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Opinion 130 deals with a Request for an Opinion asking the Judicial Commission to clarify whether the genus name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate. The Request is approved and an answer is given. The name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate because it is a later homonym of the validly published cyanobacterial name Rhodococcus Hansgirg 1884. The Judicial Commission also clarifies that it has the means to resolve such cases by conserving a name over an earlier homonym. It is concluded that the name Rhodococcus Zopf 1891 (Approved Lists 1980) is significantly more important than the name Rhodococcus Hansgirg 1884 and therefore the former is conserved over the latter. This makes the name Rhodococcus Zopf 1891 (Approved Lists 1980) legitimate.

Rhodococcus equi is a rare human opportunistic pathogen that has been increasingly reported in recent decades. It mainly affects immunosuppressed patients, and in particular human immunodeficiency virus (HIV)–infected patients, where it typically presents as cavitary pneumonia. Early treatment with combined and effective antimicrobials and antiretroviral therapy after prompt diagnosis is essential to ensure an optimal outcome. We present a case series of three human Rhodococcus equi infections in HIV‐infected patients with advanced immune suppression, treated at the University Hospital of Antwerp, Belgium. [ABSTRACT FROM AUTHOR]

Summary: Daqu is an essential saccharification and fermentation agent in Baijiu brewing, and its characteristics affect the yield, quality, and flavour of Baijiu. The fundamental reason is that Daqu can provide rich microbial resources, complex enzyme systems, and raw materials for the Baijiu brewing process. In this study, three sauce‐flavour Daqu from two production areas, Beijing and Guizhou, were selected to focus on discussing and analysing the main contributions of sauce‐flavour Daqu itself to Baijiu brewing without interference from the external environment. The differences in the flavour composition and microbial communities of three Daqu were analysed. Microbial biomarkers were analysed by Lefse multilevel discriminant analysis for three Daqu. We found that different regions have their own biomarkers. Citrobacter, Rhodococcus, and Pseudomonas, were biomarkers of HD Daqu. Oceanobacillus, Aspergillus and Pichia were biomarkers of MT Daqu. Bacillus, Pediococcus and Fusarium were biomarkers of WM Daqu. A solid‐state simulation fermentation experiment was carried out to analyse changes in the flavour composition and microbial communities of fermented grains after 35 days of fermentation. The results showed that the microbial communities and the flavour composition in the Daqu and fermented samples differed significantly. The dominant microorganism genus evolved from Citrobacter, Rhodococcus, and Thermomyces to Lactobacillus, Pediococcus, and Pichia HD sample. The dominant microorganism genus in WM sample changed from Virgibacillus, Oceanobacillus, and Thermomyces to Lactobacillus, Pediococcus, and Pichia. Whereas in MT sample, the dominant microorganism genus evolved from Virgibacillus, Kroppenstedtia, and Thermomyces to Lactobacillus, Pediococcus, and Pichia. Additionally, the main flavour composition also changed after fermentation, which in the late fermentation period were phenylethyl alcohol, ethyl palmitate, tetramethylpyrazine, and 3‐methylbutanoic acid. These findings can provide support to explain the importance and contribution of sauce‐flavour Daqu in Baijiu brewing scientifically. [ABSTRACT FROM AUTHOR]

In order to analyze the high-temperature Daqu bacterial taxa and their physicochemical properties in Linyi area, Shandong Province, Illumina MiSeq high-throughput sequencing technology and pure culture technology were used to analyze the bacterial taxa of high-temperature Daqu in Lanling wine, and then the physicochemical indexes were determined by conventional detection methods in this study. Finally, the correlation between bacterial taxa and physicochemical indexes in Daqu was explored. The results showed that the main genera of bacteria in Daqu were Kroppenstedtia, Thermoactinomyces, Saccharopolyspora, Staphylococcus, Rhodococcus, Weissella and Bacillus, et al. Bacillus subtilis, Bacillus licheniformis and Bacillus coagulans were cultureable dominant bacterial isolates. There was a large difference in saccharification, esterification, alcoholization and liquefaction between the 15 parts of high-temperature Daqu. Kroppenstedtia, Staphylococcus, Leucobacter, Rhodococcus and Weissella were significantly positively correlated with esterification, fermentation, alcoholization, esterification and liquefaction (P<0.05). Thus, there are a large number of core bacterial taxa in high-temperature Daqu in Lanling wine, and there is a significant correlation between various bacterial genera and physicochemical indexes, which further provides a reference for the improvement and enhancement of the quality of high-temperature Daqu in this area. [ABSTRACT FROM AUTHOR]

The present study describes the case of a 33-year-old male patient, who was diagnosed with concurrent infections of Rhodococcus hoagii (R. hoagii), Mycobacterium intracellulare (M. intracellulare), human immunodeficiency virus (HIV) and syphilis. This patient, a homeless farm laborer with no prior medical treatments, exhibited symptoms including persistent fever and cough, and was admitted to hospital. Treatment was initiated with a combination of anti-retroviral therapy with emtricitabine/tenofovir alafenamide/dolutegravir, and antibiotics (azithromycin, rifampicin, amikacin and ethambutol) targeted at both R. hoagii and M. intracellulare, alongside adjustments for drug-drug interactions due to rifampicin administration. Despite initial improvements and discharge after 21 days with scheduled outpatient follow-ups, the patient did not return for further treatment monitoring. The case presented herein underscores the challenges in managing complex infections in severely immunocompromised patients and highlights the need for integrated treatment approaches, careful drug management, and robust follow-up systems to ensure adherence and prevent relapse. In addition, the present case report contributes to the limited literature available on R. hoagii infections in HIV-infected individuals and highlights the need for early intervention and comprehensive management in similar clinical scenarios [ABSTRACT FROM AUTHOR]

This study was designed to recover representative culturable actinomycetes from the Atacama Desert, and to detect their ability to promote plant growth under drought conditions. Environmental samples were taken from three Atacama Desert habitats, namely, from the Aguas Calientes, Lomas Bayas and Yungay core regions. With one exception higher actinomycete counts were obtained when isolation media were inoculated with mineral particles than with corresponding aliquots of serial dilution. Comparative 16S rRNA gene sequencing showed that representative isolates belonged to thirteen genera including putative novel Blastococcus, Kocuria, Micromonospora, Pseudonocardia, Rhodococcus and Streptomyces species. Representative isolates produced indole-3-acetic acid, siderophore and solubilized phosphate as well as displaying an ability to grow under drought conditions. In conclusion, the current findings open up exciting prospects for the promising potential of actinomycetes from the Atacama Desert to be used as bioinoculants to promote plant growth in arid and semi-arid biomes. [ABSTRACT FROM AUTHOR]

The actinomycete genus Rhodococcus is known for its diverse biosynthetic enzymes, with potential in pollutant degradation, chemical biocatalysis, and natural product exploration. Comparative genomics have analyzed the distribution patterns of non-ribosomal peptide synthetases (NRPSs) in Rhodococcus. The diversity and specificity of its secondary metabolism offer valuable insights for exploring natural products, yet remain understudied. In the present study, we analyzed the distribution patterns of biosynthetic gene clusters (BGCs) in the most comprehensive Rhodococcus genome data to date. The results show that 86.5% of the gene cluster families (GCFs) are only distributed in a specific phylogenomic-clade of Rhodococcus, with the most predominant types of gene clusters being NRPS and ribosomally synthesized and post-translationally modified peptides (RiPPs). In-depth mining of RiPP gene clusters revealed that Rhodococcus encodes many clade-specific novel RiPPs, with thirteen core peptides showing antibacterial potential. High-throughput elicitor screening (HiTES) and non-targeted metabolomics revealed that a marine-derived Rhodococcus strain produces a large number of new aurachin-like compounds when exposed to specific elicitors. The present study highlights the diversity and specificity of secondary biosynthetic potential in Rhodococcus, and provides valuable information for the targeted exploration of novel natural products from Rhodococcus, especially for phylogenomic-clade-specific metabolites. [ABSTRACT FROM AUTHOR]

Introduction: The genus Rhodococcus, first described by Zopf in 1891, comprises 56 species with validly published names. This bacterium belongs to the phylum Actinobacteria, class Actinobacteria, order Mycobacteriales, and family Nocardiaceae. Notable characteristics of this bacterial genus include: Gram-positive, partially acid-fast positive, catalase-positive, non-spore-forming, and non-motile. The use of molecular methods such as 16S rRNA gene sequencing, along with phenotypic methods, has been suggested for the identification of this bacterium. To date, nine species of the genus Rhodococcus have been reported from clinical specimens. Currently, microbroth dilution is the standard method for assessing the antibiotic susceptibility testing of Rhodococcus species. The pattern of antibiotic resistance in Rhodococcus species varies based on geographical region, and it is recommended that antibiotic susceptibility testing be performed for clinical isolates.

