Draft genome sequence of propane- and butane-oxidizing Rhodococcus ruber IEGM 333 able to accumulate cesium

A genome of Rhodococcus ruber IEGM 333 was sequenced and annotated. This bacterium had pronounced propane- and n-butane-oxidizing and cesium-accumulating activities. The obtained sequence could be used to reveal the genetic mechanisms of these activities and efficiently exploit the biotechnological potential of propanotrophic Rhodococcus.

The roles of Rhodococcus ruber in denitrification with quinoline as the electron donor

Denitrification is an important step in domestic wastewater treatment, but providing bioavailable electron donors is an expense. However, some industrial wastewaters contain organic compounds that could be a no-cost or low-cost electron donor, because they otherwise must be treated separately. In this work, quinoline was used as an electron donor to drive denitrification through bioaugmentation with Rhodococcus ruber, which is able to biodegrade quinoline. When quinoline-acclimated biomass (QAB) was used for denitrification, addition of R. ruber accelerated biodegradation of quinoline and its first mono-oxygenation intermediate (2-hydroxyquinoline). Although R. ruber was not directly active in denitrification, its biodegradation of quinoline and 2-hydroxyquinoline supplied products that other bacteria used to respire nitrate. In contrast, glucose-acclimated biomass (GAB) could not achieve effective denitrification with quinoline, whether or not R. ruber was added. Analysis by high-throughout sequencing showed that genera Ignavibacterium, Ferruginibacter, Limnobacter, and Denitrosoma were important during quinoline biodegradation with denitrification by QAB. In summary, bioaugmented R. ruber and endogenous bacterial strains had complementary roles when biodegrading quinoline to enhance denitrification. The significance of this study is to enable the use of industrial wastewater to provide electron donor to drive denitrification.

Mitigating the inhibition of antibacterial agent chloroxylenol on nitrification system-The role of Rhodococcus ruber in a bioaugmentation system

The chloroxylenol (PCMX) degrading strain was successfully isolated from sludge and identified as Rhodococcus ruber (R. ruber). Afterwards, a bioaugmentation system was constructed by seeding R. ruber into nitrifying sludge to fasten degradation efficiency of highly toxic PCMX from wastewater. Results showed that R. ruber presented high PCMX-degrading performance under aerobic conditions, 25 °C, pH 7.0 and inoculum sizes of 4% (v/v). These optimized conditions were used in subsequent bioaugmentation experiment. In bioaugmentation system, R. ruber could detoxify nitrifiers by degrading PCMX, and the content of polysaccharide in extracellular polymeric substances increased. The quantitative polymerase chain reaction results exhibited that the absolute abundance of 16S rRNA gene and ammonia oxidizing bacteria (AOB) slightly elevated in bioaugmentation system. After analyzing the results of high-throughput sequencing, it was found that the loaded R. ruber can colonize successfully and turn into dominant strains in sludge system. Molecular docking simulation showed that PCMX had a weaker suppressed effect on AOB than nitrite oxidizing bacteria, and R. ruber can alleviate the adverse effect. This study could provide a novel strategy for potential application in reinforcement of PCMX removal in wastewater treatment.

A stable isotope assay with 13C-labeled polyethylene to investigate plastic mineralization mediated by Rhodococcus ruber

Methods that unambiguously prove microbial plastic degradation and allow for quantification of degradation rates are necessary to constrain the influence of microbial degradation on the marine plastic budget. We developed an assay based on stable isotope tracer techniques to determine microbial plastic mineralization rates in liquid medium on a lab scale. For the experiments, ¹³C-labeled polyethylene (¹³C-PE) particles (irradiated with UV-light to mimic exposure of floating plastic to sunlight) were incubated in liquid medium with Rhodococcus ruber as a model organism for proof of principle. The transfer of ¹³C from ¹³C-PE into the gaseous and dissolved CO₂ pools translated to microbially mediated mineralization rates of up to 1.2 % yr^-1 of the added PE. After incubation, we also found highly ¹³C-enriched membrane fatty acids of R. ruber including compounds involved in cellular stress responses. We demonstrated that isotope tracer techniques are a valuable tool to detect and quantify microbial plastic degradation.

