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Pistachio bushy top syndrome (PBTS) is a serious problem for pistachio growers in the western United States, but the cause of this disorder remains controversial. Recently, it was proposed that the Rhodococcus species R. fascians and R. corynebacterioides caused PBTS outbreaks in 2011 and 2015. To investigate the association of Rhodococcus spp. with PBTS in California's pistachio-growing region, Rhodococcus-like isolates were collected from diverse hosts and environments, including pistachio nurseries and orchards. Whole genome sequence analysis of 231 isolates revealed their evolutionary relationships and identified six Rhodococcus species. Combined with data on geography and host of origin, the data reveal that Rhodococcus generally, and R. fascians specifically, is ubiquitous in nature, frequently occurring in both symptomatic and asymptomatic pistachio trees and on other woody and native species. Core gene and single nucleotide polymorphism-based phylogenies and pangenome analyses differentiate R. fascians into distinct genotypes. Although we found examples of common genotypes shared between nurseries and orchards, the observed patterns are most consistent with an environmental source of strains and do not support a scenario in which individual nurseries are point sources of Rhodococcus. Moreover, none of the collected strains harbored known virulence genes, calling into question the role of these common environmental bacteria in causing PBTS. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Little is known about the prevalence, functionality and ecological roles of temperate phages for members of the mycolic acid producing bacteria, the Mycolata. While many lytic phages infective for these organisms have been isolated, and assessed for their suitability for use as biological control agents of activated sludge foaming, no studies have investigated how temperate phages might be induced for this purpose. Bioinformatic analysis using the PHAge Search Tool (PHAST) on Mycolata whole genome sequence data in GenBank for members of the genera Gordonia, Mycobacterium, Nocardia, Rhodococcus, and Tsukamurella revealed 83% contained putative prophage DNA sequences. Subsequent prophage inductions using mitomycin C were conducted on 17 Mycolata strains. This led to the isolation and genome characterization of three novel Caudovirales temperate phages, namely GAL1, GMA1, and TPA4, induced from Gordonia alkanivorans, Gordonia malaquae, and Tsukamurella paurometabola, respectively. All possessed highly distinctive dsDNA genome sequences.

A new pluramycin-class polyketide, rausuquinone (1), and its known congener hydramycin (2) were isolated from the culture extract of the deep-sea water-derived Rhodococcus sp. RD015140. Compound 1 possesses a γ-pyrone-fused anthraquinone core with a 3-butene-1,2-diol side chain. Structures of 1 was determined by extensive analysis of 1D and 2D NMR spectroscopic data. Compound 1 showed antimicrobial activity against Gram-positive bacteria. This is the first discovery of aromatic polyketides from the genus Rhodococcus.

The development of effective measures for the remediation of lindane contaminated sites is the need of the hour. In this study, a potent lindane degrading bacteria, identified as Rhodococcus rhodochrous NITDBS9 was isolated from an agricultural field of Odisha that could utilize up to 87% of 100 mg L−1 lindane when grown under liquid culture conditions in mineral salt media in 10 days. The bacteria could produce biofilm in lindane-containing media. Rhodococcus rhodochrous NITDBS9 was further characterized for its plant growth-promoting properties and it was found that the bacteria showed abilities for phytohormone, ammonia and biosurfactant production, etc. This could be beneficial for the bioremediation and improvement of crop production in contaminated sites. Ecotoxicity studies carried out for lindane, and its degradation products in mung bean and mustard seeds showed a reduction in toxicity of lindane after treatment with NITDBS9. NITDBS9 was used with a previously isolated potent lindane degrading strain Paracoccus sp. NITDBR1 in a dual mixed culture for the enhanced removal of lindane in the liquid system i.e. up to 93% in 10 days. Cytotoxicity studies were conducted with lindane before and after treatment with the single and dual mixed cultures on human skin fibroblast and HCT116 cell lines. They revealed a significant reduction in toxicity of lindane after it was bioremediated with the single and dual mixed cultures. Therefore, our proposed strategy could be efficiently used for the detoxification of the lindane-contaminated system, and further work should be done to study the use of these cultures in the contaminated soil system.

In order to study some aspects of pathogenesis of Rhodococcus equi, 60 white Swiss mice were used. They were randomly divided into 2 groups. The 1s' group (40 animals) was inoculated subcutaneously with a dose of 4x10° CFU .of R.equi while the 2nd group was kept as a control. Four animals from the 1st group and 2 animals from the 2nd group were sacrified at day, 1,2,4,8,12,16,20,24,28 and 30 postinoculation (P.I) Six animals of 1stgroup were died during the first and second days P.I. Microscopical examination showed acute to subacute suppurative inflammation in the liver, lung and spleen at I to 4 days PI. While pyogranulomatous lesions and epithelioid granuloma were seen in liver, lungs and spleen at 4 to 24 days PI R.equi was isolated liver, lungs, spleen, kidney and brain in the first day PI. The bacteria persisted in the spleen from and brain up to 20th day, in the liver up to 24" day while in the lungs, and kidney bacterial isolation continuous till 28th day PI.

The development of microbial cell factories requires robust synthetic biology tools to reduce design uncertainty and accelerate the design-build-test-learn process. Herein, we developed a suite of integrative genetic tools to facilitate the engineering of Rhodococcus, a genus of bacteria with considerable biocatalytic potential. We first created pRIME, a modular, copy-controlled integrative-vector, to provide a robust platform for strain engineering and characterizing genetic parts. This vector was then employed to benchmark a series of strong promoters. We found PM6 to be the strongest constitutive rhodococcal promoter, 2.5- to 3-fold stronger than the next in our study, while overall promoter activities ranged 23-fold between the weakest and strongest promoters during exponential growth. Next, we used an optimized variant of PM6 to develop hybrid-promoters and integrative vectors to allow for tetracycline-inducible gene expression in Rhodococcus. The best of the resulting hybrid-promoters maintained a maximal activity of ∼50% of PM6 and displayed an induction factor of ∼40-fold. Finally, we developed and implemented a uLoop-derived Golden Gate assembly strategy for high-throughput DNA assembly in Rhodococcus. To demonstrate the utility of our approaches, pRIME was used to engineer Rhodococcus jostii RHA1 to grow on vanillin at concentrations 10-fold higher than what the wild-type strain tolerated. Overall, this study provides a suite of tools that will accelerate the engineering of Rhodococcus for various biocatalytic applications, including the sustainable production of chemicals from lignin-derived aromatics.

Plasmid-mediated bioaugmentation has potential application in the cleanup of recalcitrant environmental pollutants. In this study, we examined the influence of various contaminants (in different categories or different amounts) as a selection pressure on the spread of catabolic plasmids within an activated sludge bacteria community bioaugmented with Rhodococcus sp. strain p52 harboring pDF01 and pDF02. The distinguishable genera of transconjugants were isolated under the stresses of phenanthrene, dibenzothiophene, and dibenzo-p-dioxin. The three contaminants exerted different degrees of influence on the activated sludge bacteria bearing the catabolic plasmids. The relatively high ratios of transconjugant-bearing catabolic plasmids were detected in the reactor fed with dibenzo-p-dioxin. As dibenzo-p-dioxin from 10 to 80 mg/L was fed into the reactors, the ratios of transconjugant-bearing catabolic plasmids increased. Additionally, levels of ROS and extracellular LDH of activated sludge bacteria in the contaminants-fed reactors increased, comparing with that in the control reactor, indicating that the contaminants exerted toxicity which promoted the cell membrane permeability of the activated sludge bacteria. Our study provides a characterization of the recalcitrant contaminants as a selection pressure that can modulate catabolic plasmid transfer during genetic bioaugmentation for the removal of contaminants.

