial PHB.

Cytochrome P450 enzymes have tremendous potential as industrial biocatalysts, including in biological lignin valorization. Here, we describe P450s that catalyze the O-demethylation of lignin-derived guaiacols with different ring substitution patterns. Bacterial strains Rhodococcus rhodochrous EP4 and Rhodococcus jostii RHA1 both utilized alkylguaiacols as sole growth substrates. Transcriptomics of EP4 grown on 4-propylguaiacol (4PG) revealed the up-regulation of agcA, encoding a CYP255A1 family P450, and the aph genes, previously shown to encode a meta-cleavage pathway responsible for 4-alkylphenol catabolism. The function of the homologous pathway in RHA1 was confirmed: Deletion mutants of agcA and aphC, encoding the meta-cleavage alkylcatechol dioxygenase, grew on guaiacol but not 4PG. By contrast, deletion mutants of gcoA and pcaL, encoding a CYP255A2 family P450 and an ortho-cleavage pathway enzyme, respectively, grew on 4-propylguaiacol but not guaiacol. CYP255A1 from EP4 catalyzed the O-demethylation of 4-alkylguaiacols to 4-alkylcatechols with the following apparent specificities (k cat/K M): propyl > ethyl > methyl > guaiacol. This order largely reflected AgcA’s binding affinities for the different guaiacols and was the inverse of GcoAEP4’s specificities. The biocatalytic potential of AgcA was demonstrated by the ability of EP4 to grow on lignin-derived products obtained from the reductive catalytic fractionation of corn stover, depleting alkylguaiacols and alkylphenols. By identifying related P450s with complementary specificities for lignin-relevant guaiacols, this study facilitates the design of these enzymes for biocatalytic applications. We further demonstrated that the metabolic fate of the guaiacol depends on its substitution pattern, a finding that has significant implications for engineering biocatalysts to valorize lignin.

Background Plant-microbe interactions are essential for mitigating abiotic and biotic stressors by shaping the rhizosphere environment. However, how rhizosphere beneficial bacteria and plant metabolites respond to glufosinate (GLU)-induced toxicity remains largely unknown. Results Our study investigates the impact of GLU on chili plant growth and rhizosphere microbiome, emphasizing GLU-induced alterations in amino acid profiles, secondary metabolites, and microbial community composition, with notable enrichment of the Rhodococcus genus. To uncover the underlying mechanisms of Rhodococcus genus-root exudate interactions under GLU stress, we successfully isolated an efficient Rhodococcus gordoniae strain TR-5 from soil samples contaminated with GLU. This strain, isolated from GLU-contaminated soil, demonstrates potential for bioremediation and achieved over 95% GLU degradation efficiency at 35 °C, pH 6.38, and 1% inoculation rate. Through growth analysis, chemotaxis analysis, and molecular docking, caffeic acid disrupts the bacterial strain’s metabolic pathways and impedes TR-5 development. In contrast, jasmonic acid (JA) acts as a chemoattractant, promoting bacterial growth and metabolic activity to degrade GLU residues, thereby effectively degrading GLU residues in the soil. Conclusions This research indicates that GLU significantly influences the metabolic mechanisms of pepper plants. The optimization of microbial remediation strategies may improve soil remediation efficiency and reduce environmental impacts, highlighting opportunities for integrating microbial remediation into sustainable agricultural practices. Our findings provide insights into the role of JA in attracting and promoting the growth and metabolic activities of the Rhodococcus genus, which could be harnessed to improve soil remediation and plant health under GLU stress. Bpan91VuLfcPc8VpwQR5Me Video Abstract Graphical Abstract