Aerobic Degradation Characteristics of Decabromodiphenyl ether through Rhodococcus ruber TAW-CT127 and Its Preliminary Genome Analysis

Decabromodiphenyl ether (BDE-209), a polybrominated diphenyl ether (PBDE) homolog, seriously threatens human health. In this study, a Rhodococcus ruber strain with high BDE-209 degradation activity, named TAW-CT127, was isolated from Tong’an Bay, Xiamen. Under laboratory conditions, the strain’s optimal growth temperature, pH, and salinity are 45 °C, 7.0, and 0–2.5%, respectively. Scanning electron microscopy (SEM) analysis shows that TAW-CT127 is damaged when grown in manual marine culture (MMC) medium with BDE-209 as the sole carbon source instead of eutrophic conditions. In the dark, under the conditions of 28 °C, 160 rpm, and 3 g/L (wet weight) TAW-CT127, the degradation rate of 50 mg/L BDE-209 is 81.07%. The intermediate metabolites are hexabromo-, octabromo-, and nonabromo-diphenyl ethers. Through whole-genome sequencing, multiple dehalogenases were found in the genome of TAW-CT127; these may be involved in the production of lower-brominated diphenyl ethers. Additionally, biphenyl-2,3-dioxygenase (BDO) in TAW-CT127 may catalyze the debromination reaction of BDE-209. Our research provides a new high-efficiency strain for bioremediation of BDE-209 pollution, and lays the foundation for the preliminary exploration of genes associated with BDE-209 degradation.

Further Studies on the 3-Ketosteroid 9α-Hydroxylase of Rhodococcus ruber Chol-4, a Rieske Oxygenase of the Steroid Degradation Pathway

The biochemistry and genetics of the bacterial steroid catabolism have been extensively studied during the last years and their findings have been essential to the development of biotechnological applications. For instance, metabolic engineering of the steroid-eater strains has allowed to obtain intermediaries of industrial value. However, there are still some drawbacks that must be overcome, such as the redundancy of the steroid catabolism genes in the genome and a better knowledge of its genetic regulation. KshABs and KstDs are key enzymes involved in the aerobic breakage of the steroid nucleus. Rhodococcus ruber Chol-4 contains three kshAs genes, a single kshB gene and three kstDs genes within its genome. In the present work, the growth of R. ruber ΔkshA strains was evaluated on different steroids substrates; the promoter regions of these genes were analyzed; and their expression was followed by qRT-PCR in both wild type and ksh mutants. Additionally, the transcription level of the kstDs genes was studied in the ksh mutants. The results show that KshA2B and KshA1B are involved in AD metabolism, while KshA3B and KshA1B contribute to the cholesterol metabolism in R. ruber. In the kshA single mutants, expression of the remaining kshA and kstD genes is re-organized to survive on the steroid substrate. These data give insight into the fine regulation of steroid genes when several isoforms are present.

Expression, Rapid Purification and Functional Analysis of DnaK from Rhodococcus ruber

BACKGROUND

Heat shock proteins (HSPs) represent a group of important proteins which are produced by all kinds of organisms especially under stressful conditions. DnaK, an Hsp70 homolog in prokaryotes, has indispensable roles when microbes was confronted with stress conditions. However, few data on DnaK from Rhodococcus sp. were available in the literature. In a previous study, we reported that toluene and phenol stress gave rise to a 29.87-fold and 3.93-fold increase for the expression of DnaK from R. ruber SD3, respectively. Thus, we deduced DnaK was in correlation with the organic solvent tolerance of R. ruber SD3.

OBJECTIVE

To elucidate the role of DnaK in the organic solvent tolerance of R. ruber SD3, expression, purification and functional analysis of Dnak from R. ruber SD3 were performed in the present paper.