Rhodococcus spp. strains are widespread in diverse natural and anthropized environments thanks to their high metabolic versatility, biodegradation activities, and unique adaptation capacities to several stress conditions such as the presence of toxic compounds and environmental fluctuations. Additionally, the capability of Rhodococcus spp. strains to produce high value-added products has received considerable attention, mostly in relation to lipid accumulation. In relation with this, several works carried out omic studies and genome comparative analyses to investigate the genetic and genomic basis of these anabolic capacities, frequently in association with the bioconversion of renewable resources and low-cost substrates into triacylglycerols. This review is focused on these omic analyses and the genetic and metabolic approaches used to improve the biosynthetic and bioconversion performance of Rhodococcus. In particular, this review summarizes the works that applied heterologous expression of specific genes and adaptive laboratory evolution approaches to manipulate anabolic performance. Furthermore, recent molecular toolkits for targeted genome editing as well as genome-based metabolic models are described here as novel and promising strategies for genome-scaled rational design of Rhodococcus cells for efficient biosynthetic processes application.

Isolation of culturable actinobacteria from coastal wetlands and screening of their potential biological activities are important for the development of new marine natural products. We collected and isolated 109 actinobacteria from the Sanggou Bay and the Swan Lake wetlands, in the coast of Weihai, China. Of the 109 isolates, 104 had antimicrobial activity against at least one indicator strain. The 35 strains with the strongest inhibitory effects were chosen for the screening of the biosynthesis gene clusters of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS). Four strains with the PKS gene, six strains with the NRPS gene, and three strains with both genes were detected. Eight of the 13 strains with PKS or NRPS genes belong to the genera Streptomyces, and other strains belonged to genus Micromonospora, Nocardiopsis, Rhodococcus, Saccharomonospora, and Staphylococcus. Our results reveal that the culturable actinobacteria isolated from coastal wetlands showed broad-spectrum antimicrobial activities, and some strains with antimicrobial activities possessed PKS and NRPS genes. Thus, culturable actinobacteria from coastal wetlands may contain potential new bioactive substances.

The article presents the results of allergic and bacteriological studies of cattle from a tuberculosis-free farm. The presence of cattle reacting to an allergen from atypical mycobacteria was established in three allergic simultaneous tests during 2019–2020. Based on the results obtained, the causative agent of tuberculosis and atypical mycobacteria were not isolated during the bacteriological examination of a biological material from animals slaughtered for diagnostic purposes (n = 17), as well as soil (n = 5) and straw (n = 3) samples. However, microorganisms of the genera Nocardia (n = 2), Rhodococcus (n = 10), and Actinomyces (n = 5) were isolated from the biomaterial according to the results of microscopy, culture and biochemical tests. These microorganisms were also isolated from the soil and straw samples. Short-term non-specific reactions in cattle to mycobacterial allergens were due to the persistence and circulation of the aforementioned microorganisms closely related to mycobacteria. It was determined that the genera Nocardia and Rhodococcus are sensitive to the 1.0%, 2.0%, 3.0% solutions of glutaraldehyde, formaldehyde and sodium hydroxide. Thus, it is necessary to take into account the epizootic situation as to the presence of nocardioform microorganisms in the herd during routine allergic studies, as well as in case of differentiation between specific reactions and paraallergic and pseudoallergic ones. It is necessary to carry out comprehensive systematic studies of livestock and feed quality assessment. For the purpose of disinfection, glutaraldehyde and formaldehyde at a concentration of 1.0% are effective in destroying microorganisms of the genera Nocardia and Rhodococcus with 3-hour exposure or more.

Enantiopure esomeprazole is an important drug in the treatment of gastric ulcer. The asymmetric sulfoxidation of omeprazole thioether was catalyzed by immobilized cells of a mutant of Rhodococcus rhodocrous ATCC 4276 to synthesize esomeprazole. The bioreaction was carried out in a biphasic system (chloroform-water), at a high substrate concentration (200 mM), and optimized using response surface methodology (RSM). The optimal yield of esomeprazole obtained was 94.8% with e.e. (>99%) without the formation of the sulfone form as a byproduct, under the optimal conditions: the concentration of immobilized cells, 283.5 g/L, the incubation temperature, 37.05 °C, and pH of phosphate buffer, 7.35, respectively. A quadratic polynomial model was developed with R2 of 0.9998, which indicates that the model predicts the observed data with very high accuracy. The mutant exhibited a high enantioselective activity and substrate and product tolerance. The small size of immobilized cell beads (0.5–1 mm) creates a large reaction interface. The aerated flask provides enough oxygen for a high concentration of cells. The significant improvement of substrate tolerance may mainly be attributed to employing the chloroform-water biphasic system because organic substrates may be partitioned in the organic phase, eliminating potential damage and inhibition to cells. Based on the above, the asymmetric sulfoxidation catalyzed by immobilized bacterial cells is therefore more promising for efficient synthesis of chiral sulfoxides.

2,4-Dinitrophenol (2,4-DNP) is an important organic environmental pollutant that is highly toxic to all forms of living organisms. A gram-positive strain (designated XM24D) was isolated from 2,4-DNP-contaminated soil by an enrichment technique. The study was designed to analyze the ability of XM24D to degrade 2,4-DNP and its analogs and to reveal the degradation pathways of these aromatic compounds. The degradation ability of XM24D was tested by a growth experiment. 2,4-DNP and its analog degradation pathways were predicted by genome and comparative transcriptome sequencing. Growth profiles showed that XM24D was able to utilize 2,4-DNP as the sole source of carbon, nitrogen and energy. Analogs of 2,4-DNP, including 4-nitrophenol (PNP) and 2-chloro-4-nitrophenol (2C4NP), can also be degraded by XM24D. Genome analysis showed that the XM24D genome contains two chromosomes with a combined size of 9.08 Mb and an average GC content of 67.07 %. Average nucleotide identity analysis indicated that Rhodococcus imtechensis RKJ300 is the most closely related strain to XM24D. Comparative transcriptome analysis revealed that the 2,4-DNP/PNP/2C4NP degradation pathway in XM24D is highly similar in sequence and organization to the 2,4-DNP degradation pathway in Rhodococcus opacus HL PM-1, the PNP degradation pathway in Rhodococcus opacus SAO101 and the 2C4NP degradation pathway in Rhodococcus imtechensis RKJ300. These results suggested that 2,4-DNP/PNP/2C4NP was degraded via the 2,4-dinitrocyclohexanone/4-nitrocatechol/hydroxyquinol pathway in XM24D. Genomic and transcriptomic information on XM24D provides a valuable reference for further investigating the evolutionary characteristics of nitrophenol degradation pathways in microorganisms.

Introduction. The microbiota of the gastrointestinal tract (GIT) plays an essential role in maintaining human health. Many factors, including industrial pollutions with biotechnological strains of microbes, can affect the normal balance of intestinal microbiota. The biotechnological industry nowadays produces a wide range of products for medical and veterinary use, agriculture, food, chemical industries, etc. To develop hygienic standards that regulate the possible adverse effect of biotechnological strains of microorganisms on workers’ health, the intestinal microflora of rats in the experiment can be studied. The data obtained were used as the basic concept in elaborating state sanitary standards for limitations of the concentrations of biotechnological strains of microorganisms in the ambient air of the working area and settlements’ atmosphere. Materials and methods. We have tested 52 strains of microorganisms applied in biotechnology as producers of a variety of biological substances. They included members of different taxonomic groups: gram-positive and gram-negative bacteria, actinomycetes, molds, and yeasts. The experiments were carried out on conventional male and female white rats (290-320 g, body weight). Each test and control group of animals included eight animals. The strains of microorganisms mentioned above were given to animals by inhalation of minimal effective doses of microbes in the concentrations of 10 3 -10 8 CFU/m 3 during one month. To demonstrate possible adverse effects to gut microflora, the routine bacteriological examination of animal feces was performed. To do this, after the priming, the 10-fold dilutions of animal feces in sterile saline were inoculated onto a set of general-purpose and selective culture media for Enterobacteriaceae members, staphylococci, enterococci, clostridia, bifidobacteria, lactobacilli, and fungi, with subsequent identification of the genus of the isolated microorganism. After that, the concentrations of microorganisms were calculated and measured in lg of CFU/g of feces. The Institutional Ethical Committee of Animal Care and Use of the Pirogov Russian National Research Medical University approved all procedures involving animals. The results of experiments were analyzed with a simple t-test using Statistica (v.6.0, Stat Soft, USA) and Microsoft Office Excel 2007. Results were considered statistically significant when p < 0.05. Results. The most notable changes in the composition of the intestinal microbiota were observed after inhaling of yeasts of genus Candida at the level of 10 3 –10 4 CFU/m 3 and in cases of exposure to molds (Aspergillus awamori, Penicillium funiculosum, and Tolypocladium cylindrosporum) in the concentration of 2•10 4 CFU/m 3 , and gram-negative bacteria of the genus Alcaligenes and genus Pseudomonas at 5•10 5 CFU/m 3 . We observed a dramatic decrease of Escherichia coli and the increase of gram-positive bacteria (staphylococci, enterococci). For some genera of biotechnological strains, a significant decline in the content of lactobacilli was also shown. On the other hand, Rhodococcus did not cause any disturbances even at high concentrations in the ambient air. Conclusion. The obtained data can be used to develop biosafety and hygienic standards for industrial microbes to help decrease or minimize the occupational risk of infection or undesirable allergic effect when working with biotechnological strains of microbes in the ambient air of residential areas.

