Rhodococcus Species Research Articles

Using axenic and gnotobiotic insects to examine the role of different microbes on the development and reproduction of the kissing bug Rhodnius prolixus (Hemiptera: Reduviidae).

Kissing bugs (Hempitera: Reduviidae) are obligately and exclusively blood feeding insects. Vertebrate blood is thought to provide insufficient B vitamins to insects, which rely on symbiotic relationships with bacteria that provision these nutrients. Kissing bugs harbour environmentally acquired bacteria in their gut lumen, without which they are unable to develop to adulthood. Rhodococcus rhodnii was initially identified as the sole symbiont of Rhodnius prolixus, but modern studies of the kissing bug microbiome suggest that R. rhodnii is not always present or abundant in wild-caught individuals. We asked whether R. rhodnii or other bacteria alone could function as symbionts of R. prolixus. We produced insects with no bacteria (axenic) or with known microbiomes (gnotobiotic). Gnotobiotic insects harbouring R. rhodnii alone developed faster, had higher survival, and laid more eggs than those harbouring other bacterial monocultures, including other described symbionts of kissing bugs. R. rhodnii grew to high titre in the guts of R. prolixus while other tested species were found at much lower abundance. Rhodococcus species tested had nearly identical B vitamin biosynthesis genes, and dietary supplementation of B vitamins had a relatively minor effect on development and survival of gnotobiotic R. prolixus. Our results indicate that R. prolixus have a higher fitness when harbouring R. rhodnii than other bacteria tested, that this may be due to R. rhodnii existing at higher titres and providing more B vitamins to the host, and that symbiont B vitamin synthesis is probably a necessary but not sufficient function of gut bacteria in kissing bugs.

Mechanisms of biostimulant-enhanced biodegradation of PAHs and BTEX mixed contaminants in soil by native microbial consortium

Despite the co-occurrence of polycyclic aromatic hydrocarbons (PAHs) and benzene, toluene, ethylbenzene, and xylene (BTEX) in the field, to date, knowledge on the bioremediation of benzene and benzo[a]pyrene (BaP) mixed contaminants is limited. In this study, the mechanisms underlying the biodegradation of benzene and BaP under individual and co-contaminated conditions followed by the enhanced biodegradation using methanol, ethanol, and vegetable oil as biostimulants were investigated. The results demonstrated that the benzene biodegradation was highly reduced under the co-contaminated condition compared to the individual benzene contamination, whereas the BaP biodegradation was slightly enhanced with the co-contamination of benzene. Moreover, biostimulation significantly improved the biodegradation of both contaminants under co-contaminated conditions. A trend of significant reduction in the bioavailable BaP contents was observed in all biostimulant-enhanced groups, implying that the bioavailable BaP was the preferred biodegradable BaP fraction. Furthermore, the enzymatic activity analysis revealed a significant increase in lipase and dehydrogenase (DHA) activities, as well as a reduction in the catalase and polyphenol oxidase, suggesting that the increased hydrolysis of fats and proton transfer, as well as the reduced oxidative stress, contributed to the enhanced benzene and BaP biodegradation in the vegetable oil treatment. In addition, the microbial composition analysis results demonstrated that the enriched functional genera contributed to the increased biodegradation efficiency, and the functional genera in the microbial consortium responded differently to different biostimulants, and competitive growth was observed in the biostimulant-enhanced treatments. In addition, the enrichment of Pseudomonas and Rhodococcus species was noticed during the biostimulation of benzene and BaP co-contamination soil, and was positively correlated with the DHA enzyme activities, indicating that these species encode DHA genes which contributed to the higher biodegradation. In conclusion, multiple lines of evidence were provided to shed light on the mechanisms of biostimulant-enhanced biodegradation of PAHs and BTEX co-contamination with native microbial consortiums.