METHODS

In this article, DnaK from R. ruber SD3 was heterologously expressed in E. coli BL21(DE3) and purified by affinity chromatography. Functional analysis of DnaK was performed using determination of kinetics, docking, assay of chaperone activity and microbial growth.

RESULTS

The recombinant DnaK was rapidly purified by affinity chromatography with the purification fold of 1.9 and the recovery rate of 57.9%. Km, Vmax and Kcat for Dnak from R. ruber SD3 were 80.8 μM, 58.1 nmol/min and 374.3 S-1, respectively. The recombinant protein formed trimer in vitro, with the calculated molecular weight of 214 kDa. According to In-silico analysis, DnaK interacted with other molecular chaperones and some important proteins in the metabolism. The specific activity of catalase in the presence of recombinant DnaK was 1.85 times or 2.00 times that in the presence of BSA or Tris-HCl buffer after exposure to 54 °C for 1h. E. coli transformant with pET28-dnak showed higher growth than E. coli transformant with pET28 at 43°C and in the presence of phenol, respectively.

CONCLUSION

The biochemical properties and the interaction analysis of DnaK from R. ruber SD3 deepened our understanding of DnaK function. DnaK played an important role in microbial growth when R. ruber was subjected to various stress such as heating and organic solvent.

Bioaugmentation potential evaluation of a bacterial consortium composed of isolated Pseudomonas and Rhodococcus for degrading benzene, toluene and styrene in sludge and sewage

Bioaugmentation was conducted using a bacterial consortium of Pseudomonas putida SW-3 and Rhodococcus ruber SS-4, to test their ability to degrade benzene, toluene, and styrene (BTS). SW-3 and SS-4 were isolated from domestic sludge and sewage samples to establish a synthetic consortium with an optimized ratio of 2:1 to reach a degradation efficiency of 82.5-89.8% of BTS. The bacterial consortium was inoculated with sludge and sewage samples at a ratio of 2:1, resulting in a degradation efficiency of 97.9% and 92.7%, respectively, at a BTS concentration of 1800 mg·L^-1. Analysis of bacterial community structure following bioaugmentation indicated an increase in abundance of BTS-degrading bacteria, particularly Acinetobacter and Pseudoxanthomonas in sludge and Pseudomonas in sewage, enhancing the collective BTS degradation ability of the bacterial community. Principal component analysis demonstrated that a more balanced bacterial community structure was established following intervention. This indicated that the selected bacteria are excellent candidates for bioaugmentation.

Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 11: suitability of taxonomic units notified to EFSA until September 2019

Qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance are assessed. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA was updated with 54 biological agents, received between April and September 2019; 23 already had QPS status, 14 were excluded from the QPS exercise (7 filamentous fungi, 6 Escherichia coli, Sphingomonas paucimobilis which was already evaluated). Seventeen, corresponding to 16 TUs, were evaluated for possible QPS status, fourteen of these for the first time, and Protaminobacter rubrum, evaluated previously, was excluded because it is not a valid species. Eight TUs are recommended for QPS status. Lactobacillus parafarraginis and Zygosaccharomyces rouxii are recommended to be included in the QPS list. Parageobacillus thermoglucosidasius and Paenibacillus illinoisensis can be recommended for the QPS list with the qualification 'for production purposes only' and absence of toxigenic potential. Bacillus velezensis can be recommended for the QPS list with the qualification 'absence of toxigenic potential and the absence of aminoglycoside production ability'. Cupriavidus necator, Aurantiochytrium limacinum and Tetraselmis chuii can be recommended for the QPS list with the qualification 'production purposes only'. Pantoea ananatis is not recommended for the QPS list due to lack of body of knowledge in relation to its pathogenicity potential for plants. Corynebacterium stationis, Hamamotoa singularis, Rhodococcus aetherivorans and Rhodococcus ruber cannot be recommended for the QPS list due to lack of body of knowledge. Kodamaea ohmeri cannot be recommended for the QPS list due to safety concerns.