Abstract Microbial degradation of fluorinated compounds raised significant attention because of their widespread distribution and potential environmental impacts. Here, we report a bacterial isolate, Rhodococcus sp. NJF-7 capable of defluorinating monofluorinated medium-chain length alkanes. This isolate consumed 2.29 ± 0.13 mmol L− 1 of 1-fluorodecane (FD) during a 52 h incubation period, resulting in a significant release of inorganic fluoride amounting to 2.16 ± 0.03 mmol L− 1. The defluorination process was strongly affected by the initial FD concentration and pH conditions, with lower pH increasing fluoride toxicity to bacterial cells and inhibiting enzymatic defluorination activity. Stoichiometric conversion of FD to fluoride was observed at neutral pH with resting cells, while defluorination was significantly lower at reduced pH (6.5). The discovery of the metabolites decanoic acid and methyl decanoate suggests that the initial attack by monooxygenases may be responsible for the biological defluorination of FD. The findings here provide new insights into microbial defluorination processes, specifically aiding in understanding the environmental fate of organic semi-fluorinated alkane chemicals.

This study explored the enantiocomplementary bioreduction of substituted 1-(arylsulfanyl)propan-2-ones in batch mode using four wild-type yeast strains and two different recombinant alcohol dehydrogenases from Lactobacillus kefir and Rhodococcus aetherivorans. The selected yeast strains and recombinant alcohol dehydrogenases as whole-cell biocatalysts resulted in the corresponding 1-(arylsulfanyl)propan-2-ols with moderate to excellent conversions (60–99%) and high selectivities (ee > 95%). The best bioreductions—in terms of conversion (>90%) and enantiomeric excess (>99% ee)—at preparative scale resulted in the expected chiral alcohols with similar conversion and selectivity to the screening reactions. [ABSTRACT FROM AUTHOR]

This study was undertaken in order to explore the correlation between the quality changes and microbial community in sauced duck necks during cold storage. Commercial sauced duck necks in modified atmosphere packaging were stored at 4 °C for 1, 4, 7, 10, and 13 days, and the changes in pH, thiobarbituric acid reactive substances (TBARS) value, color, texture, total bacterial count, total volatile base nitrogen (TVB-N) content, and microbial community were analyzed. The results showed that the pH initially decreased and then increased with storage time, while brightness (L*), redness (a*), yellowness (b*) and hardness exhibited a decreasing trend, and elasticity, chewiness, cohesiveness and adhesiveness showed an initial increase followed by a decrease. The total bacterial count, TVB-N and TBARS values all gradually increased during storage, with the total bacterial count and TVB-N exceeding the acceptable limits on the 10th day. Microbial diversity diminished gradually with storage time. At the initial stage of storage, the dominant bacteria were Rhodococcus, Acinetobacter, Ureibacillus and Symbiobacterium, while those in the late storage period were Rhodococcus, Acinetobacter, Leuconostoc and Lactobacillus. Principal co-ordinate analysis indicated the two principal coordinates explained 74.03% of the variation, and differences in microbial community composition occurred after 4 days of storage. Correlation analysis showed that Leuconostoc was positively correlated with pH, total bacterial count, TVB-N content and TBARS value during cold storage of sauced duck necks, indicating that Leuconostoc was the primary spoilage bacteria during storage. [ABSTRACT FROM AUTHOR]

Soil-dwelling Actinomycetes are a diverse and ubiquitous component of the global microbiome but largely lack genetic tools comparable to those available in model species such as Escherichia coli or Pseudomonas putida, posing a fundamental barrier to their characterization and utilization as hosts for biotechnology. To address this, we have developed a modular plasmid assembly framework, along with a series of genetic control elements for the previously genetically intractable Gram-positive environmental isolate Rhodococcus ruber C208, and demonstrate conserved functionality in 11 additional environmental isolates of Rhodococcus, Nocardia, and Gordonia. This toolkit encompasses five Mycobacteriale origins of replication, five broad-host-range antibiotic resistance markers, transcriptional and translational control elements, fluorescent reporters, a tetracycline-inducible system, and a counter-selectable marker. We use this toolkit to interrogate the carotenoid biosynthesis pathway in Rhodococcus erythropolis N9T-4, a weakly carotenogenic environmental isolate and engineer higher pathway flux toward the keto-carotenoid canthaxanthin. This work establishes several new genetic tools for environmental Mycobacteriales and provides a synthetic biology framework to support the design of complex genetic circuits in these species. [ABSTRACT FROM AUTHOR]

To clarify the growth mechanisms of Rhodococcus in the alkane phase, we measured oxygen utilization in the alkane phase. The results showed that dissolved oxygen decreased significantly when viable cells were present in the alkane phase. The findings suggested that Rhodococcus strains can grow in alkanes and utilize the resident dissolved oxygen. [ABSTRACT FROM AUTHOR]

Complete genome sequencing of R. pyridinivorans strain 5Ap revealed the pSID plasmid (CP063453.1) 250 428 bp in size. The gene responsible for replication of this plasmid is, most probably, dnaB. The genes which may be involved in the replication (dnaB, ssb) and plasmid separation after replication (parA) showed the highest similarity to the determinants located on large (224‒343 kb) plasmids of rhodococci: unnamed1 of R. pyridinivorans YF3, unnamed1 of R. rhodochrous LH-B3, pRJH1 of R. pyridinivorans YC-JH2, pRDE01 of Rhodococcus sp. RDE2, and pRho-VOC14-C342 of R. opacus VOC-14. The pSID plasmid was found to contain two loci responsible for the synthesis of secondary metabolites, one of them determining the synthesis of a polyketide compound (similar sequences have been revealed on plasmids of other rhodococci) and the other one probably determines the synthesis of a siderophore: the genes for biosynthesis of this compound (sid1–5) exhibited the highest similarity (not exceeding 75%) with the sequences from Streptomyces vilmorinianum YP1 (CP040244.1), S. ficellus NRRL 8067 (CP034279.1), Streptomyces sp. NBC00162 (CP102509.1), and some other streptomycetes, while showing no similarity to the known siderophore biosynthesis genes of rhodococci. The locus of the pSID plasmid responsible for the siderophore synthesis had a unique organization, since transcription of the sid5 (iucC) gene occurs in the opposite direction, while in other bacteria it belongs to an operon and is located at one of its termini. Inactivation of the sid1 gene was found to result in decreased antagonistic activity of R. pyridinivorans 5Ap against plant-pathogenic bacteria P. carotovorum 2.18, lower resistance to iron and cadmium ions and arsenate, as well as in emergence of phytotoxic properties against radish, while wild-type bacteria exhibit plant growth-promoting activity. [ABSTRACT FROM AUTHOR]