Exposure to metal nanoparticles changes zeta potentials of Rhodococcus cells

Nanoparticles (NPs) of transition metals and their oxides are widely used in industries and exhibit diverse biological activities – from antimicrobial to growth promoting and regulating biofilms. In this study, the concentration-dependent effects of negatively charged metal and metal oxide NPs on the viability and net surface charge of Rhodococcus cells were revealed. Our hypothesis that zeta potential values of bacterial cells approach the zeta potential of NPs with an increase in the concentration of nanoparticles was statistically validated, thus suggesting the accumulation of nanoparticles on the cell surface. Thus, based on the dynamics of zeta potential, it would be possible to predict the accumulation of metal NPs on the cell surface of particular Rhodococcus species. It seemed that more toxic nanometals (e.g. CuO) accumulate more intensively on the bacterial cell wall than less toxic nanometals (Bi, Ni and Co). Physical properties of NPs, such as shape, size, dispersity and zeta potential, were characterized at different nanoparticle concentrations, in order to explain their diverse effects on bacterial viability, cellular charge and adhesion to hydrocarbons. Interestingly, an increase in Rhodococcus adhesion to n-hexadecane was observed in the presence of Cu and CuO NPs, while treatment with Fe3O4 NPs resulted in a decrease in the adhesive activity. The obtained data help to clarify the mechanisms of nano-bio interaction and make it possible to select metal and metal oxide nanoparticles to modify the surface of bacterial cells without toxic effects.

Biosynthesis and Characterization of Gold Nanoparticles Produced Using Rhodococcus Actinobacteria at Elevated Chloroauric Acid Concentrations.

The growing industrial and medical use of gold nanoparticles (AuNPs) requires environmentally friendly methods for their production using microbial biosynthesis. The ability of actinobacteria of the genus Rhodococcus to synthesize AuNPs in the presence of chloroauric acid (HAuCl4) was studied. The effect of elevated (0.8-3.2 mM) concentrations of HAuCl4 on bacterial viability, morphology, and intracellular accumulation of AuNPs by different Rhodococcus species was shown. An increase in surface roughness, a shift of the zeta potential to the positive region, and the formation of cell aggregates of R. erythropolis IEGM 766 and R. ruber IEGM 1135 during nanoparticle synthesis were revealed as bacterial adaptations to toxic effects of HAuCl4. The possibility to biosynthesize AuNPs at a five times higher concentration of chloroauric acid compared to chemical synthesis, for example, using the citrate method, suggests greater efficiency of the biological process using Rhodococcus species. The main parameters of biosynthesized AuNPs (size, shape, surface roughness, and surface charge) were characterized using atomic force microscopy, dynamic and electrophoretic light scattering, and also scanning electron microscopy in combination with energy-dispersive spectrometry. Synthesized by R. erythropolis spherical AuNPs have smaller (30-120 nm) dimensions and are positively (12 mV) charged, unlike AuNPs isolated from R. ruber cells (40-200 nm and -22 mV, respectively). Such differences in AuNPs size and surface charge are due to different biomolecules, which originated from Rhodococcus cells and served as capping agents for nanoparticles. Biosynthesized AuNPs showed antimicrobial activity against Gram-positive (Micrococcus luteus) and Gram-negative (Escherichia coli) bacteria. Due to the positive charge and high dispersion, the synthesized by R. erythropolis AuNPs are promising for biomedicine, whereas the AuNPs formed by R. ruber IEGM 1135 are prone to aggregation and can be used for biotechnological enrichment of gold-bearing ores.