New insights into the genome of Rhodococcus ruber strain Chol-4

Background

Rhodococcus ruber strain Chol-4, a strain isolated from a sewage sludge sample, is able to grow in minimal medium supplemented with several compounds, showing a broad catabolic capacity. We have previously determined its genome sequence but a more comprehensive study of their metabolic capacities was necessary to fully unravel its potential for biotechnological applications.

Results

In this work, the genome of R. ruber strain Chol-4 has been re-sequenced, revised, annotated and compared to other bacterial genomes in order to investigate the metabolic capabilities of this microorganism. The analysis of the data suggests that R. ruber Chol-4 contains several putative metabolic clusters of biotechnological interest, particularly those involved on steroid and aromatic compounds catabolism.

To demonstrate some of its putative metabolic abilities, R. ruber has been cultured in minimal media containing compounds belonging to several of the predicted metabolic pathways. Moreover, mutants were built to test the naphtalen and protocatechuate predicted catabolic gene clusters.

Conclusions

The genomic analysis and experimental data presented in this work confirm the metabolic potential of R. ruber strain Chol-4. This strain is an interesting model bacterium due to its biodegradation capabilities. The results obtained in this work will facilitate the application of this strain as a biotechnological tool.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5677-2) contains supplementary material, which is available to authorized users.

Biodegradation of Di-(2-ethylhexyl) Phthalate by Rhodococcus ruber YC-YT1 in Contaminated Water and Soil

Di-(2-ethylehxyl) phthalate (DEHP) is one of the most broadly representative phthalic acid esters (PAEs) used as a plasticizer in polyvinyl chloride (PVC) production, and is considered to be an endocrine-disrupting chemical. DEHP and its monoester metabolites are responsible for adverse effects on human health. An efficient DEHP-degrading bacterial strain Rhodococcus ruber YC-YT1, with super salt tolerance (0⁻12% NaCl), is the first DEHP-degrader isolated from marine plastic debris found in coastal saline seawater. Strain YC-YT1 completely degraded 100 mg/L DEHP within three days (pH 7.0, 30 °C). According to high-performance liquid chromatography⁻mass spectrometry (HPLC-MS) analysis, DEHP was transformed by strain YC-YT1 into phthalate (PA) via mono (2-ethylehxyl) phthalate (MEHP), then PA was used for cell growth. Furthermore, YC-YT1 metabolized initial concentrations of DEHP ranging from 0.5 to 1000 mg/L. Especially, YC-YT1 degraded up to 60% of the 0.5 mg/L initial DEHP concentration. Moreover, compared with previous reports, strain YC-YT1 had the largest substrate spectrum, degrading up to 13 kinds of PAEs as well as diphenyl, p-nitrophenol, PA, benzoic acid, phenol, protocatechuic acid, salicylic acid, catechol, and 1,2,3,3-tetrachlorobenzene. The excellent environmental adaptability of strain YC-YT1 contributed to its ability to adjust its cell surface hydrophobicity (CSH) so that 79.7⁻95.9% of DEHP-contaminated agricultural soil, river water, coastal sediment, and coastal seawater were remedied. These results demonstrate that R. ruber YC-YT1 has vast potential to bioremediate various DEHP-contaminated environments, especially in saline environments.

Functional differentiation of 3-ketosteroid Δ1-dehydrogenase isozymes in Rhodococcus ruber strain Chol-4

Background

The Rhodococcus ruber strain Chol-4 genome contains at least three putative 3-ketosteroid Δ¹-dehydrogenase ORFs (kstD1, kstD2 and kstD3) that code for flavoenzymes involved in the steroid ring degradation. The aim of this work is the functional characterization of these enzymes prior to the developing of different biotechnological applications.