This is the first report on the isolation of Rhodococcus aetherivorans-specific bacteriophages and of applicability of such invertebrates as Hyalophora cecropia and Eisenia fetida as objects for screening the phages capable of growth on Rhodococcus species. Some of the isolated phages were capable of reproduction on R. ruber and R. qingshengii. An efficient procedure for bacteriophage reproduction in the liquid culture of R. aetherivorans was developed. The revealed bacteriophages may be used for development of efficient genetic tools for Rhodococcus strains, including the industrially significant ones. [ABSTRACT FROM AUTHOR]

Rhodococcus rhodochrous strain М8 is a platform for development of the biotechnologies for biocatalytic production of acrylic monomers, the raw material for synthesis of acrylic heteropolymers. A genetic system for investigation of the cobalt-dependent transcription of nitrile hydratase genes in this strain was constructed, based on the reporter gene of the metal-independent acylamidase from Rhodococcus qingshengii TA37. The cobalt-regulated promoter was shown to be located at a significant distance (~0.5 kb) from nitrile hydratase genes. Excision of the region between the promoter and the nitrile hydratase genes decreased significantly both the promoter activity and the degree of regulation by cobalt. Our results improve the possibilities for rational design of regulated expression cassettes using the promoter of nitrile hydratase genes in Rhodococcus, and for further development of biocatalysts based on these bacteria. [ABSTRACT FROM AUTHOR]

A genome of Rhodococcus rhodochrous IEGM 1362 was sequenced and annotated. This strain can transform monoterpene alcohol (–)-isopulegol with the formation of two novel pharmacologically promising metabolites. Nine genes encoding cytochrome P450, presumably involved in (–)-isopulegol transformation, were found in the genome of R. rhodochrous IEGM 1362. Primers and PCR conditions for their detection were selected. The obtained data can be used for the further investigation of genes encoding enzymes involved in monoterpene biotransformation. [ABSTRACT FROM AUTHOR]

The use of fossil fuels leads to environmental contamination during their extraction, processing and distribution. Microbial biodegradation provides a sustainable method for cleaning contaminated areas which follows the principles of sustainability. This paper presents the dynamics of biodegradation of hydrocarbon fractions of diesel oil, using Planomicrobium sp. and Rhodococcus sp. isolated from petroleum-contaminated sites. GC–MS analysis was employed to analyse abundances of the specific compounds such as n-alkanes, isoprenoids, sesquitepranes, hopanes, steranes and aromatic compounds (naphthalene and its methylated homologues, phenanthrene and anthracene and their methylated homologues, and dibenzothiophene and its methylated homologues). The obtained results showed that after 30 days of biodegradation of diesel, a significant degradation was achieved, with almost complete degradation of n-alkanes and a decrease in the amount of sesquiterapanes. Rhodococcus sp. had a higher efficiency in degradation of n-alkanes, while Planomicrobium sp. had a higher efficiency in the degradation of branched hydrocarbons. Both strains showed high activity in the biodegradation of sesquitepranes and demonstrate ability to degrade methylated phenanthrenes. Additionally, dimethyl-dibenzothiophenes were almost completely degraded and removed from the system. This study presents the first comprehensive report on the GC–MS analysis of the diesel biodegradation pattern of the Planomicrobium sp., compared with the well-established Rhodococcus sp. [ABSTRACT FROM AUTHOR]

Organic farming has emerged as a sustainable solution to the adverse effects (diminished nutritional value, compromised food quality, environmental contamination, and public health hazards) that are usually associated with harmful chemical pesticides. To overcome such loss, one must explore the plantassociated microbes that are the naturally occurring root commensal and could positively improve crop health. In this review, we highlight the importance of the bacterial genus Rhodococcus, a subset of Actinobacteria that carries immense potential in enhancing crop yield and is associated with bioremediation of toxic pesticides and other chemicals to improve soil health. However, it has been noticed that few species of Rhodococcus are pathogenic for the plant (R. fascians) as well as humans/animals (R. equi). But still, the majority of Rhodococcus isolates are found to be nonpathogenic and carry substantial beneficial traits. Here, we have attempted to comprise those beneficial traits of the different members of the genus Rhodococcus. The main emphasis of this review article is to explore the major areas such as enzyme production, phytohormone synthesis, growth regulation, siderophore production, bioremediation, organic compound degradation, and environmental pollution control. Opinions towards the applications of advanced methodologies for utilizing the cumulative prospective potential of the genus Rhodococcus have also been discussed in the different sections of the review. Conclusively, this article gathers the scattered information from the past and recent literature about this bacteria and provides the future direction about how it can improve plant/soil health and eliminate toxic chemicals and environmental pollutants. [ABSTRACT FROM AUTHOR]

Microorganisms harbor catabolic plasmids to tackle refractory organic pollutants, which is crucial for bioremediation and ecosystem health. Understanding the impacts of plasmids on hosts provides insights into the behavior and adaptation of degrading bacteria in the environment. Here, we examined alterations in the physiological properties and gene expression profiles of Rhodococcus sp. strain p52 after losing two conjugative dioxin-catabolic megaplasmids (pDF01 and pDF02). The growth of strain p52 accelerated after pDF01 loss, while it decelerated after pDF02 loss. During dibenzofuran degradation, the expression levels of dibenzofuran catabolic genes on pDF01 were higher compared to those on pDF02; accordingly, pDF01 loss markedly slowed dibenzofuran degradation. It was suggested that pDF01 is more beneficial to strain p52 under dibenzofuran exposure. Moreover, plasmid loss decreased biofilm formation, especially after pDF02 loss. Transcriptome profiling revealed different pathways enriched in upregulated and downregulated genes after pDF01 and pDF02 loss, indicating different adaptation mechanisms. Based on the transcriptional activity variation, pDF01 played roles in transcription and anabolic processes, while pDF02 profoundly influenced energy production and cellular defense. This study enhances our knowledge of the impacts of degradative plasmids on native hosts and the adaptation mechanisms of hosts, contributing to the application of plasmid-mediated bioremediation in contaminated environments. [ABSTRACT FROM AUTHOR]

Terpenoids and steroids are secondary plant and animal metabolites and are widely used to produce highly effective pharmacologically significant compounds. One of the promising approaches to the transformation of these compounds to form bioactive metabolites is their transformation using microorganisms. Rhodococcus spp. are one of the most developed objects in biotechnology due to their exceptional metabolic capabilities and resistance to extreme environmental conditions. In this review, information on the processes of biotransformation of terpenoid and steroid compounds by actinomycetes of the genus Rhodococcus and their molecular genetic bases are most fully collected and analyzed for the first time. Examples of the use of both native whole-cell catalysts and mutant strains and purified enzyme systems for the production of derivatives of terpenoids and steroids are given. [ABSTRACT FROM AUTHOR]

Rhodococcus equi (R. equi) is a zoonotic opportunistic pathogen that mainly causes fatal lung and extrapulmonary abscesses in foals and immunocompromised individuals. To date, no commercial vaccine against R. equi exists. We previously screened all potential vaccine candidates from the complete genome of R. equi using a reverse vaccinology approach. Five of these candidates, namely ABC transporter substrate-binding protein (ABC transporter), penicillin-binding protein 2 (PBD2), NlpC/P60 family protein (NlpC/P60), esterase family protein (Esterase), and M23 family metallopeptidase (M23) were selected for the evaluation of immunogenicity and immunoprotective effects in BALB/c mice model challenged with R. equi. The results showed that all five vaccine candidate-immunized mice experienced a significant increase in spleen antigen-specific IFN-γ- and TNF-α-positive CD4 + and CD8 + T lymphocytes and generated robust Th1- and Th2-type immune responses and antibody responses. Two weeks after the R. equi challenge, immunization with the five vaccine candidates reduced the bacterial load in the lungs and improved the pathological damage to the lungs and livers compared with those in the control group. NlpC/P60, Esterase, and M23 were more effective than the ABC transporter and PBD2 in inducing protective immunity against R. equi challenge in mice. In addition, these vaccine candidates have the potential to induce T lymphocyte memory immune responses in mice. In summary, these antigens are effective candidates for the development of protective vaccines against R. equi. The R. equi antigen library has been expanded and provides new ideas for the development of multivalent vaccines. [ABSTRACT FROM AUTHOR]