Microbe-based decontamination of phenol-polluted environments has significant advantages over physical and chemical approaches by being relatively cheaper and ensuring complete phenol degradation. There is a need to search for commercially prospective bacterial strains that are resistant to phenol and other co-pollutants, e.g. oil hydrocarbons, in contaminated environments, and able to carry out efficient phenol biodegradation at a variable range of concentrations. This research characterizes the phenol-biodegrading ability of a new actinobacteria strain isolated from a lubricant-contaminated soil environment. Phenotypic and phylogenetic analyses showed that the novel strain UCM Ac-603 belonged to the species Rhodococcus aetherivorans, and phenol degrading ability was quantitatively characterized for the first time. R. aetherivorans UCM Ac-603 tolerated and assimilated phenol (100% of supplied concentration) and various hydrocarbons (56.2–94.4%) as sole carbon sources. Additional nutrient supplementation was not required for degradation and this organism could grow at a phenol concentration of 500 mg L−1 without inhibition. Complete phenol assimilation occurred after 4 days at an initial concentration of 1750 mg L−1 for freely-suspended cells and at 2000 mg L−1 for vermiculite-immobilized cells: 99.9% assimilation of phenol was possible from a total concentration of 3000 mg L−1 supplied at daily fractional phenol additions of 750 mg L−1 over 4 days. In terms of phenol degradation rates, R. aetherivorans UCM Ac-602 showed efficient phenol degradation over a wide range of initial concentrations with the rates (e.g. 35.7 mg L−1 h−1 at 500 mg L−1 phenol, and 18.2 mg L−1 h−1 at 1750 mg L−1 phenol) significantly exceeding (1.2–5 times) reported data for almost all other phenol-assimilating bacteria. Such efficient phenol degradation ability compared to currently known strains and other beneficial characteristics of R. aetherivorans UCM Ac-602 suggest it is a promising candidate for bioremediation of phenol-contaminated environments.

Background Rhodococcus equi is an intracellular bacterial pathogen that can cause infections in various hosts, including humans and animals. Host-associated virulence plasmids have been identified as key contributors to the pathogenicity of R. equi and potentially play a role in determining the host tropism of the bacteria. The investigation of additional clinical and environmental isolates is likely to provide novel insights into the population structure, infection pathways, and drug resistance of this important pathogen. We combined whole-genome sequencing and antimicrobial-susceptibility testing of 37 selected R. equi isolates from animal, human, and environmental sources, collected in Switzerland over a 21 year period. In addition, we gathered a total of 251 whole-genome sequences and 141 multi-locus sequence (MLST) typing records from public sources. Although large geographical areas are not represented due to missing genomes we used a phylogenetic approach to define diversity patterns, distribution, and host tropism of R. equi . Results Horse isolates, irrespective of the country of isolation, exhibited distinct sequence types (ST), notably ST-1 and ST-24 among others, and carried the VAPA plasmid, implying a strain-specific affinity for particular plasmid types. Several STs including ST-62 and ST-76 associated with the VAPN plasmid included both human and ruminant isolates from Switzerland, hinting at a potential common infection source. Similarly, isolates from porcine and human sources, documented in various European countries and China, exhibited common ST, including ST-18 and ST-36, and were found to harbour VAPB plasmids upon testing, suggesting potential zoonotic implications. Conclusions Using a genomic approach we report host-specific strains that serve as carriers of virulence-associated plasmids, indicating an adaptation strategy within distinct R. equi lineages. The existence of shared plasmid profiles between farm animals and humans suggests a common infection source. Our results contribute to an improved understanding of the global genetic diversity of virulent and environmental R. equi strains, which will benefit from additional molecular epidemiological studies including strains from unrepresented geographical areas.

Plastic waste management has become a global issue. Polyethylene (PE) is the most abundant synthetic plastic worldwide, and one of the most resistant to biodegradation. Indeed, few bacteria can degrade polyethylene. In this paper, the transcriptomic analysis unveiled for the first time Rhodococcus opacus R7 complex genetic system based on diverse oxidoreductases for polyethylene biodegradation. The RNA-seq allowed uncovering genes putatively involved in the first step of oxidation. In-depth investigations through preliminary bioinformatic analyses and enzymatic assays on the supernatant of R7 grown in the presence of PE confirmed the activation of genes encoding laccase-like enzymes. Moreover, the transcriptomic data allowed identifying candidate genes for the further steps of short aliphatic chain oxidation including alkB gene encoding an alkane monooxygenase, cyp450 gene encoding cytochrome P450 hydroxylase, and genes encoding membrane transporters. The PE biodegradative system was also validated by FTIR analysis on R7 cells grown on polyethylene.