Цель исследования – изучение возможности применения микробиологического препарата, изначально разработанного для переработки нефтепродуктов, в качестве средства, утилизирующего полициклические ароматические углеводороды (ПАУ) в техногенно-загрязнённых почвах промышленно-урбанизированных территорий. Методы. В ходе проведённых исследований проанализированы известные способы деструкции ПАУ и наиболее распространённые способы рекультивации, применяемые в настоящее время. Показано, что задача улучшения качества загрязнённых почв может быть решена с помощью препарата, содержащего неспорообразующие микроорганизмы родов Candida, Pseudomonas и Rhodococcus, разработанного в ООО «НПО Биотехсоюз» и ранее не использовавшегося для утилизации ПАУ. Эффективность данного препарата продемонстрирована на примере 64 образцов почвы, отобранных по 4 направлениям в радиусе 5 км от двух промышленных предприятий города Москвы и Московской области (мусоросжигательный завод No 3 и НПО «Луч», город Подольск, производящий металлические изделия, соответственно). Результаты представлены в виде пространственных схем, демонстрирующих текущие уровни загрязнения почв (не обработанных препаратом) и ожидаемые уровни загрязнения (после обработки). Зонирование исследованных территорий основано на использовании ранее предложенного одним из авторов статьи индекса общего токсического воздействия биологически доступных полициклических ароматических углеводородов, который учитывает не только концентрации отдельных загрязнителей в почве, но также степень их воздействия на живые организмы. Выводы. Выявлены некоторые общие закономерности и особенности переработки ПАУ микроорганизмами, относящимися к вышеперечисленным родам. Показано, что степень переработки этих соединений зависит от их молекулярного строения.

Emission of sulfur-based compounds create problem for environment as well as for on human health. To remove sulfur compounds from sulfur-rich fossil fuel, various techniques have been proposed and studied. Based on problem associated with environment as well as for human health, current study focused on DBT removal using novel Rhodococcus spp. (SL-9). Furthermore, study focused on kinetic modeling and simulation of biodesulfurization process for calculating the efficiency of newly isolated bacteria Rhodococcus spp. (SL-9), effect of cell growth, and degradation rate for DBT (dibenzothiophene). Rhodococcus spp. (SL-9) degrade 0.39 mM DBT within 7 days via 4S pathway. The efficiency of Rhodococcus spp. (SL-9) for maximum degradation and conversion of DBT into 2-HBP (2-hydroxybiphenyl) at optimized parameters are 30 °C, 7 pH, and glucose as carbon source. It has been observed through the study that an increase in degradation rate of model DBT compound at 3 mM about 70 hr of incubation period. Rhodococcus sp-SL-9 shows maximum rate of growth about 0.067 h−1 along with biodegradation of DBT rate about 0.89 h−1, which endorses its application in coal desulfurization process.

Rhodococcus bacteria are a promising platform for biodegradation, biocatalysis, and biosynthesis, but the use of rhodococci is hampered by the insufficient number of both platform strains for expression and promoters that are functional and thoroughly studied in these strains. To expand the list of such strains and promoters, we studied the expression capability of the Rhodococcus rhodochrous M33 strain, and the functioning of a set of recombinant promoters in it. We showed that the strain supports superexpression of the target enzyme (nitrile hydratase) using alternative inexpensive feedings-acetate and urea-without growth factor supplementation, thus being a suitable expression platform. The promoter set included Ptuf (elongation factor Tu) and Psod (superoxide dismutase) from Corynebacterium glutamicum ATCC13032, Pcpi (isocitrate lyase) from Rhodococcus erythropolis PR4, and Pnh (nitrile hydratase) from R. rhodochrous M8. Activity levels, regulation possibilities, and growth-phase-dependent activity profiles of these promoters were studied in derivatives of the M33 strain. The activities of the promoters were significantly different (Pcpi < Psod ≪ Ptuf < Pnh), covering 103-fold range, and the most active Pnh and Ptuf produced up to a 30-50% portion of target protein in soluble intracellular proteins. On the basis of the mRNA quantification and amount of target protein, the production level of Pnh was positioned close to the theoretical upper limit of expression in a bacterial cell. A selection method for the laboratory evolution of such active promoters directly in Rhodococcus was also proposed. Concerning regulation, Ptuf could not be regulated (2-fold change), while others were tunable (6-fold for Psod, 79-fold for Pnh, and 44-fold for Pcpi). The promoters possessed four different activity profiles, including three with peak of activity at different growth phases and one with constant activity throughout the growth phases. Ptuf and Pcpi did not change their activity profile under different growth conditions, whereas the Psod and Pnh profiles changed depending on the growth media. The results allow flexible construction of Rhodococcus strains using the studied promoters, and demonstrate a valuable approach for complex characterization of promoters intended for biotechnological strain construction.

It was established that groEL genes can be used as molecular genetic markers for species identification of Rhodococcus bacteria. A restriction analysis scheme was developed for the PCR products of groEL genes using restriction enzymes BglI, NarI, SfiI, SinI, and RseI to identify the species of natural Rhodococcus bacteria. Fifty-two genome loci determining the resistance to stressful environmental condition were annotated in genome of R. pyridinivorans strain 5Ap (i.e. 49 structural and 4 regulatory genes that determine the synthesis of 23 heat shock proteins, 9 universal stress proteins, 17 P450 cytochromes). The unique nucleotide sequences encoding the synthesis of the heat shock protein DnaK (1 plasmid gene) and P450 cytochromes (2 chromosomal and 1 plasmid) were found among these genes. Thus, they can be used for molecular typing of the biotechnological R. pyridinivorans strain 5Ap.

Rhodococcus erythropolis S43 is an arsenic-tolerant actinobacterium isolated from an arsenic contaminated soil. It has been shown to produce siderophores when exposed to iron-depleting conditions. In this work, strain S43 was shown to have the putative heterobactin production cluster htbABCDEFGHIJ(K). To induce siderophore production, the strain was cultured in iron-depleted medium in presence and absence of sodium arsenite. The metabolites produced by S43 in the colorimetric CAS and As-mCAS assays, respectively, showed iron- and arsenic-binding properties reaching a chelating activity equivalent to 1.6 mM of desferroxamine B in the supernatant of the culture without arsenite. By solid-phase extraction and two subsequent HPLC separations from both cultures, several fractions were obtained, which contained CAS and As-mCAS activity and which were submitted to LC-MS analyses including fragmentation of the major peaks. The mixed-type siderophore heterobactin B occurred in all analyzed fractions, and the mass of the "Carrano heterobactin A" was detected as well. In addition, generation of a molecular network based on fragment spectra revealed the occurrence of several other compounds with heterobactin-like structures, among them a heterobactin B variant with an additional CH2O moiety. 1H NMR analyses obtained for preparations from the first HPLC step showed signals of heterobactin B and of "Carrano heterobactin A" with different relative amounts in all three samples. In summary, our results reveal that in R. erythropolis S43, a pool of heterobactin variants is responsible for the iron- and arsenic-binding activities. KEY POINTS: • Several heterobactin variants are the arsenic-binding compounds in Rhodococcus erythropolis S43. • Heterobactin B and the compound designated heterobactin A by Carrano are of importance. • In addition, other heterobactins with ornithine in the backbone exist, e.g., the new heterobactin C.