Mining-related lead (Pb) pollution of the soil poses serious hazards to ecosystems and living organisms, including humans. Improved heavy metal phytoremediation efficacy, achieved by using phytostabilizing plants assisted by plant-growth-promoting (PGP) microorganisms, has been presented as an effective strategy for remediating polluted soils. The objective of this research was to examine the response and potential of the plant-growth-promoting bacterium LMR356, a Rhodococcus qingshengii strain isolated from an abandoned mining soil, under lead stress conditions. Compared to non-contaminated culture media, the presence of lead induced a significant decrease in auxin production (from 21.17 to 2.65 μg mL−1) and phosphate solubilization (from 33.60 to 8.22 mg L−1), whereas other PGP traits increased drastically, such as 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity (from 38.17 to 71.37 nmol mg−1 h−1 α-ketobutyrate), siderophore production (from 69 to 83%), exopolysaccharide production (from 1952.28 to 3637.72 mg mL−1), biofilm formation, and motility. We, therefore, investigated the behavior of Sulla spinosissima L. in the presence or absence of this strain under a variety of experimental conditions. Under hydroponic conditions, Sulla plants showed endurance to varying lead concentrations (500–1000 μM). Inoculation of plants with Rhodococcus qingshengii strain LMR356 enhanced plant tolerance, as demonstrated by the increase in plant biomass (ranging from 14.41 to 79.12%) compared to non-inoculated Pb-stressed and non-stressed control plants. Antioxidant enzyme activities (increasing by −42.71 to 126.8%) and chlorophyll (383.33%) and carotenoid (613.04%) content were also augmented. In addition to its impact on plant lead tolerance, strain LMR356 showed a growth-promoting effect on Sulla plants when cultivated in sterilized non-contaminated sand. Parameters such as plant biomass (16.57%), chlorophyll (24.14%), and carotenoid (30%) contents, as well as ascorbate peroxidase (APX), peroxidase (POD), and catalase (CAT) activities, were all elevated compared to non-inoculated plants. Furthermore, when the same plant species was cultivated in highly polluted soil, inoculation increased plant biomass and improved its physiological properties. These findings demonstrate that LMR356 is a phytobeneficial bacterial strain capable of enhancing Sulla growth under normal conditions and improving its heavy metal tolerance in multi-polluted soils. Thus, it can be considered a promising biofertilizer candidate for growing Sulla spinosissima L. or other selected plants intended for application in restoration and stabilization initiatives aimed at reviving and safeguarding environmentally compromised and polluted soils after mining activities. [ABSTRACT FROM AUTHOR]

Marine hydrocarbonoclastic bacteria can use polycyclic aromatic hydrocarbons as carbon and energy sources, that makes these bacteria highly attractive for bioremediation in oil-polluted waters. However, genomic and metabolic differences between species are still the subject of study to understand the evolution and strategies to degrade PAHs. This study presents Rhodococcus ruber MSA14, an isolated bacterium from marine sediments in Baja California, Mexico, which exhibits adaptability to saline environments, a high level of intrinsic pyrene tolerance (> 5 g L− 1), and efficient degradation of pyrene (0.2 g L− 1) by 30% in 27 days. Additionally, this strain demonstrates versatility by using naphthalene and phenanthrene as individual carbon sources. The genome sequencing of R. ruber MSA14 revealed a genome spanning 5.45 Mbp, a plasmid of 72 kbp, and three putative megaplasmids, lengths between 110 and 470 Kbp. The bioinformatics analysis of the R. ruber MSA14 genome revealed 56 genes that encode enzymes involved in the peripheral and central pathways of aromatic hydrocarbon catabolism, alkane, alkene, and polymer degradation. Within its genome, R. ruber MSA14 possesses genes responsible for salt tolerance and siderophore production. In addition, the genomic analysis of R. ruber MSA14 against 13 reference genomes revealed that all compared strains have at least one gene involved in the alkanes and catechol degradation pathway. Overall, physiological assays and genomic analysis suggest that R. ruber MSA14 is a new haloalkalitolerant and hydrocarbonoclastic strain toward a wide range of hydrocarbons, making it a promising candidate for in-depth characterization studies and bioremediation processes as part of a synthetic microbial consortium, as well as having a better understanding of the catabolic potential and functional diversity among the Rhodococci group. [ABSTRACT FROM AUTHOR]

Ethylene glycol (EG) is a widely used industrial chemical with manifold applications and also generated in the degradation of plastics such as polyethylene terephthalate. Rhodococcus jostii RHA1 (RHA1), a potential biocatalytic chassis, grows on EG. Transcriptomic analyses revealed four clusters of genes potentially involved in EG catabolism: the mad locus, predicted to encode mycofactocin-dependent alcohol degradation, including the catabolism of EG to glycolate; two GCL clusters, predicted to encode glycolate and glyoxylate catabolism; and the mft genes, predicted to specify mycofactocin biosynthesis. Bioinformatic analyses further revealed that the mad and mft genes are widely distributed in mycolic acid-producing bacteria such as RHA1. Neither ΔmadA nor ΔmftC RHA1 mutant strains grew on EG but grew on acetate. In resting cell assays, the ΔmadA mutant depleted glycolaldehyde but not EG from culture media. These results indicate that madA encodes a mycofactocin-dependent alcohol dehydrogenase that initiates EG catabolism. In contrast to some mycobacterial strains, the mad genes did not appear to enable RHA1 to grow on methanol as sole substrate. Finally, a strain of RHA1 adapted to grow ~3× faster on EG contained an overexpressed gene, aldA2, predicted to encode an aldehyde dehydrogenase. When incubated with EG, this strain accumulated lower concentrations of glycolaldehyde than RHA1. Moreover, ecotopically expressed aldA2 increased RHA1's tolerance for EG further suggesting that glycolaldehyde accumulation limits growth of RHA1 on EG. Overall, this study provides insights into the bacterial catabolism of small alcohols and aldehydes and facilitates the engineering of Rhodococcus for the upgrading of plastic waste streams. [ABSTRACT FROM AUTHOR]

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In this study, a new strain of bacteria, named Rhodococcus sp. KLW-1, was isolated from farmland soil contaminated by plastic mulch for more than 30 years. To improve the application performance of free bacteria and find more ways to use waste biochar, KLW-1 was immobilised on waste biochar by sodium alginate embedding method to prepare immobilised pellet. Response Surface Method (RSM) predicted that under optimal conditions (3% sodium alginate, 2% biochar and 4% CaCl2), di (2-ethylhexyl) phthalate (DEHP) degradation efficiency of 90.48% can be achieved. Under the adverse environmental conditions of pH 5 and 9, immobilisation increased the degradation efficiency of 100 mg/L DEHP by 16.42% and 11.48% respectively, and under the high-stress condition of 500 mg/L DEHP concentration, immobilisation increased the degradation efficiency from 71.52% to 91.56%, making the immobilised pellets have strong stability and impact load resistance to environmental stress. In addition, immobilisation also enhanced the degradation efficiency of several phthalate esters (PAEs) widely existing in the environment. After four cycles of utilisation, the immobilised particles maintained stable degradation efficiency for different PAEs. Therefore, immobilised pellets have great application potential for the remediation of the actual environment. [ABSTRACT FROM AUTHOR]