It has been reported that an indigenous quorum quenching bacterium, Rhodococcus sp. BH4, which was isolated from a real plant of membrane bioreactor (MBR) has promising potential to control biofouling in MBR. However, little is known about quorum quenching mechanisms by the strain BH4. In this study, various characteristics of strain BH4 were investigated to elucidate its behavior in more detail in the mixed liquor of MBR. The N-acyl homoserine lactone hydrolase (AHL–lactonase) gene of strain BH4 showed a high degree of identity to qsdA in Rhodococcus erythropolis W2. The LC-ESI-MS analysis of the degradation product by strain BH4 confirmed that it inactivated AHL activity by hydrolyzing the lactone bond of AHL. It degraded a wide range of N-acyl homoserine lactones (AHLs), but there was a large difference in the degradation rate of each AHL compared to other reported AHL–lactonase-producing strains belonging to Rhodococcus genus. Its quorum quenching activity was confirmed not only in the Luria-Bertani medium, but also in the synthetic wastewater. Furthermore, the amount of strain BH4 encapsulated in the vessel as well as the material of the vessel substantially affected the quorum quenching activity of strain BH4, which provides useful information, particularly for the biofouling control in a real MBR plant from an engineering point of view.

Equation (2.10) in Costa, Brandt & Picano (2020) for the lift force model used in the point-particle direct numerical simulations (DNS), and which is derived from the classical lift force of Saffman (1965), (Equation presented) does not correspond to the force model actually used in the point-particle DNS with lift force presented in the manuscript. Instead, the following equation was used: (Equation presented) which replaces the first occurrence of the term |Us| on the right-hand-side of (1) with |ω|D. We recall that two cases were considered in the manuscript depending on the value of J in the lift force equation: J = 1 in the case denoted PP-Saffman; and J given by (Equation presented) with ϵ = √|ω|ν/|Us|, in the case denoted PP-McLaughlin. Also, equation (2.13) of the manuscript - describing the perfectly elastic hard-sphere rebound - is incorrect; the term D/2 should be D: (Equation presented) Despite the lapse in the manuscript, equation (4) was implemented correctly (Costa et al. 2020). The results from the point-particle DNS with the model reported in (2.10) of Costa et al. (2020) ((1) above) differ from those reported in the manuscript, and are shown (Figure presented) in figure 1 (cf. figures 7 and 8 of Costa et al. (2020)). The statistics presented here have been collected in the fully developed state from 600 samples over a time interval of 250h/Ub, which ensured statistical convergence of the results. The results from the point-particle cases presented in the original manuscript are also reproduced here with this (higher) statistical sampling, and show very minor differences with respect to figures 7 and 8 of Costa et al. (2020). In light of these results, the conclusions drawn from the results in the last section of § 3 of the manuscript must be therefore reformulated: (i) The Saffman lift model does not correctly predict the near-wall statistics of the interface-resolved DNS very close to the wall, including the near-wall concentration peak. (ii) The equation proposed by Mei (1992) that fits the model of McLaughlin (1991) shows results similar to those reported in the original manuscript for this model. That is, it predicts well the near-wall concentration peak, and fails to predict the other observables near the wall. (iii) Equation (2) for Fl presented above, with J = 1, predicts very well all the observables in figure 1. We have therefore accidentally discovered that the expression (2) for Fl predicts the observed particle statistics very well. Still, the reason for the strikingly good agreement remains elusive to us. We hope that this result can be further exploited for the improvement lift force models for point-particle simulations of wall-bounded turbulent flows.