The bacterial diversity retained in Al/Fe-pillared interlayered clay and Fe-functionalized granular activated carbon absorbent was characterized after their saturation with mature landfill leachate either before and after a tertiary, catalytic wet peroxide oxidation treatment. The 454 pyrosequencing analyses showed bacteria belonging to Phyla: Proteobacteria, Bacteroidetes and Actinobacteria. Flavobacterium was the most representative genus detected in three out of four studied adsorbents: the pillared clay before the catalytic oxidation and the granular activated carbon at both stages before and after the catalytic oxidation, whereas Haliscomenobacter, Rhodococcus Pseudomonas, Thermomonas, Aequorivita, and Acidovorax, were also found according to the type of absorbent. It was demonstrated the efficiency of the oxidizing treatment in the elimination of the immobilized leachate’s microorganisms when in the presence of the Al/Fe-pillared clay adsorbent; this exhibited the highest catalytic response, since no DNA was detected on this material after its catalytic treatment. Only in the case of the functionalized activated carbon, it was found the presence of microorganisms of environmental interest after the advanced oxidation stage. Although the bacterial community detected in the activated carbon after oxidizing treatment showed lower voltage output than that one before oxidation, such resistant bacteria could be potentially useful driving microbial fuel cells for degradation of more complex and harmful substrates. Thus, further studies should be done assessing the degradation of toxic and hazardous substances by microbial fuel cells in the presence of catalytic wet peroxide oxidation- and other advanced oxidation-resistant bacteria, including contaminants of emerging concern widely spread in wastewaters.

Humic substances (HS) in soil are widely distributed in cold environments and account for a significant fraction of soil's organic carbon. Bacterial strains (n = 281) were isolated at 15 °C using medium containing humic acids (HA), a principal component of HS, from a variety of polar soil samples: 217 from the Antarctic and 64 from the Arctic. We identified 73 potential HA-degrading bacteria based on 16S rRNA sequence similarity, and these sequences were affiliated with phyla Proteobacteria (73.9%), Actinobacteria (20.5%), and Bacteroidetes (5.5%). HA-degrading strains were further classified into the genera Pseudomonas (51 strains), Rhodococcus (10 strains), or others (12 strains). Most strains degraded HA between 10 and 25 °C, but not above 30 °C, indicating cold-adapted degradation. Thirty unique laccase-like multicopper oxidase (LMCO) gene fragments were PCR-amplified from 71% of the 73 HA-degrading bacterial strains, all of which included conserved copper-binding regions (CBR) I and II, both essential for laccase activity. Bacterial LMCO sequences differed from known fungal laccases; for example, a cysteine residue between CBR I and CBR II in fungal laccases was not detected in bacterial LMCOs. This suggests a bacterial biomarker role for LMCO to predict changes in HS-degradation rates in tundra regions as global climate changes. Computer-aided molecular modeling showed these LMCOs contain a highly-conserved copper-dependent active site formed by three histidine residues between CBR I and CBR II. Phylogenetic- and modeling-based methods confirmed the wide occurrence of LMCO genes in HA-degrading polar soil bacteria and linked their putative gene functions with initial HS-degradation processes.

Study of carbohydrate-active enzymes (CAZymes) can reveal information about the lifestyle and behavior of an organism. Rhodococcus species is well known for xenobiotic metabolism; however, their carbohydrate utilization ability has been less discussed till date. This study aimed to present the CAZyme analysis of two Rhodococcus strains, PAMC28705 and PAMC28707, isolated from lichens in Antarctica, and compare them with other Rhodococcus, Mycobacterium, and Corynebacterium strains. Genome-wide computational analysis was performed using various tools. Results showed similarities in CAZymes across all the studied genera. All three genera showed potential for significant polysaccharide utilization, including starch, cellulose, and pectin referring their biotechnological potential. Keeping in mind the pathogenic strains listed across all three genera, CAZymes associated to pathogenicity were analyzed too. Cutinase enzyme, which has been associated with phytopathogenicity, was abundant in all the studied organisms. CAZyme gene cluster of Rhodococcus sp. PAMC28705 and Rhodococcus sp. PAMC28707 showed the insertion of cutinase in the cluster, further supporting their possible phytopathogenic properties.

A bacterial strain that could effectively degrade DEHP was isolated from the activated sludge and identified as Bacillus sp. by DNA sequencing. The biochemical degradation pathway of DEHP was further analyzed by GC-MS, and the results showed that DEHP was first decomposed into phthalates (DBP). Diuretic sylycol (DEP) was then generated, and phthalates (PA) were generated by a continuous de-ehelateization reaction. Phthalic acid (PA) was oxidized, dehydrogenated, and decarboxylated into protocatechins. Protocatechins enter the TCA cycle through orthotopic ring opening. To enhance DEHP degradation, sodium alginate and calcium chloride were used as embedding and cross-linking materials, and the strain was immobilized. The immobilization conditions were optimized via an orthogonal experiment, and the results showed that the optimal immobilization conditions were SA mass fraction of 4%, CaCl2 mass fraction of 5%, ratio of bacteria to SA of 1:1, and the crosslinking time of 6 hours. The immobilized bacteria agent was further applied to MBR systems. The results showed that the removal rate of DEHP (5mg/L) in the system by immobilized bacteria was 91.9%, which is significantly higher than that of free bacteria. The 3, 4-dioxygenase gene and microbial community dynamics were analyzed by q-PCR and Illumina Miseq sequencing. The q-PCR results showed that the number of copies of 3, 4-dioxygenase gene in the immobilized system was significantly higher than that of free bacteria. Illumina Miseq sequencing results showed that Micromonospora, Rhodococcus, Bacteroides and Pseudomonas were the dominant generas in the MBR system. The analysis of bacterial community structure indicated that immobilization technology had a positive impact on the system stability. The results implied that this immobilized technique had potential applications in DEHP wastewater treatment.

The diversity and succession of microbial community and antioxidant activity present during the preparation of red raspberry Enzymes with and without starter cultures were investigated by high‐throughput sequencing of 16S rRNA and ITS1 genes and correlation analysis of the microbial diversity and antioxidant activity. The results showed that the sample inoculated with mixed fermentation had higher antioxidant activity than the sample without inoculated fermentation. The antioxidant capacity of red raspberry Enzymes increased significantly as the fermentation time increased. Firmicutes and Ascomycota were the predominant phyla of bacteria and fungi in all samples. At the genus level, Rhodococcus and Lactobacillus were the predominating bacteria throughout the fermentation process. The genus Kodamaea dominated the fungal community of early‐fermentation samples with microbial inoculated fermentation. Candida spp. grew rapidly in the late stage of fermentation in the samples with spontaneous fermentation. Unweighted pair‐group and PCA analysis revealed that the microbiota structures differed between the two groups. RDA and CCA showed that Rhodococcus and Kodamaea had positive effects on the DPPH scavenging ability and other antioxidant indicators, and the total phenol content had a significant and positive correlation coefficient with Gluconobacter. The results indicated that the fermentation by microorganisms significantly improves the oxidation resistance and helps to improve the quality of the red raspberry Enzymes., Red raspberry Enzymes inoculated with mixed fermentation had higher antioxidant activity than the sample without inoculated fermentation. The microbiota structures differed between the two samples. The results indicated that the fermentation by microorganisms significantly improves the oxidation resistance and helps to improve the quality of the Enzymes.