Isolation and characterization of a rare polar carotenoid 1’-OH-4-keto-ϒ-carotene from an indigenously isolated Rhodococcus kroppenstedtii MH715196

The catabolic diversity and biocatalytic potential in members of genus Rhodococcus makes it an ideal industrial workhouse for metabolite production. Despite their applicability, Rhodococci are least explored for carotenoids, located in their cell membrane. The goal of the present study was to identify the carotenoids of Rhodococcus kroppenstedtii MH715196. UV-Vis spectral data and molecular mass estimates showed that the principal carotenoid extracted from R. kroppenstedtii MH715196 was 1’-OH-4-keto-ϒ-carotene. Biosynthetic route of 1’-OH-4-keto-ϒ-carotene in R. kroppenstedtii MH715196 was postulated on the basis of molecular mass estimates in co-relation with putative carotenoid biosynthetic genes identified in the genome of the reference strains of R. kroppenstedtii. Three key enzymes, were then considered for phylogenetic analysis to establish the phylogenetic relationship across the Rhodococcus genus leading the way for carotenoid identification in other Rhodococcus species. The present study would be the first report on identification of a rare polar carotenoid from R. kroppenstedtii MH715196 which could be potentially explored as a food colorant in hydrophilic food matrices like jams, jellies, beverages etc.

Environmental Adaptability and Organic Pollutant Degradation Capacity of a Novel Rhodococcus Species Derived from Soil in the Uninhabited Area of the Qinghai-Tibet Plateau.

The Qinghai-Tibet Plateau (QTP) is known for extreme natural environments and, surprisingly, has been reported to contain widespread organic pollutants. Rhodococcus can survive a variety of extreme environments and degrade many organic contaminants. Here, we isolated a Rhodococcus strain (FXJ9.536 = CGMCC 4.7853) from a soil sample collected in the QTP. Phylogenomic analysis indicated that the strain represents a novel Rhodococcus species, for which the name Rhodococcus tibetensis sp. nov. is proposed. Interestingly, R. tibetensis FXJ9.536 maintained a fast growth rate and degraded 6.2% of p-nitrophenol (4-NP) and 50.0% of malathion even at 10 °C. It could degrade 53.6% of 4-NP and 99.9% of malathion at a moderate temperature. The genome of R. tibetensis FXJ9.536 contains 4-hydroxyphenylacetate 3-monoxygenase and carboxylesterase genes, which are likely associated with the degradation of 4-NP and malathion, respectively. Further genomic analysis revealed that the strain might employ multiple strategies to adapt to the harsh QTP environment. These include synthesizing cold shock proteins, compatible solutes, secondary metabolites, and storage compounds, utilizing inorganic compounds as energy and nutrition sources, as well as degrading a range of organic pollutants. Overall, our study reveals the potential of a QTP-derived new actinobacterial species for environmental adaptation and remediation in cold regions.

Genome-Based Exploration of Rhodococcus Species for Plastic-Degrading Genetic Determinants Using Bioinformatic Analysis.

Plastic polymer waste management is an increasingly prevalent issue. In this paper, Rhodococcus genomes were explored to predict new plastic-degrading enzymes based on recently discovered biodegrading enzymes for diverse plastic polymers. Bioinformatics prediction analyses were conducted using 124 gene products deriving from diverse microorganisms retrieved from databases, literature data, omic-approaches, and functional analyses. The whole results showed the plastic-degrading potential of Rhodococcus genus. Among the species with high plastic-degrading potential, R. erythropolis, R. equi, R. opacus, R. qingshengii, R. fascians, and R. rhodochrous appeared to be the most promising for possible plastic removal. A high number of genetic determinants related to polyester biodegradation were obtained from different Rhodococcus species. However, score calculation demonstrated that Rhodococcus species (especially R. pyridinivorans, R. qingshengii, and R. hoagii) likely possess PE-degrading enzymes. The results identified diverse oxidative systems, including multicopper oxidases, alkane monooxygenases, cytochrome P450 hydroxylases, para-nitrobenzylesterase, and carboxylesterase, and they could be promising reference sequences for the biodegradation of plastics with C−C backbone, plastics with heteroatoms in the main chain, and polyesters, respectively. Notably, the results of this study could be further exploited for biotechnological applications in biodegradative processes using diverse Rhodococcus strains and through catalytic reactions.