The purpose of this study was to evaluate the potential of microbial-enhanced Brassica oleracea for the phytoremediation of seleniferous soils. The effect of selenite (Se(IV)) and selenate (Se(VI)) on B. oleracea (1–100 mg.L−1) was examined through germination (7 d) and pot (30 d) trials. Microbial analysis was conducted to verify the toxic effect of various Se concentrations (1–500 mg.L−1) on Rhodococcus opacus PD360, and to determine if it exhibits plant growth promoter traits. R. opacus PD630 was found to tolerate high concentrations of both Se(IV) and Se(VI), above 100 mg.L−1. R. opacus PD630 reduced Se(IV) and Se(VI) over 7 days, with a Se conversion efficiency between 60 and 80%. Germination results indicated lower concentrations (0–10 mg.L−1) of Se(IV) and Se(VI) gave a higher shoot length (> 4 cm). B. oleracea accumulated 600–1,000 mg.kg−1 dry weight (DW) of Se(IV) and Se(VI), making it a secondary accumulator of Se. Moreover, seeds inoculated with R. opacus PD360 showed increased Se uptake (up to 1,200 mg Se.kg−1 DW). In addition, bioconcentration and translocation factors were greater than one. The results indicate a synergistic effect between R. opacus PD630 and B. oleracea for Se phytoextraction from polluted soils. This article examines how Brassica oleracea may be used to improve seleniferous soils and how Rhodococcus opacus can be added to increase biofortification. The research shows great potential for combining Brassica species with bacterial isolates to remove selenium from heavily contaminated soils. [ABSTRACT FROM AUTHOR]

Lignocellulosic biomass is currently underutilized, but it offers promise as a resource for the generation of commercial end-products, such as biofuels, detergents, and other oleochemicals. Rhodococcus opacus PD630 is an oleaginous, Gram-positive bacterium with an exceptional ability to utilize recalcitrant aromatic lignin breakdown products to produce lipid molecules such as triacylglycerols (TAGs), which are an important biofuel precursor. Lipid carbon storage molecules accumulate only under growth-limiting low nitrogen conditions, representing a significant challenge toward using bacterial biorefineries for fuel precursor production. In this work, we screened overexpression of 27 native transcriptional regulators for their abilities to improve lipid accumulation under nitrogen-rich conditions, resulting in three strains that accumulate increased lipids, unconstrained by nitrogen availability when grown in phenol or glucose. Transcriptomic analyses revealed that the best strain (#13) enhanced FA production via activation of the β-ketoadipate pathway. Gene deletion experiments confirm that lipid accumulation in nitrogen-replete conditions requires reprogramming of phenylalanine metabolism. By generating mutants decoupling carbon storage from low nitrogen environments, we move closer toward optimizing R. opacus for efficient bioproduction on lignocellulosic biomass. [ABSTRACT FROM AUTHOR]

The selection of oleaginous bacteria, potentially applicable to biotechnological approaches, is usually carried out by different expensive and time-consuming techniques. In this study, we used Oil Red O (ORO) as an useful dye for staining of neutral lipids (triacylglycerols and wax esters) on thin-layer chromatography plates. ORO could detect minimal quantities of both compounds (detection limit, 0.0025 mg of tripalmitin or 0.005 mg of cetylpalmitate). In addition, we developed a specific, rapid, and inexpensive screening methodology to detect triacylglycerol-accumulating microorganisms grown on the agar plate. This staining methodology detected 9/13 strains with a triacylglycerol content higher than 20% by cellular dry weight. ORO did not stain polyhydroxyalkanoates-producing bacteria. The four oleaginous strains not detected by this screening methodology exhibited a mucoid morphology of their colonies. Apparently, an extracellular polymeric substance produced by these strains hampered the entry of the lipophilic dye into cells. The utilization of the developed screening methodology would allow selecting of oleaginous bacteria in a simpler and faster way than techniques usually used nowadays, based on unspecific staining protocols and spectrophotometric or chromatographic methods. Furthermore, the use of ORO as a staining reagent would easily characterize the neutral lipids accumulated by microorganisms as reserve compounds. Key points: • Oil Red O staining is specific for triacylglycerols • Oil Red O staining is useful to detect oleaginous bacteria • Fast and inexpensive staining to isolate oleaginous bacteria from the environment [ABSTRACT FROM AUTHOR]

Ethylene glycol (EG) is an industrially important two-carbon diol used as a solvent, antifreeze agent, and building block of polymers such as poly(ethylene terephthalate) (PET). Recently, the use of EG as a starting material for the production of bio-fuels or bio-chemicals is gaining attention as a sustainable process since EG can be derived from materials not competing with human food stocks including CO2, syngas, lignocellulolytic biomass, and PET waste. In order to design and construct microbial process for the conversion of EG to value-added chemicals, microbes capable of catabolizing EG such as Escherichia coli, Pseudomonas putida, Rhodococcus jostii, Ideonella sakaiensis, Paracoccus denitrificans, and Acetobacterium woodii are candidates of chassis for the construction of synthetic pathways. In this mini-review, we describe EG catabolic pathways and catabolic enzymes in these microbes, and further review recent advances in microbial conversion of EG to value-added chemicals by means of metabolic engineering. Key points: • Ethylene glycol is a potential next-generation feedstock for sustainable industry. • Microbial conversion of ethylene glycol to value-added chemicals is gaining attention. • Ethylene glycol-utilizing microbes are useful as chassis for synthetic pathways. [ABSTRACT FROM AUTHOR]

Withmore than 100 rubber-degrading strains being reported, only 9 Lcp proteins isolated from Nocardia, Gordonia, Streptomyces, Rhodococcus, Actinoplanes, and Solimonas have been purified and biochemically characterized. A new strain, Dactylosporangium sp. AC04546 (strain JCM34239), isolated from soil samples collected in Sarawak Forest, was able to grow and utilize natural or synthetic rubber as the sole carbon source. Complete genome of Strain AC04546 was obtained from the hybrid assembly of PacBio Sequel II and Illumina MiSeq. Strain AC04546 has a large circular genome of 13.08 Mb with a G+C content of 72.1%. The genome contains 11,865 protein-coding sequences with 3 latex clearing protein (lcp) genes located on its chromosome. The genetic organization of the lcp gene cluster is similar to two other reported rubber-degrading strains--Actinoplanes sp. OR16 and Streptomyces sp. CFMR 7. All 3 Lcp from strain AC04546 were expressed in Escherichia coli and exhibited degrading activity against natural rubber. The distinctiveness of strain AC04546, along with other characterized rubber-degrading strains, is reported here. [ABSTRACT FROM AUTHOR]

Microbial degradation of fluorinated compounds raised significant attention because of their widespread distribution and potential environmental impacts. Here, we report a bacterial isolate, Rhodococcus sp. NJF-7 capable of defluorinating monofluorinated medium-chain length alkanes. This isolate consumed 2.29 ± 0.13 mmol L− 1 of 1-fluorodecane (FD) during a 52 h incubation period, resulting in a significant release of inorganic fluoride amounting to 2.16 ± 0.03 mmol L− 1. The defluorination process was strongly affected by the initial FD concentration and pH conditions, with lower pH increasing fluoride toxicity to bacterial cells and inhibiting enzymatic defluorination activity. Stoichiometric conversion of FD to fluoride was observed at neutral pH with resting cells, while defluorination was significantly lower at reduced pH (6.5). The discovery of the metabolites decanoic acid and methyl decanoate suggests that the initial attack by monooxygenases may be responsible for the biological defluorination of FD. The findings here provide new insights into microbial defluorination processes, specifically aiding in understanding the environmental fate of organic semi-fluorinated alkane chemicals. [ABSTRACT FROM AUTHOR]