Background Evidence regarding the efficacy of equine hyperimmune plasma to prevent pneumonia in foals caused by Rhodococcus equi is limited and conflicting. Hypothesis Opsonization with R. equi‐specific hyperimmune plasma (HIP) will significantly increase phagocytosis and decrease intracellular replication of R. equi by alveolar macrophages (AMs) compared to normal plasma (NP). Animals Fifteen adult Quarter Horses were used to collect bronchoalveolar lavage cells. Methods In the first experiment, AMs from 9 horses were pretreated (incubated) with either HIP, NP, or media only (control) and then infected with nonopsonized R. equi. In a second experiment, AMs from 6 horses were infected with R. equi either opsonized with HIP or opsonized with NP. For both experiments, AMs were lysed at 0 and 48 hours and the number of viable R. equi quantified by culture were compared among groups using linear mixed‐effects modeling with significance set at P

Objectives Study of the rifampicin resistance of Rhodococcus equi strains isolated from French horses over a 20-year period. Methods Rifampicin susceptibility was tested by disk diffusion (DD) and broth macrodilution methods, and rpoB gene sequencing and MLST were performed on 40 R. equi strains, 50.0% of which were non-susceptible to rifampicin. Results Consistency of results was observed between rifampicin susceptibility testing and rpoB sequencing. Strains non-susceptible to rifampicin by DD had a substitution at one of the sites (Asp516, His526 and Ser531) frequently encountered and conferring rifampicin resistance. High-level resistance was correlated with His526Asp or Ser531Leu substitutions; low-level resistance was correlated with Asp516Tyr substitution, a novel substitution for R. equi. Strains susceptible to rifampicin by DD showed no substitution in the three sites, except for two strains carrying, respectively, the His526Asn and Asp516Val substitutions (previously correlated with low-level rifampicin resistance). Both strains were isolated from an animal from which ten other strains were also isolated and found to be rifampicin-non-susceptible by DD. MLST showed the presence of 10 STs (including the novel ST43), but no association was observed with rifampicin resistance. Conclusions This study confirms that certain substitutions in RpoB are more likely to confer high- or low-level rifampicin resistance, describes a new substitution conferring rifampicin resistance in R. equi and suggests non-clonal dissemination of rifampicin-resistant strains in France. Standard DD may miss strains with a low-level rifampicin-resistant substitution; further studies are needed to remedy the absence of R. equi-specific clinical breakpoints.

The genusRhodococcuscontains several species with agricultural, biotechnological and ecological importance. Within this genus, many phyllosphere, rhizosphere and endosphere strains are plant growth promoting bacteria, whereas strains designated asR. fasciansare plant pathogens. In this study, we isolated 47Rhodococcusstrains from a range of herbaceous and woody plant species. Phylogenetic analysis based on 16S rDNA,gyrB andalkB genes was used to compare our strains with type strains ofRhodococcus. For most of our strains, sequence similarity of the 16S rDNA,gyrB andalkB regions to type strains ranged from 98–100 %. Results of the concatenated gene sequence comparisons identified 18 strains ofR. fasciansand three strains ofR. kroppenstedtii. The remaining strains were unclassified, and may represent novel species ofRhodococcus. Phylogenetic analysis based ongyrB sequences provided a more precise classification of our strains to species level than 16S rDNA sequences, whereas analysis ofalkB sequences was unable to identify strains with orange-coloured colonies to species level.

The use of microbial phosphotriesterases in the degradation of organophosphorus compounds employed as pesticides, plasticizers and petroleum additives is a sustainable alternative for bioremediation of water and soils, decontamination of particular foods and as poisoning antidote. Whole cells of six wild type microorganisms-Streptomyces phaeochromogenes, Streptomyces setonii, Nocardia corynebacterioides, Nocardia asteroides and two Arthrobacter oxydans-selected in our lab as phosphotriesterase sources, were further tested as biocatalysts in the hydrolysis of paraoxon, methyl paraoxon, methyl parathion, coroxon, coumaphos, dichlorvos and chlorpyrifos, highlighting 98% conversion of chlorpyrifos into its hydrolysis products using whole cells of S. phaeochromogenes at pH 8 and 40 °C. Immobilized whole cells and enzyme extracts were also assessed, observing as a general trend, that there is no significant variation in hydrolytic activity between them. These results suggest that according to the circumstances, immobilized whole cells (avoiding cellular disruption and centrifugation) or enzyme extracts (which can be handled more easily) could be used.

Oil spills are events that frequently lead to petroleum pollution. This pollution may cause stress to microbial communities, which require long adaption periods. Soil petroleum pollution is currently considered one of the most serious environmental problems. In the present work, processes occurring in the bacterial communities of three soil samples with different physicochemical characteristics, artificially polluted with 12% of crude oil, were investigated in 120-day laboratory experiment. It was found that the total petroleum hydrocarbon content did not decrease during this time; however, the proportion of petroleum fractions was altered. Petroleum pollution led to a short-term decrease in the bacterial 16S rRNA gene copy number. On the basis of amplicon sequencing analysis, it was concluded that bacterial community successions were similar in the three soils investigated. Thus, the phyla Actinobacteria and Proteobacteria and candidate TM7 phylum (Saccaribacteria) were predominant with relative abundances ranging from 35 to 58%, 25 to 30%, and 15 to 35% in different samples, respectively. The predominant operational taxonomic units (OTUs) after pollution belonged to the genera Rhodococcus and Mycobacterium, families Nocardioidaceae and Sinobacteraceae, and candidate class ТМ7-3. Genes from the alkIII group encoding monoxygenases were the most abundant compared with other catabolic genes from the alkI, alkII, GN-PAH, and GP-PAH groups, and their copy number significantly increased after pollution. The copy numbers of expressed genes involved in the horizontal transfer of catabolic genes, FlgC, TraG, and OmpF, also increased after pollution by 11-33, 16-63, and 11-71 times, respectively. The bacterial community structure after a high level of petroleum pollution changed because of proliferation of the cells that initially were able to decompose hydrocarbons, and in the second place, because proliferation of the cells that received these catabolic genes through horizontal transfer.

Microbial terephthalic acid (TPA) catabolic pathways are conserved among the few bacteria known to turnover this xenobiotic aromatic compound. However, to date there are few reported cases in which this pathway has been successfully expressed in heterologous hosts to impart efficient utilization of TPA as a sole carbon source. In this work, we aimed to engineer TPA conversion in Acinetobacter baylyi ADP1 via the heterologous expression of catabolic and transporter genes from a native TPA-utilizing bacterium. Specifically, we obtained ADP1-derived strains capable of growing on TPA as the sole carbon source using chromosomal insertion and targeted amplification of the tph catabolic operon from Comamonas sp. E6. Adaptive laboratory evolution was then used to improve growth on this substrate. TPA consumption rates of the evolved strains, which retained multiple copies of the tph genes, were ~0.2 g/L/h (or ~1 g TPA/g cells/h), similar to that of Comamonas sp. E6 and almost 2-fold higher than that of Rhodococcus jostii RHA1, another native TPA-utilizing strain. To evaluate TPA transport in the evolved ADP1 strains, we engineered a TPA biosensor consisting of the transcription factor TphR and a fluorescent reporter. In combination with whole-genome sequencing, the TPA biosensor revealed that transport of TPA was not mediated by the heterologous proteins from Comamonas sp. E6. Instead, the endogenous ADP1 muconate transporter MucK, a member of the major facilitator superfamily, was responsible for TPA transport in several evolved strains in which MucK variants were found to enhance TPA uptake. Furthermore, the IclR-type transcriptional regulator DcaS was identified as a repressor of mucK expression. Overall, this work presents an unexpected function of a native protein identified through gene amplification, adaptive laboratory evolution, and a combination of screening methods. This study also provides a TPA biosensor for application in ADP1 and identifies transporter variants for use in metabolic engineering applications focused on plastic upcycling of polyesters.