Rhodococcus pseudokoreensis sp. nov. isolated from the rhizosphere of young M26 apple rootstocks

The Gram-positive strain R79T, isolated from the rhizosphere of young M26 apple rootstocks, was investigated by a polyphasic taxonomic approach. Phylogenetic identification based on the full-length 16S rRNA gene sequence revealed highest 16S rRNA gene sequence similarity to the type strains of Rhodococcus wratislaviensis (99.6%) and Rhodococcus opacus (99.2%) followed by Rhodococcus imtechensis (98.9%). All other 16S rRNA gene sequence similarities were below 98.65%. A phylogenomic tree calculated based on a whole-genome sequence also showed a distinct clustering with the type strain of Rhodococcus koreensis. Average nucleotide identity (ANI) values between whole-genome sequences of R79T and the closest related type strains were below 95% supported the novel species status. The DNA G + C content of R79T was 67.24% mol. Predominant fatty acids were C16:0, C15:0 and C17:1ω8c. The strain contained MK8-H2 as the major respiratory quinone. The polar lipid profile consists of diphosphatidylglycerol and phosphatidylethanolamine, as well as of some unidentified lipids. The peptidoglycan type of the strain is A1γ meso-diaminopimelic acid. Based on the obtained genotypic and phenotypic, including chemotaxonomic data, we conclude that R79T represents a novel species of the genus Rhodococcus, for which the name Rhodococcus pseudokoreensis sp. nov. is proposed. The type strain is R79T (= DSM 113102T = LMG 32444T = CCM 9183T).

Diversity of Alkane-1-Monooxygenase Genes in Actinobacteria of the Genus Rhodococcus

By analyzing genetic similarity of rhodococci actinobacteria seven phylogenetic groups are allocated on the base on alkane- 1-monooxygenases sequences. R. qingshengii F2-2 genome have been shown to have alkane-1-monooxygenase genes affiliated to five different types. We assume the use of alkane-1-monooxygenase genes diversity as a molecular marker to identify Rhodococcus species.

Genomic Sequence Data of Bacterial Isolates from Pistachio Trees and Other Woody Plants in California Are Inconsistent with the Role of Rhodococcus as the Causative Agent of Pistachio Bushy Top Syndrome

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 .

Cell wall channels of Rhodococcus species: identification and characterization of the cell wall channels of Rhodococcus corynebacteroides and Rhodococcus ruber

The cell wall of Rhodococcus corynebacteroides formerly known as Nocardia corynebacteroides contains cell wall channels that are responsible for the cell wall permeability of this bacterium. Based on partial sequencing of the polypeptide subunits and a BLAST search, we identified one polypeptide of R. corynebacteroides (PorARc) and two polypeptides (PorARr and PorBRr) from the closely related bacterium Rhodococcus ruber. The corresponding genes, porARc (606 bp), porARr (702 bp), and porBRr (540 bp) are constituents of the known genome of R. corynebacteroides DSM-20151 and R. ruber DSM-43338, respectively. porARr and porBRr of R. ruber are possibly forming a common operon coding for the polypeptide subunits of the cell wall channel. The genes coding for PorARc and for PorARr and PorBRr without signal peptide were separately expressed in the porin-deficient Escherichia coli BL21DE3Omp8 strain and the proteins were purified to homogeneity. All proteins were checked for channel formation in lipid bilayers. PorARc formed channels with characteristics that were very similar to those of a previous study. The proteins PorARr and PorBRr expressed in E. coli could alone create channels in lipid bilayer membranes, despite the possibility that the two corresponding genes form a porin operon and that both subunits possibly form the cell wall channels in vivo. Based on amino acid sequence comparison of a variety of proteins forming cell wall channels in bacteria of the suborder Corynebacterineae, it seems very likely that PorARc, PorARr, and PorBRr are members of a huge family of proteins (PF09203) that form MspA-like cell wall channels.