Taxonomic diversity and quantitative distribution of cultured forms of Fe- and Mn-oxidizing microorganisms in Fe–Mn nodules of different sizes and fine earth of Gleyic Luvisols formed in the territory not affected by direct anthropogenic impact, were analyzed. The results were obtained using a combination of microbiological, molecular and analytical methods and noninvasive techniques. Most of the microorganisms which were cultured from the nodules were Mn oxidizers. Bacteria of the genera Bacillus, Rhodococcus, Lysinibacillus, Pseudomonas, and Priestia were identified in the nodules. Quantitative distribution of Fe- and Mn-oxidizing microorganisms in the outer and inner zones of the nodules of different sizes demonstrated that Mn-oxidizing microorganisms were involved in all stages of nodules formation and development, while Fe-oxidizing microorganisms participated in the initial phase of their formation. Spherules and porous structures of bacterial nature were observed in the studied nodules. The host soil fine earth was characterized by differences in the relative abundance of the dominant microbial groups in the profile. Manganese-oxidizing bacteria were represented in the soil fine earth by the genera Prestia and Methylobacterium. [ABSTRACT FROM AUTHOR]

Zearalenone (ZEN) is a prevalent mycotoxin found in grains and grain-derived products, inducing adverse health effects in both animals and humans. The in-field application of microorganisms to degrade and detoxify ZEN is a promising strategy to enhance the safety of food and feed. In this study, we investigated the potential of three actinobacterial strains to degrade and detoxify ZEN in vitro and in planta on wheat ears. The residual ZEN concentration and toxicity in the samples were analysed with UHPLC-MS/MS and a bioluminescence BLYES assay, respectively. Streptomyces rimosus subsp. rimosus LMG19352 could completely degrade and detoxify 5 mg/L ZEN in LB broth within 24 h, along with significant reductions in ZEN concentration both in a minimal medium (MM) and on wheat ears. Additionally, it was the only strain that showed a significant colonisation of these ears. Rhodococcus sp. R25614 exhibited partial but significant degradation in LB broth and MM, whereas Streptomyces sp. LMG16995 degraded and detoxified ZEN in LB broth after 72 h by 39% and 33%, respectively. Although all three actinobacterial strains demonstrated the metabolic capability to degrade and detoxify ZEN in vitro, only S. rimosus subsp. rimosus LMG19352 showed promising potential to mitigate ZEN in planta. This distinction underscores the importance of incorporating in planta screening assays for assessing the potential of mycotoxin-biotransforming microorganisms as biocontrol agents. [ABSTRACT FROM AUTHOR]

Cyanides and nitriles, characterized by their R-CN chains, are known for their toxicity, mutagenicity, and carcinogenicity, posing significant threats to environmental and human health. This study aims to explore the biodegradation capabilities of Rhodococcus sp. in breaking down cyanide and nitrile bonds. Rhodococcus pyridinivorans strain I-benzo was isolated from tanning waste and cultured in mineral media with a 20 mM benzonitrile substrate. The activity of this strain was tested using substrates such as benzonitrile, acetonitrile, acrylonitrile, benzamide, acetamide, and acrylamide, revealing positive reactions of nitrile hydratase and amidase enzymes through the Nessler measurement method, which indicated the production of ammonia and carboxylic acids. Furthermore, the degradation tests showed that the Vmax values for the biodegradation of potassium cyanide and sodium cyanide were 0.56 ppm/minute and 0.21 ppm/minute, respectively. These findings highlight the potential application of Rhodococcus pyridinivorans strain I-benzo in mitigating the environmental impact of cyanide and nitrile pollutants through efficient biodegradation. [ABSTRACT FROM AUTHOR]

To investigate the etiological role of vapB-positive Rhodococcus equi in pigs, R. equi was isolated from the submaxillary lymph nodes with or without macroscopically detectable lesions of apparently healthy growing-finishing pigs at a slaughterhouse in Toyama Prefecture, Japan. R. equi was isolated from 57 (24.6%) of 232 pigs with macroscopically detectable lymph node lesions, and 56 (98.2%) of the 57 isolates were vapB-positive. R. equi was isolated from 10 (2.4%) of 420 pigs without lymph node lesions, and six (60%) of the 10 isolates were vapB-positive. Plasmid DNA was isolated from the 62 vapB-positive isolates and digested with EcoRI and NsiI to obtain the plasmid profile. Fifty-two (83.9%), three (4.8%), and four (6.5%) isolates contained pVAPB subtypes 1, 2, and 3, respectively, while the remaining three isolates were of pVAPB subtypes 9, 13, and 14, respectively. Twelve specimens from lymph nodes with macroscopically detectable lesions were randomly selected for histopathological staining. Granulomatous lesions resembling tuberculosis were found in 11 of the 12 specimens, and the remaining specimen showed typical foci of malakoplakia in the lymph node. The isolation rates of R. equi and vapB-positive R. equi from lymph nodes with macroscopically detectable lesions were significantly higher (P<0.05) than those of lymph nodes without lesions, suggesting an etiologic association between vapB-positive R. equi and macroscopically detectable granulomatous lesions in porcine submaxillary lymph nodes. Previous reports on the prevalence of vapB-positive R. equi in pigs are reviewed and discussed. [ABSTRACT FROM AUTHOR]

Abstract Background Belonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, more rarely, in humans. Over 100 phages that infect Rhodococcus species have been isolated but despite their importance for Rhodococcus ecology and biotechnology applications, little is known regarding the molecular genetic interactions between phage and host during infection. To address this need, we report RNA-Seq analysis of a novel Rhodococcus erythopolis phage, WC1, analyzing both the phage and host transcriptome at various stages throughout the infection process. Results By five minutes post-infection WC1 showed upregulation of a CAS-4 family exonuclease, putative immunity repressor, an anti-restriction protein, while the host showed strong upregulation of DNA replication, SOS repair, and ribosomal protein genes. By 30 min post-infection, WC1 DNA synthesis genes were strongly upregulated while the host showed increased expression of transcriptional and translational machinery and downregulation of genes involved in carbon, energy, and lipid metabolism pathways. By 60 min WC1 strongly upregulated structural genes while the host showed a dramatic disruption of metal ion homeostasis. There was significant expression of both host and phage non-coding genes at all time points. While host gene expression declined over the course of infection, our results indicate that phage may exert more selective control, preserving the host’s regulatory mechanisms to create an environment conducive for virion production. Conclusions The Rhodococcus genus is well recognized for its ability to synthesize valuable compounds, particularly steroids, as well as its capacity to degrade a wide range of harmful environmental pollutants. A detailed understanding of these phage-host interactions and gene expression is not only essential for understanding the ecology of this important genus, but will also facilitate development of phage-mediated strategies for bioremediation as well as biocontrol in industrial processes and biomedical applications. Given the current lack of detailed global gene expression studies on any Rhodococcus species, our study addresses a pressing need to identify tools and genes, such as F6 and rpf, that can enhance the capacity of Rhodococcus species for bioremediation, biosynthesis and pathogen control.