The halophilic consortium enriched from seagrass present in Jeddah coast region, Saudi Arabia, potently degraded different petroleum hydrocarbons such as phenanthrene (PHE), fluorene (FLU), pyrene (PY) and hexadecane (HD) under saline condition (4%). The halophilic consortium recorded complete degradation of PHE and FLU up to 400 ppm. At 600 ppm of PHE and FLU, the consortium revealed 98% and 99% degradation in 10 days. Further increase in concentration to 800 ppm showed slight decline in the percent degradation of PHE (92%) and FLU (95%) by the halophilic consortium. Pyrene was selected as model compound from high molecular weight hydrocarbons recorded 84% and 78% degradation by the consortium at 50 ppm and 100 ppm in 8 and 10 days, respectively. The halophilic consortium revealed complete degradation of HD at 0.5% and 1% concentration under saline condition. The consortium was able to degrade 93% and 71% of HD at 1.5 and 2% concentration in 6 and 8 days under saline condition. Under different high saline conditions such as 8%, 12%, 16% and 20%, the halophilic consortium exhibited PHE (95%, 90%, 85%, 65%) and FLU (97%, 92%, 86%, 66%) degradation in 7, 10, 14 and 18 days. Addition of urea and yeast extract at high salinity enhanced the biomass production and reduced the time taken for degradation. The surface tension of the biosurfactant produced by the consortium was 36 ± 1 mN/m. The treatment of hydrocarbons-contaminated boat fuel station wastewater in continuous stirred tank reactor recorded 92% Chemical Oxygen Demand removal in 40 days. The potential halophilic strains present in the consortium responsible for petroleum hydrocarbon degradation were identified as Marinobacter, Rhodococcus, Ochrobactrum, Martelella, Pseudomonas, Stenotrophomonas and Sedimentibacter.

Certain metal (loid)-resistant bacteria that inhabit the rhizosphere have shown to improve plant growth and tolerance under toxic metal stress. In this study, we tested if six native, arsenic-resistant and plant growth promoting bacteria (PGPB) were able to enhance soybean (Glycine max L.) growth and modulate arsenic (As) uptake. As a previous work, we tested all single isolates and all possible binary combinations without arsenic stress to identify the combinations that would have the greatest plant growth promoting effect. In this study, a screening assay was performed with only five inoculation options selected after first stage (Pseudomonas sp. AW4, Pseudomonas sp. AW6, AW4+AW6, Rhodococcus sp. AW3+Pseudomonas sp. AW5 and Enterobacter sp. AW1+AW6). In both stages, inoculation was implemented by imbibition of soybean seeds with bacterial suspensions, and plant growth was carried out in pots using perlite as substrate in a chamber with controlled conditions. In the third stage, we performed similar assays, under As stress, using the three most promising inoculation options (AW4, AW6 and AW3+AW5). Treatments were performed by irrigation with 25 μM arsenite (As3+), 25 μM arsenate (As5+), 25 μM equimolar As3+/As5+ solution or water (control). Biometric and biochemical parameters indicated that inoculation with Pseudomonas sp. AW4 significantly promoted soybean growth under As3+/As5+ treatment and did not modified As accumulation pattern. Further field studies are needed to determine if some of these inoculation options are useful to improve in situ soybean growth under arsenic stress and could become a tool for the development of sustainable agriculture in As-impacted environments.

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 GcoA(EP4)’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.

Abstract Bacteria belonging to Rhodococcus genus represent ideal candidates for microbial biotechnology applications because of their metabolic versatility, ability to degrade a wide range of organic compounds, and resistance to various stress conditions, such as metal toxicity, desiccation, and high concentration of organic solvents. Rhodococcus spp. strains have also peculiar biosynthetic activities that contribute to their strong persistence in harsh and contaminated environments and provide them a competitive advantage over other microorganisms. This review is focused on the metabolic features of Rhodococcus genus and their potential use in biotechnology strategies for the production of compounds with environmental, industrial, and medical relevance such as biosurfactants, bioflocculants, carotenoids, triacylglycerols, polyhydroxyalkanoate, siderophores, antimicrobials, and metal-based nanostructures. These biosynthetic capacities can also be exploited to obtain high value-added products from low-cost substrates (industrial wastes and contaminants), offering the possibility to efficiently recover valuable resources and providing possible waste disposal solutions. Rhodococcus spp. strains have also recently been pointed out as a source of novel bioactive molecules highlighting the need to extend the knowledge on biosynthetic capacities of members of this genus and their potential utilization in the framework of bioeconomy. Key points • Rhodococcus possesses promising biosynthetic and bioconversion capacities. • Rhodococcus bioconversion capacities can provide waste disposal solutions. • Rhodococcus bioproducts have environmental, industrial, and medical relevance.

The information on the use of microorganisms and mixed consortia in the biological desulfurization of coal is summarized. The ecological problems that accompany the burning of high-sulfur coals are shown, and the prospects of environmentally friendly and resource-saving biotechnological approaches to coal desulfurization are considered. Analysis of available literature indicates the enormous role of microorganisms of various taxonomic groups in the removal of inorganic and organic sulfur in coals. Mesophilic and moderately thermophilic acidophilic chemolithotrophic bacteria (ACB) of the genus Acidithiobacillus—A. ferrooxidans, A. thiooxidans, A. caldus, as well as some heterotrophic bacteria Bacillus subtilis and paenibacillus polymyxa—play the dominant role in the removal of inorganic sulfur. Mixed cultures and associations of mesophilic and thermophilic bacteria isolated from coal mines or from the coal surface structure are considered an effective tool in the biosulfurization of pyrite sulfur. The prospects of microbial desulfurization of organic coal sulfur with the use of heterotrophic microorganisms of the genera Pseudomonas, Sulfolobus, Rhodococcus, the fungi Agrocybe aegerita and Alterneria sp., the bacterial–fungal consortia Sulfolobus solfataricus and Phanerochaeta chrysosporium ME446, and the laccase enzyme of the basidiomycetes Trametes versicolor ATCC 20080 are examined.

Biodegradable materials, namely pure polylactide (PLA), poly (3,4-hydroxybutyrate) (PHB), poly(ε-caprolactone) (PCL) were investigated to assess their degradability by activated sludge. The study aimed at the isolation of biofilm-forming bacteria and the determination of their hydrolytic activity toward the PLA, PHB, and PCL with embedded PHMG derivatives. The biological oxygen demand and physical properties (tensile strength, water vapor permeability, surface structure) of materials indicated that PCL was the best biodegradable film. Aeromonas and Rhodococcus isolated from the polymers' surface during the process of decomposition showed the ability to form biofilms. The introduction of PHMG derivatives into PLA, PCL, and PHB films did not affect biofilm formation and hydrolase activity for most of the isolates. PHMG derivatives at the concentration of 1% disturbed the degradation process.

The conditions for the quantitative determination of acetylsalicylic acid (ASA) in Rhodococcus culture fluids via the reverse-phase high-performance liquid chromatography are developed. The rate of biodegradation process and the half-life of acetylsalicylic acid as a pharmaceutical substance and tablets are found.

Low-density polyethylene (LDPE) polymer is mainly used in the production of plastic bags and food packaging making up the largest volume of plastic pollutions. These polymers are potential substrates for bacteria in the bioremediation process. In this study, soil samples were collected from different plastic landfills in Iran and subsequently enriched in specific media (polyethylene as carbon source) to increase the population of LDPE-degrading bacteria. Seventeen PE-degrading bacteria, some novel, were isolated from Iranian soil samples and identified using 16S rDNA gene sequencing. These isolates were capable of degrading PE in a limited incubation period without the need for physicochemical pretreatments and comprise mostly of Actinobacteria which include the three genera of Streptomyces, Nocardia, and Rhodococcus. The isolates belonged to 17 different species of gram-positive Actinobacteria. In all, 11 species of the genus Streptomyces, 3 species of the genus Rhodococcus, and 3 species of the genus Nocardia were identified. The isolates with less than 99% 16S rRNA gene similarity to previously known species were suspected to be new species. Various analyses (weight loss, SEM, FTIR, and tensile strength test) to determine polyethylene biodegradation rate were carried out after a 60-day incubation period. Analysis of polyethylene biodegradation elucidates that Actinobacteria have a high ability for biodegradation of polyethylene-based plastics. Streptomyces sp. IR-SGS-T10 showed the highest reduction in weight of the LDPE film (1.58 mg/g/day) after 60 days of incubation without any pretreatments. Rhodococcus sp. IR-SGS-T11 shows the best reduction in the tensile property of LDPE film, while results from FTIR study for Streptomyces sp. IR-SGS-Y1 indicated a significant change in structural analysis.