Isolation and identification of microorganism’s resistant to soil salinization

315 variants of halotolerant bacteria were isolated from soil samples taken around Starobin potash deposit mined by Belaruskali concern. Nitrogen-fixing isolate CA-6 and phosphate-solubilizing isolate Cp-1 capable to withstand abiotic stress caused by sodium chloride in concentration 1710 and 2565 mM, respectively and water deficiency characterized by osmotic potential -0.20 and -0.42 MPa were sorted out. Isolate Cp-1 may dissolve phosphates yielding halo zones 9 mm in diameter while isolate CA-6 displays nitrogenase activity 44.0 nM C2H2/vial/3 days. Both isolates are growth-promoting organisms, distinguished by the ability to synthesize IAA in concentrations 89.7 and 37.8 μg IAA/ml of cultural liquid, respectively. The selected salt-resistant isolates were identified based on analysis of the nucleotide sequence of the 16S rRNA gene and data of MALDI-TOF mass spectrometry and were referred to the species Rhodococcus jostii and Priestia megaterium. Halotolerant strains Priestia megaterium Cp-1 and Rhodococcus jostii CA-6 were deposited in Belarusian collection of non-pathogenic microorganisms under the respective registration numbers BIM B-1314D and BIM B-1353D.

Effect of Culture Condition and Growth Kinetics on Phenol Biodegradation by an Indigenous Rhodococcus pyridinivorans Strain PDB9T NS-1

The US Environmental Protection Agency listed phenolic compounds as priority pollutants, and their occurrence in water systems poses serious health risks to humans and other living species. The culture conditions are extremely crucial for microbial growth, enzymatic and cellular metabolic activities. Thus, the effects of different culture parameters like pH, temperature (°C), and agitation speed (RPM) on the indigenous Rhodococcus pyridinivorans strain PDB9T NS-1 were modeled using response surface methodology (RSM) and central composite design (CCD). The results showed that the main effect of pH and interaction between pH and agitation speed had a significant to a moderately significant effect on phenol degradation by the indigenous R. pyridinivorans strain PDB9T NS-1. Almost complete phenol degradation was obtained at an optimal setting of pH 7.5, 187 rpm, and 34 °C in 18 h. Growth and phenol degradation kinetics of the actinomycetes was examined in a batch shake flask under the optimized conditions. The growth of Rhodococcus species at varying initial levels of the phenol followed a Pamukoglu and Kargi substrate inhibition model with half-saturation constant (Ks ) of 54.21 mg/l, maximum specific growth rate (µ max) of 0.169 (1/h), substrate inhibition constant (Ksi ) of 243.26 mg/l. The results obtained from the optimization of culture conditions and growth kinetics by the indigenous R. Pyridinivorans strain PDB9T NS-1 suggest the potential of the system in the treatment of phenolic wastewater.

Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species.

Under conditions of increasing environmental pollution, true saprophytes are capable of changing their survival strategies and demonstrating certain pathogenicity factors. Actinobacteria of the genus Rhodococcus, typical soil and aquatic biotope inhabitants, are characterized by high ecological plasticity and a wide range of oxidized organic substrates, including hydrocarbons and their derivatives. Their cell adaptations, such as the ability of adhering and colonizing surfaces, a complex life cycle, formation of resting cells and capsule-like structures, diauxotrophy, and a rigid cell wall, developed against the negative effects of anthropogenic pollutants are discussed and the risks of possible pathogenization of free-living saprotrophic Rhodococcus species are proposed. Due to universal adaptation features, Rhodococcus species are among the candidates, if further anthropogenic pressure increases, to move into the group of potentially pathogenic organisms with “unprofessional” parasitism, and to join an expanding list of infectious agents as facultative or occasional parasites.

Benchmarking DNA Extraction Methods for Phylogenomic Analysis of Sub-Antarctic Rhodococcus and Williamsia Species.