High concentration of phenol residues in soil are harmful to human health and ecological safety. However, limited information is available on the in-situ bioremediation of phenol-contaminated soil using biochar as a carrier for bacteria. In this study, bamboo -derived biochar was screened as a carrier to assemble microorganism-immobilized composite with Rhodococcus pyridinivorans B403. Then, SEM used to observe the micromorphology of composite and its bioactivity was detected in solution and soil. Finally, we investigated the effects of free B403 and biochar-immobilized B403 (BCJ) on phenol biodegradation in two types of soils and different initial phenol concentrations. Findings showed that bacterial cells were intensively distributed in/onto the carriers, showing high survival. Immobilisation increased the phenol degradation rate of strain B403 by 1.45 times (37.7 mg/(L·h)). The phenol removed by BCJ in soil was 81% higher than free B403 on the first day. Moreover, the removal of BCJ remained above 51% even at phenol concentration of 1,500 mg/kg, while it was only 15% for free B403. Compared with the other treatment groups, BCJ showed the best phenol removal effect in both tested soils. Our results indicate that the biochar-B403 composite has great potential in the remediation of high phenol-contaminated soil. [ABSTRACT FROM AUTHOR]

Diterpenoids are an important class of secondary metabolites in nature with diverse applications such as pharmaceuticals, flavors and fragrances. Sclareol, a plant-derived diterpene alcohol from Salvia sclarea, is most commonly used as the starting material for the production of hemisynthetic Ambrox, a valuable substitute for ambergris from sperm whales used in perfumery. Here, we engineered the oleaginous yeast Yarrowia lipolytica as a chassis for sclareol overproduction. We constructed a de novo sclareol biosynthetic pathway by screening and engineering heterologous LPP synthase (Lpps) and sclareol synthase (Scs). By constructing a two-layer geranylgeranyl diphosphate (GGPP) accumulation pathway and scaffold-free multienzyme complexes, the metabolic flux was redirected toward sclareol synthesis, enabling significantly improved production of sclareol and reduced levels of by-products. The engineered strain was capable of producing 12.9 g L-1 of sclareol in a 5 L bioreactor, with this being the highest titer achieved to date. To the best of our knowledge, this is the first report of sclareol biosynthesis in Y. lipolytica, and this chassis strain may offer a groundbreaking foundation for the sustainable, large-scale fermentation of diterpenoids. [ABSTRACT FROM AUTHOR]

The bacterial genus Rhodococcus comprises organisms performing oleaginous behaviors under certain growth conditions and ratios of carbon and nitrogen availability. Rhodococci are outstanding producers of biofuel precursors, where lipid and glycogen metabolisms are closely related. Thus, a better understanding of rhodococcal carbon partitioning requires identifying catalytic steps redirecting sugar moieties to storage molecules. Here, we analyzed two GT4 glycosyl-transferases from Rhodococcus jostii (RjoGlgAb and RjoGlgAc) annotated as α-glucan-α-1,4-glucosyl transferases, putatively involved in glycogen synthesis. Both enzymes were produced in Escherichia coli cells, purified to homogeneity, and kinetically characterized. RjoGlgAb and RjoGlgAc presented the "canonical" glycogen synthase activity and were actives as maltose-1P synthases, although to a different extent. Then, RjoGlgAc is a homologous enzyme to the mycobacterial GlgM, with similar kinetic behavior and glucosyl-donor preference. RjoGlgAc was two orders of magnitude more efficient to glucosylate glucose-1P than glycogen, also using glucosamine-1P as a catalytically efficient aglycon. Instead, RjoGlgAb exhibited both activities with similar kinetic efficiency and preference for short-branched α-1,4-glucans. Curiously, RjoGlgAb presented a super-oligomeric conformation (higher than 15 subunits), representing a novel enzyme with a unique structure-to-function relationship. Kinetic results presented herein constitute a hint to infer on polysaccharides biosynthesis in rhodococci from an enzymological point of view. [ABSTRACT FROM AUTHOR]

The oil-bearing rose (Rosa damascena Miller) is the most important essential oil crop in Bulgaria. In May 2023 in rose plantations located in the region of Zelenikovo village the rose soft scale Rhodococcus perornatus (Hemiptera: Coccidae) was found in high density of 5% infested rose bushes (Cockerell & Parrott, 1899). The rose plantations are growing within the conventional farming. Two chemical (Closer – 0.02%, 0.04% and Sivanto prime – 0.05%, 0.1%) and one biological (Naturalis – 0.1%, 0.2%) insecticides were tested against the rose soft scale. All tested products showed better results in higher concentrations. Closer indicated the fastest initial action. In the concentration of 0.04% on the 1st day after the treatment its efficacy was 100%. Sivanto prime in the concentration of 0.1% on the 5th day after the treatment showed an efficacy of 100%. The biological insecticide Naturalis had a slower action and in the concentration of 0.2% on the 7th day after the treatment its efficacy was 90%. [ABSTRACT FROM AUTHOR]

Microorganism lipid droplet small regulator (MLDSR) is a transcriptional regulator of the major lipid droplet (LD)‐associated protein MLDS in Rhodococcus jostii RHA1 and Rhodococcus opacus PD630. In this study, we investigated the role of MLDSR on lipid metabolism and triacylglycerol (TAG) accumulation in R. jostii RHA1 at physiological and molecular levels. MLDSR gene deletion promoted a significant decrease of TAG accumulation, whereas inhibition of de novo fatty acid biosynthesis by the addition of cerulenin significantly repressed the expression of the mldsr‐mlds cluster under nitrogen‐limiting conditions. In vitro and in vivo approaches revealed that MLDSR‐DNA binding is inhibited by fatty acids and acyl‐CoA residues through changes in the oligomeric or conformational state of the protein. RNAseq analysis indicated that MLDSR not only controls the expression of its own gene cluster but also of several genes involved in central, lipid, and redox metabolism, among others. We also identified putative MLDSR‐binding sites on the upstream regions of genes coding for lipid catabolic enzymes and validated them by EMSA assays. Overexpression of mldsr gene under nitrogen‐rich conditions promoted an increase of TAG accumulation, and further cell lysis with TAG release to the culture medium. Our results suggested that MLDSR is a fatty acid‐responsive regulator that plays a dual role in cells by repression or activation of several metabolic genes in R. jostii RHA1. MLDSR seems to play an important role in the fine‐tuning regulation of TAG accumulation, LD formation, and cellular lipid homeostasis, contributing to the oleaginous phenotype of R. jostii RHA1 and R. opacus PD630. [ABSTRACT FROM AUTHOR]

Background: Belonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, more rarely, in humans. Over 100 phages that infect Rhodococcus species have been isolated but despite their importance for Rhodococcus ecology and biotechnology applications, little is known regarding the molecular genetic interactions between phage and host during infection. To address this need, we report RNA-Seq analysis of a novel Rhodococcus erythopolis phage, WC1, analyzing both the phage and host transcriptome at various stages throughout the infection process. Results: By five minutes post-infection WC1 showed upregulation of a CAS-4 family exonuclease, putative immunity repressor, an anti-restriction protein, while the host showed strong upregulation of DNA replication, SOS repair, and ribosomal protein genes. By 30 min post-infection, WC1 DNA synthesis genes were strongly upregulated while the host showed increased expression of transcriptional and translational machinery and downregulation of genes involved in carbon, energy, and lipid metabolism pathways. By 60 min WC1 strongly upregulated structural genes while the host showed a dramatic disruption of metal ion homeostasis. There was significant expression of both host and phage non-coding genes at all time points. While host gene expression declined over the course of infection, our results indicate that phage may exert more selective control, preserving the host's regulatory mechanisms to create an environment conducive for virion production. Conclusions: The Rhodococcus genus is well recognized for its ability to synthesize valuable compounds, particularly steroids, as well as its capacity to degrade a wide range of harmful environmental pollutants. A detailed understanding of these phage-host interactions and gene expression is not only essential for understanding the ecology of this important genus, but will also facilitate development of phage-mediated strategies for bioremediation as well as biocontrol in industrial processes and biomedical applications. Given the current lack of detailed global gene expression studies on any Rhodococcus species, our study addresses a pressing need to identify tools and genes, such as F6 and rpf, that can enhance the capacity of Rhodococcus species for bioremediation, biosynthesis and pathogen control. [ABSTRACT FROM AUTHOR]