Pretreatment can improve the hydrolysis efficiency of cellulose, in which biological pretreatment plays an important role. In the present study, we uncovered that Rhodococcus has the ability of lig...

The biosurfactant monoacyltrehalose fraction isolated from Rhodococcus ruber IEGM 231 actinobacterium suppresses antibody production, bactericidal potential, and production of IL-1β by mouse peritoneal cells after intraperitoneal and intramuscular injection and stimulates the production of IL-10 after intraperitoneal injection. The data of in vitro experiments attest to an important role of bacterial glycolipids in the regulation of the functions of splenocytes and peritoneal macrophages.

Inadequate use of antibiotics has led to spread of microorganisms resistant to effective antimicrobial compounds for humans and animals. This study was aimed to isolate cultivable strains of actinobacteria associated with Baikal endemic alga Draparnaldioides baicalensis and estimate their antibiotic properties. During this study, we isolated both widespread and dominant strains related to the genus Streptomyces and representatives of the genera Saccharopolyspora, Nonomuraea, Rhodococcus, and Micromonospora. For the first time, actinobacteria belonging to the genera Nonomuraea and Saccharopolyspora were isolated from Baikal ecosystem. Also, it was the first time when actinobacteria of the genus Nonomuraea were isolated from freshwater algae. Some rare strains demonstrated activity inhibiting growth of bacteria and yeasts. Also, it has been shown that the strains associated with Baikal alga D. baicalensis are active against both Gram-positive and Gram-negative bacteria. According to this study and previously published materials, diversity of cultivable actinobacteria and rare strains isolated from D. baicalensis is comparable to that of cultivable actinobacteria previously isolated from plant sources of Lake Baikal. Also, it exceeds the cultivable actinobacteria diversity previously described for macroinvertebrates, water, or sediments of Lake Baikal. The large number of rare and active strains associated with the endemic alga D. baicalensis could be the promising sources for biopharmaceutical and biotechnological developments and discovery of new natural compounds.

A Gram-reaction-positive, strictly aerobic, catalase-positive, oxidase-negative, non-motile actinobacterium, designated C1-24T, was isolated from a soil sample collected inside a natural cave. The organism exhibited a rod–coccus developmental cycle during its growth phase. Results of 16S rRNA gene-based phylogenetic analysis showed that the novel strain belonged to the genus Rhodococcus and formed a distinct sublineage at the base of the radiation including a Rhodococcus enclensis–Rhodococcus kroppenstedtii–Rhodococcus corynebacterioides–Rhodococcus trifoli cluster. In the results of phylogenomic analysis, the novel strain was loosely associated to Rhodococcus corynebacterioides . The closest relatives were Rhodococcus qingshengii (98.01 % 16S rRNA gene sequence similarity) and Rhodococcus degradans (98.01 %). The genome size was 5.66 Mbp and the DNA G+C content was 64.30 mol%. Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose and galactose as the diagnostic diamino acid and sugars. MK-8(H2) was the predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid and three unidentified phospholipids. Mycolic acids were present. The major fatty acids were C16 : 0, C18 : 1 ω9c, C16 : 1 ω7c and/or C16 : 1 ω6c and 10-methyl C18 : 0. Digital DNA–DNA hybridization and average nucleotide identity values revealed that the novel strain should be assigned to a different species. Based on the combined data obtained here, strain C1-24T (=KACC 19964T=DSM 109484T) represents a new species of the genus Rhodococcus , for which Rhodococcus cavernicola sp. nov. is proposed. Also, it is proposed that R. degradans is a later heterosynonym of R. qingshengii based on analyses of 16S rRNA gene and whole-genome sequences.

The level of CO2 production and the growth dynamics of the biomass of Rhodococcus erythropolis VKM Ac2017D (Russia) and the yeast strain Saccharomyces cerevisiae OenofermC2 (France) were determined in cultivation media with variously reduced (from 10 to 150 ppm) deuterium concentration. The maximum increase in the rhodococcal biomass was shown in the media with a deuterium concentration of 50 ppm or less. It was noted that the production of CO2 as an integral indicator of the biological activity of cells is more pronounced in Rhodococcus compared to the yeast. With generally similar dynamics of CO2 emission curves, prokaryotes showed broader temporal dynamics of its production.

N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) plays a major role in development of biofilms, which contribute to rise in infections and biofouling in water-related industries. Interference in QS, called quorum quenching (QQ), has recieved a lot of attention in recent years. Rhodococcus spp. are known to have prominent quorum quenching activity and in previous reports it was suggested that this genus possesses multiple QQ enzymes, but only one gene, qsdA, which encodes an AHL-lactonase belonging to phosphotriesterase family, has been identified. Therefore, we conducted a whole genome sequencing and analysis of Rhodococcus sp. BH4 isolated from a wastewater treatment plant. The sequencing revealed another gene encoding a QQ enzyme (named jydB) that exhibited a high AHL degrading activity. This QQ enzyme had a 46% amino acid sequence similarity with the AHL-lactonase (AidH) of Ochrobactrum sp. T63. HPLC analysis and AHL restoration experiments by acidification revealed that the jydB gene encodes an AHL-lactonase which shares the known characteristics of the α/β hydrolase family. Purified recombinant JydB demonstrated a high hydrolytic activity against various AHLs. Kinetic analysis of JydB revealed a high catalytic efficiency (kcat/KM) against C4-HSL and 3-oxo-C6 HSL, ranging from 1.88 × 106 to 1.45 × 106 M-1 s-1, with distinctly low KM values (0.16 - 0.24 mM). This study affirms that the AHL degrading activity and biofilm inhibition ability of Rhodococcus sp. BH4 may be due to the presence of multiple quorum quenching enzymes, including two types of AHL-lactonases, in addition to AHL-acylase and oxidoreductase, for which the genes have yet to be described.