Bacteria containing mycolic acids in their cell envelope are often recalcitrant to cell lysis, so extracting DNA of sufficient quality for third-generation sequencing and high-fidelity genome assembly requires optimization, even when using commercial kits with protocols for hard-to-lyse bacteria. We benchmarked three spin-column-based kits against a classical DNA extraction method employing lysozyme, proteinase K and SDS for six lysozyme-resistant, sub-Antarctic strains of Corynebaceriales. Prior cultivation in broths containing glycine at highly growth-inhibitory concentrations (4.0–4.5%) improved cell lysis using both classical and kit methods. The classical method produced DNA with average fragment sizes of 27–59 Kbp and tight fragment size ranges, meeting quality standards for genome sequencing, assembly and phylogenomic analyses. By 16S rRNA gene sequencing, we classified two strains as Williamsia and four strains as Rhodococcus species. Pairwise comparison of average nucleotide identity (ANI) and alignment fraction (AF), plus genome clustering analysis, confirmed Rhodococcus sp. 1163 and 1168 and Williamsia sp. 1135 and 1138 as novel species. Phylogenetic, lipidomic and biochemical analyses classified psychrotrophic strains 1139 and 1159 as R. qingshengii and R. erythropolis, respectively, using ANI similarity of >98% and AF >60% for species delineation. On this basis, some members of the R. erythropolis genome cluster groups, including strains currently named as R. enclensis, R. baikonurensis, R. opacus and R. rhodochrous, would be reclassified either as R. erythropolis or R. qingshengii.

Complete genome sequencing and comparative CAZyme analysis of Rhodococcus sp. PAMC28705 and PAMC28707 provide insight into their biotechnological and phytopathogenic potential.

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.

Metabolic profiling of phenol biodegradation by an indigenous Rhodococcus pyridinivorans strain PDB9T N-1 isolated from paper pulp wastewater

In the present study, a phenol degrading actinomycetes strain was isolated from paper pulp wastewater. The isolated strain was identified as Rhodococcus pyridinivorans PDB9TN-1 using 16S rRNA gene sequencing technique, which yielded the complete degradation of 1600 mg l−1 of phenol within 56 h. Moreover, the Rhodococcus species could remove over 97.5% of total organic carbon (TOC) at an initial phenol concentration of 1000 mg l−1. The metabolic profile of phenol biodegradation by the actinomycetes species has been investigated using liquid chromatography–mass spectrometry (LC-MS) and Fourier-transform infrared spectroscopy (FT-IR). The key intermediate products detected in the actinomycetes culture were hydroquinone, protocatechuic acid, beta-carboxycis-cismuconate, maleyl acetate, 4–oxalocrotonic acid and 3-fumarylpyruvic acid. Further, a tentative oxalocrotonic acid pathway has been proposed on the basis of the detected intermediate products. The culture medium constituents are highly indispensable for the microbial growth, enzyme and other cellular metabolic activities associated with phenol biodegradation. Therefore, the effect of media components were modelled with the help of response surface methodology (RSM) and central composite design (CCD). A reliable quadratic model was established which predicted the degradation efficiency as high as 99.5% with an appreciable correlation coefficient (R2) of 0.98. Moreover, phenol degradation efficiency was improved with concentrations beyond the central values for all media components except K2HPO4 and NaCl.

Different genome-wide transcriptome responses of Nocardioides simplex VKM Ac-2033D to phytosterol and cortisone 21-acetate