Introduction: Microplastics (MPs) are widely distributed in the environment, causing damage to biota and human health. Due to their physicochemical characteristics, they become resistant particles to environmental degradation, leading to their accumulation in large quantities in the terrestrial ecosystem. Thus, there is an urgent need for measures to mitigate such pollution, with biological degradation being a viable alternative, where bacteria play a crucial role, demonstrating high efficiency in degrading various types of MPs. Therefore, the study aimed to identify bacteria with the potential for MP biodegradation and the enzymes produced during the process. Methods: The methodology used followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol. Results and Discussion: The research yielded 68 eligible studies, highlighting bacteria from the genera Bacillus, Pseudomonas, Stenotrophomonas, and Rhodococcus as the main organisms involved in MP biodegradation. Additionally, enzymes such as hydrolases and alkane hydroxylases were emphasized for their involvement in this process. Thus, the potential of bacterial biodegradation is emphasized as a promising pathway to mitigate the environmental impact of MPs, highlighting the relevance of identifying bacteria with biotechnological potential for large-scale applications in reducing MP pollution. [ABSTRACT FROM AUTHOR]

Chloroxylenol is a commonly used antimicrobial agent in antibacterial and disinfection products, which has been detected in various environments, such as wastewater treatment plants, rivers, seawater, and even drinking water, with concentrations ranging from ng/L to mg/L. However, the biodegradation of chloroxylenol received limited attention with only sporadic reports available so far. In this study, an efficient chloroxylenol-degrading consortium, which could degrade 20 mg/L chloroxylenol within two days, was obtained after five months of enrichment. Amplicon sequencing analysis revealed a decrease in the α-diversity (e.g., Shannon index and Inv_Simpson index) of the community during the domestication process. Microbial community dynamics were uncovered, with sequences affiliated to Achromobacter, Pseudomonas, and Rhodococcus identified as the most abundant taxonomic groups. From the consortium, five pure isolates were obtained; however, it was found that only one strain of Rhodococcus could degrade chloroxylenol. Strain Rhodococcus sp. DMU2021 could degrade chloroxylenol efficiently under the conditions of temperature 30–40 °C, and neutral/alkaline conditions. Chloroxylenol was toxic to strain DMU2021 and triggered both enzymatic and non-enzymatic antioxidant systems in response. This study provides novel insights into the biodegradation process of chloroxylenol, as well as valuable bioresources for bioremediation. [ABSTRACT FROM AUTHOR]

Pathogenic Rhodococcus equi release the virulence‐associated protein A (VapA) within macrophage phagosomes. VapA permeabilizes phagosome and lysosome membranes and reduces acidification of both compartments. Using biophysical techniques, we found that VapA interacts with model membranes in four steps: (i) binding, change of mechanical properties, (ii) formation of specific membrane domains, (iii) permeabilization within the domains, and (iv) pH‐specific transformation of domains. Biosensor data revealed that VapA binds to membranes in one step at pH 6.5 and in two steps at pH 4.5 and decreases membrane fluidity. The integration of VapA into lipid monolayers was only significant at lateral pressures <20 mN m−1 indicating preferential incorporation into membrane regions with reduced integrity. Atomic force microscopy of lipid mono‐ and bilayers showed that VapA increased the surface heterogeneity of liquid disordered domains. Furthermore, VapA led to the formation of a new microstructured domain type and, at pH 4.5, to the formation of 5 nm high domains. VapA binding, its integration and lipid domain formation depended on lipid composition, pH, protein concentration and lateral membrane pressure. VapA‐mediated permeabilization is clearly distinct from that caused by classical microbial pore formers and is a key contribution to the multiplication of Rhodococcus equi in phagosomes. [ABSTRACT FROM AUTHOR]

Emergent strategies to valorize lignin, an abundant but underutilized aromatic biopolymer, include tandem processes that integrate chemical depolymerization and biological catalysis. To date, aromatic monomers from C–O bond cleavage of lignin have been converted to bioproducts, but the presence of recalcitrant C–C bonds in lignin limits the product yield. A promising chemocatalytic strategy that overcomes this limitation involves phenol methyl protection and autoxidation. Incorporating this into a tandem process requires microbial cell factories able to transform the p-methoxylated products in the resulting methylated lignin stream. In this study, we assessed the ability of Rhodococcus jostii RHA1 to catabolize the major aromatic products in a methylated lignin stream and elucidated the pathways responsible for this catabolism. RHA1 grew on a methylated pine lignin stream, catabolizing the major aromatic monomers: p-methoxybenzoate (p-MBA), veratrate, and veratraldehyde. Bioinformatic analyses suggested that a cytochrome P450, PbdA, and its cognate reductase, PbdB, are involved in p-MBA catabolism. Gene deletion studies established that both pbdA and pbdB are essential for growth on p-MBA and several derivatives. Furthermore, a deletion mutant of a candidate p-hydroxybenzoate (p-HBA) hydroxylase, ΔpobA, did not grow on p-HBA. Veratraldehyde and veratrate catabolism required both vanillin dehydrogenase (Vdh) and vanillate O-demethylase (VanAB), revealing previously unknown roles of these enzymes. Finally, a ΔpcaL strain grew on neither p-MBA nor veratrate, indicating they are catabolized through the β-ketoadipate pathway. This study expands our understanding of the bacterial catabolism of aromatic compounds and facilitates the development of biocatalysts for lignin valorization. IMPORTANCE Lignin, an abundant aromatic polymer found in plant biomass, is a promising renewable replacement for fossil fuels as a feedstock for the chemical industry. Strategies for upgrading lignin include processes that couple the catalytic fractionation of biomass and biocatalytic transformation of the resulting aromatic compounds with a microbial cell factory. Engineering microbial cell factories for this biocatalysis requires characterization of bacterial pathways involved in catabolizing lignin-derived aromatic compounds. This study identifies new pathways for lignin-derived aromatic degradation in Rhodococcus, a genus of bacteria well suited for biocatalysis. Additionally, we describe previously unknown activities of characterized enzymes on lignin-derived compounds, expanding their utility. This work advances the development of strategies to replace fossil fuel-based feedstocks with sustainable alternatives. [ABSTRACT FROM AUTHOR]

Biodegradation of phenol is an effective method for removing this toxicant from contaminated sites. Phenol is a toxic compound for living cells, so many bacteria degrade phenol in relatively low concentrations, up to 0.75 g L−1. The Rhodococcus opacus strain 1CP is an effective destructor of a wide range of pollutants. In the absence of a carbon source in the medium, cells of the R. opacus 1CP strain easily form cyst-like resting cells (CLC). The purpose of this work was to evaluate the viability of cells during long-term storage and the efficiency of the process of phenol destruction by R. opacus 1CP cells germinating after dormancy. Resting cells were obtained by simple cultivation in a rich medium followed by storage under static conditions. This is a simple approach to obtain a large amount of biomass. Decomposition of phenol proceeded via catechol followed by ortho-cleavage of aromatic ring. The induction of three phenol hydroxylases was detected by RT-PCR in cells germinated in a mineral medium with phenol as the carbon source. The stability of the genome of cells germinating after dormancy is shown by box-PCR. Dormant R. opacus 1CP cells, both suspended and immobilized, can be directly used for the decomposition of phenol after 4–12 months storage. In addition to phenol, after 9 months of storage, immobilized germinating cells easily metabolized 4-chlorophenol and 2,4,6-trichlorophenol. The results demonstrate a potential and simple approach toward achieving long-term storage of cells for further use in bioremediation. [ABSTRACT FROM AUTHOR]