Методом биотестирования установлено, что добавление в загрязненную углеводородами почву микроорганизмов – нефтедеструкторов рода Rhodococcus оказывает положительный эффект на морфогенез и посевные качества тест-культуры – кресс-салата, что связано с микробиологическим окислением нефти бактериями исследуемых штаммов. Выявлено, что при совместном внесении гуминовых кислот и микроорганизмов положительный эффект наблюдается в 5 из 8 вариантов опыта на среде с гексадеканом. В условиях нефтяного загрязнения внесение в субстрат микроорганизмов Rh. erythropolis Х5 и Rh. erythropolis S67 с добавлением гуминовых кислот в целом оказывает стимулирующее действие на морфогенез и посевные качества кресс-салата. Следует отметить, что именно в варианте «нефть + гуминовые кислоты + микроорганизм» были получены показатели, максимально превышающие значения загрязненного контроля. Снижение токсичности нефти и гексадекана, а в ряде случаев и полное снятие негативного влияния токсикантов по отношению к тест-культуре связаны, по-видимому, с интенсификацией процесса биодеградации нефти за счет стимулирующего влияния гуминовых кислот на жизнедеятельность микроорганизмов. Доказано, что внесенные гуминовые кислоты выступают адаптогенами по отношению к микроорганизмам Rh. erythropolis Х5 и Rh. erythropolis S67, повышая их резистентность к стрессовым нагрузкам в условиях нефтяного стресса. Таким образом, полученные результаты показывают, что внесение гуминовых кислот может способствовать более эффективной биодеградации нефтяного загрязнения почв. При этом с целью направленного повышения эффективности применения гуминовых кислот более перспективным представляется использование гуминовых кислот сфагнового переходного торфа + Rh.erythropolisХ5, гуминовых кислот сфагнового верхового торфа + Rh. erythropolis Х5, гуминовых кислот тростникового низинного торфа + Rh. erythropolis S67 вусловиях загрязнения нефтью. На субстрате с гексадеканом целесообразным считаем применение гуминовых кислот сфагнового верхового торфа, так как в этом варианте были отмечены параметры, максимально превышающие загрязненный контроль., By the method of biotesting, it has been established that the addition of oil-degrading microorganisms of the genus Rhodococcus to the soil contaminated with hydrocarbonshas a positive effect on morphogenesis and sowing qualities of the cockweed test culture, which is associated with the microbiological oxidation of oil by bacteria of the studied strains. It was revealed that a positive effect was observed in 5 of 8 variants of the experiment on the medium with hexadecane with the joint introduction of humic acids and microorganisms. Under the conditions of oil pollution, the introduction of Rh. erythropolis X5 and Rh. erythropolis S67 microorganisms into the substrate with the addition of humic acids as a whole has a stimulating effect on the morphogenesis and sowing qualities of cockweed. It should be noted that it was in the “oil + humic acids + microorganism” variant that the indicators were obtained that maximally exceeded the values of the contaminated control. Reducing the toxicity of oil and hexadecane, and in some cases, the complete removal of the negative effects of toxicants in the relation to the test culture are apparently connected with the intensification of the process of oil biodegradation due to the stimulating effect of humic acids on the microorganisms. It is proved that the introduced humic acids act as adaptogens in the relation to the microorganisms Rh. erythropolis X5 and Rh. erythropolis S67, increasing their resistance to stress loads under conditions of oil stress. Thus, the results show that the introduction of humic acids can contribute to more effective biodegradation of oil pollution of soils. At the same time, in order to increase the efficiency of humic acids, the use of humic acids of sphagnum transitional peat + Rh.erythropolis X5, humic acids of sphagnum high-moor peat + Rh. erythropolis X5, humic acids of reed fen peat + Rh. erythropolis S67 in the conditions of oil pollution seems more promising. On a substrate with hexadecane, it is advisable to consider the use of humic acids of sphagnum high-moor peat, because in this variant, the parameters that maximally exceed the contaminated control were noted.

Natural rubber and synthetic poly(cis-1,4-isoprene) are used industrially in the world. Microbial utilization for the isoprene rubbers has been reported in gram-positive and gram-negative bacteria. Poly(cis-1,4-isoprene)-cleavage enzymes that are secreted by rubber-utilizing bacteria cleave the poly(cis-1,4-isoprene) chain to generate low-molecular-weight oligo(cis-1,4-isoprene) derivatives containing aldehyde and ketone groups. The resulting products are converted to the compounds including carboxyl groups, which could then be further catabolized through β-oxidation pathway. One of poly(cis-1,4-isoprene)-cleavage enzymes is latex-clearing protein (Lcp) that was found in gram-positive rubber degraders including Streptomyces, Gordonia, Rhodococcus, and Nocardia species. The other one is rubber oxygenase A and B (RoxA/RoxB) which have been identified from gram-negative rubber degraders such as Steroidobacter cummioxidans and Rhizobacter gummiphilus. Recently, the transcriptional regulation mechanisms for Lcp-coding genes in gram-positive bacteria have been characterized. Here, the current knowledge of genes and enzymes for the isoprene rubber catabolism were summarized.

Summary Chiral aromatic alcohols have received much attention due to their widespread use in pharmaceutical industries. In the asymmetric synthesis processes, the excellent performance of alcohol dehydrogenase makes it a good choice for biocatalysts. In this study, a novel and robust medium‐chain alcohol dehydrogenase RhADH from Rhodococcus R6 was discovered and used to catalyse the asymmetric reduction of aromatic ketones to chiral aromatic alcohols. The reduction of 2‐hydroxyacetophenone (2‐HAP) to (R)‐(‐)‐1‐phenyl‐1,2‐ethanediol ((R)‐PED) was chosen as a template to evaluate its catalytic activity. A specific activity of 110 U mg−1 and a 99% purity of e.e. was achieved in the presence of NADH. An efficient bienzyme‐coupled catalytic system (RhADH and formate dehydrogenase, CpFDH) was established using a two‐phase strategy (dibutyl phthalate and buffer), which highly raised the tolerated substrate concentration (60 g l−1). Besides, a broad range of aromatic ketones were enantioselectively reduced to the corresponding chiral alcohols by this enzyme system with highly enantioselectivity. This system is of the potential to be applied at a commercial scale., A novel and robust medium‐chain alcohol dehydrogenase RhADH from Rhodococcus R6 was discovered and used to catalyze the asymmetric reduction of aromatic ketones to chiral aromatic alcohols.

A Gram-stain-positive, non-motile, creamy-white actinobacterium, which has an elementary branching rod-coccus life cycle was isolated from the rhizosphere soil of rice (Oryza sativa L.) collected from Northeast Agricultural University in Harbin, Heilongjiang province, north-east PR China, and its taxonomic status was examined by using a polyphasic approach. Results from the 16S rRNA gene sequence study showed that the isolate, designated strain NEAU-CX67T, belonged to the genus Rhodococcus and formed a cluster with Rhodococcus maanshanensis DSM 44675T, Rhodococcus kronopolitis NEAU-ML12T and Rhodococcus tukisamuensis JCM 11308T (98.3, 98.1 and 97.7% gene sequence similarity, respectively). The major fatty acids were C16 : 0, 10-methyl C18 : 0, C18 : 1 ω9c and C16 : 1 ω7c. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major isoprenoid quinone was MK-8(H2). Whole-cell hydrolysates contained meso-diaminopimelic acid. Arabinose, galactose and ribose were detected as diagnostic sugars from whole-cell hydrolysates. Mycolic acids were detected. The genomic DNA G+C content of strain NEAU-CX67T was 64.6 mol%. Strain NEAU-CX67T exhibited low average nucleotide identity and digital DNA–DNA hybridization values with R. maanshanensis DSM 44675T (92.1 and 45.4 %) and R. tukisamuensis JCM 11308T (81.9 and 24.4 %). On the basis of results of phylogenetic, genotypic, physiological and chemotaxonomic analysis, strain NEAU-CX67T is considered to represent a novel species of the genus Rhodococcus for which the name Rhodococcus oryzae sp. nov. is proposed. The type strain is NEAU-CX67T (=DSM 107701T=CCTCC AB 2018233T).

The purpose of this study is to investigate the effect of soil organic matter (SOM) content levels on the biodegradation of total petroleum hydrocarbons (TPH). Batch experiments were conducted with soils with 2% or 10% organic matter that had been contaminated by diesel or fuel oil. In addition to the TPH (diesel or fuel oil) degradation efficiency, a comprehensive investigation was conducted on the TPH-degrading microbial community using molecular tools including oligonucleotide microarray technique and terminal restriction fragment length polymorphism analysis (T-RFLP). TPH was reduced from 10,000 mg/kg to 1849–4352 mg/kg dry weight soil. Higher biodegradation efficiencies and kinetic rate constants were observed in higher SOM contents. Hydrocarbon fractional analyses were conducted to explain the optimal operation with relatively low resin and aromatic fractions detected at the end of the remediation. The bacterial and fungal counts in the 10% SOM were approximately 10 CFU/g to 102 CFU/g above those in the 2% SOM, and the lowest fungal level was found when the least TPH degradability was measured. The internal transcribed spacer microarray identified the microorganisms that were introduced and proved their survival. The associated growth pattern confirmed that different kinds of contamination oils affected the microbial community diversity over time. Both the microarray and T-RFLP profiles indicated that Gordonia alkanivorans, G. desulfuricans, and Rhodococcus erythoropolis were the dominant bacteria, while Fusarium oxysporum and Aspergillus versicolor were the dominant fungi. The T-RFLP-derived nonmetric multidimensional scaling concluded that the dynamics of the microbial communities were impacted by the TPH degradation stages.