BackgroundBacterial degradation/transformation of steroids is widely investigated to create biotechnologically relevant strains for industrial application. The strain of Nocardioides simplex VKM Ac-2033D is well known mainly for its superior 3-ketosteroid Δ1-dehydrogenase activity towards various 3-oxosteroids and other important reactions of sterol degradation. However, its biocatalytic capacities and the molecular fundamentals of its activity towards natural sterols and synthetic steroids were not fully understood. In this study, a comparative investigation of the genome-wide transcriptome profiling of the N. simplex VKM Ac-2033D grown on phytosterol, or in the presence of cortisone 21-acetate was performed with RNA-seq.ResultsAlthough the gene patterns induced by phytosterol generally resemble the gene sets involved in phytosterol degradation pathways in mycolic acid rich actinobacteria such as Mycolicibacterium, Mycobacterium and Rhodococcus species, the differences in gene organization and previously unreported genes with high expression level were revealed. Transcription of the genes related to KstR- and KstR2-regulons was mainly enhanced in response to phytosterol, and the role in steroid catabolism is predicted for some dozens of the genes in N. simplex. New transcription factors binding motifs and new candidate transcription regulators of steroid catabolism were predicted in N. simplex.Unlike phytosterol, cortisone 21-acetate does not provide induction of the genes with predicted KstR and KstR2 sites. Superior 3-ketosteroid-Δ1-dehydrogenase activity of N. simplex VKM Ac-2033D is due to the kstDs redundancy in the genome, with the highest expression level of the gene KR76_27125 orthologous to kstD2, in response to cortisone 21-acetate. The substrate spectrum of N. simplex 3-ketosteroid-Δ1-dehydrogenase was expanded in this study with progesterone and its 17α-hydroxylated and 11α,17α-dihydroxylated derivatives, that effectively were 1(2)-dehydrogenated in vivo by the whole cells of the N. simplex VKM Ac-2033D.ConclusionThe results contribute to the knowledge of biocatalytic features and diversity of steroid modification capabilities of actinobacteria, defining targets for further bioengineering manipulations with the purpose of expansion of their biotechnological applications.

Discovering Decolorization Potential of Triphenylmethane Dyes by Actinobacteria from Soil

This study investigates the decolorization potential of actinobacteria from soil towards toxic triphenylmethane (TPM) dyes, i.e., malachite green (MG), methyl violet (MV), crystal violet (CV), and cotton blue (CB). The actinobacterial isolates were first isolated from fresh soil samples, plated onto actinomycetes isolation agar (AIA), and both live and dead cells were prepared to evaluate their decolorization efficiency (DE). Isolates with positive decolorization activities were identified via partial sequencing of the 16S rRNA region. They were revealed as species of Nocardiopsis (N. alba), Streptomyces (S. puniceus, S. bacillaris, S. albolongus, S. acidiscabies, S. albulus, S. pratensis, S. luridiscabiei, S. rubiginosus, S. albidochromogenes), Rhodococcus (R. sovatensis), and Kitasatospora (K. albolonga). Results indicated that all 12 actinobacterial strains (live cells and dead cells) were able to decolorize TPM dyes, although with varying degree of effectiveness. Isolate N. alba (live cells) achieved the highest DE, with 97.0, 95.1, 95.8, and 83.8% (day 14) for MG, MV, CV, and CB, respectively. This was followed by live cells of S. bacillaris with 94.7, 95.1, 90.5, and 63.9% of DE for the same dyes. Live cells appeared to be more effective in decolorizing TPM dyes, suggesting the possible biosorption and biodegradation of dyes. It is concluded that soil actinobacteria tested in this study have the potential for removal of TPM dyes.

Sequence analysis of 16S rDNA, gyrB and alkB genes of plant-associated Rhodococcus species from Tunisia

The genus Rhodococcus contains 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 as R. fascians are plant pathogens. In this study, we isolated 47 Rhodococcus strains from a range of herbaceous and woody plant species. Phylogenetic analysis based on 16S rDNA, gyrB and alkB genes was used to compare our strains with type strains of Rhodococcus. For most of our strains, sequence similarity of the 16S rDNA, gyrB and alkB regions to type strains ranged from 98-100 %. Results of the concatenated gene sequence comparisons identified 18 strains of R. fascians and three strains of R. kroppenstedtii. The remaining strains were unclassified, and may represent novel species of Rhodococcus. Phylogenetic analysis based on gyrB sequences provided a more precise classification of our strains to species level than 16S rDNA sequences, whereas analysis of alkB sequences was unable to identify strains with orange-coloured colonies to species level.