Results

The three R. ruber KstD enzymes have different substrate profiles. KstD1 shows preference for 9OHAD and testosterone, followed by progesterone, deoxy corticosterone AD and, finally, 4-BNC, corticosterone and 19OHAD. KstD2 shows maximum preference for progesterone followed by 5α-Tes, DOC, AD testosterone, 4-BNC and lastly 19OHAD, corticosterone and 9OHAD. KstD3 preference is for saturated steroid substrates (5α-Tes) followed by progesterone and DOC. A preliminary attempt to model the catalytic pocket of the KstD proteins revealed some structural differences probably related to their catalytic differences. The expression of kstD genes has been studied by RT-PCR and RT-qPCR. All the kstD genes are transcribed under all the conditions assayed, although an additional induction in cholesterol and AD could be observed for kstD1 and in cholesterol for kstD3. Co-transcription of some correlative genes could be stated. The transcription initiation signals have been searched, both in silico and in vivo. Putative promoters in the intergenic regions upstream the kstD1, kstD2 and kstD3 genes were identified and probed in an apramycin-promoter-test vector, leading to the functional evidence of those R. ruber kstD promoters.

Conclusions

At least three putative 3-ketosteroid Δ¹-dehydrogenase ORFs (kstD1, kstD2 and kstD3) have been identified and functionally confirmed in R. ruber strain Chol-4. KstD1 and KstD2 display a wide range of substrate preferences regarding to well-known intermediaries of the cholesterol degradation pathway (9OHAD and AD) and other steroid compounds. KstD3 shows a narrower substrate range with a preference for saturated substrates. KstDs differences in their catalytic properties was somehow related to structural differences revealed by a preliminary structural modelling. Transcription of R. ruber kstD genes is driven from specific promoters. The three genes are constitutively transcribed, although an additional induction is observed in kstD1 and kstD3. These enzymes have a wide versatility and allow a fine tuning-up of the KstD cellular activity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0657-1) contains supplementary material, which is available to authorized users.

Expression, purification and kinetic characterization of recombinant benzoate dioxygenase from Rhodococcus ruber UKMP-5M

In this study, benzoate dioxygenase from Rhodococcus ruber UKMP-5M was catalyzed by oxidating the benzene ring to catechol and other derivatives. The benzoate dioxygenase (benA gene) from Rhodococcus ruber UKMP-5M was then expressed, purified, characterized, The benA gene was amplified (642 bp), and the product was cloned into a pGEM-T vector. The recombinant plasmid pGEMT-benA was digested by double restriction enzymes BamHI and HindIII to construct plasmid pET28b-benA and was then ligated into Escherichia coli BL21 (DE3). The recombinant E. coli was induced with 0.5 mM isopropyl β-D-thiogalactoside (IPTG) at 22˚C to produce benzoate dioxygenase. The enzyme was then purified by ion exchange chromatography after 8 purification folds. The resulting product was 25 kDa, determined by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and western blotting. Benzoate dioxygenase activity was found to be 6.54 U/mL and the optimal pH and temperature were 8.5 and 25°C, respectively. Maximum velocity (Vmax) and Michaelis constant (Km) were 7.36 U/mL and 5.58 µM, respectively. The end metabolite from the benzoate dioxygenase reaction was cyclohexane dione, which was determined by gas chromatography mass spectrometry (GC-MS).

Diverse effects of a biosurfactant from Rhodococcus ruber IEGM 231 on the adhesion of resting and growing bacteria to polystyrene

This study evaluated the effects of a trehalolipid biosurfactant produced by Rhodococcus ruber IEGM 231 on the bacterial adhesion and biofilm formation on the surface of polystyrene microplates. The adhesion of Gram-positive (Arthrobacter simplex, Bacillus subtilis, Brevibacterium linens, Corynebacterium glutamicum, Micrococcus luteus) and Gram-negative (Escherichia coli, Pseudomonas fluorescencens) bacteria correlated differently with the cell hydrophobicity and surface charge. In particular, exponentially growing bacterial cells with increased hydrophobicities adhered stronger to polystyrene compared to more hydrophilic stationary phase cells. Also, a moderate correlation (0.56) was found between zeta potential and adhesion values of actively growing bacteria, suggesting that less negatively charged cells adhered stronger to polystyrene. Efficient biosurfactant concentrations (10-100 mg/L) were determined, which selectively inhibited (up to 76 %) the adhesion of tested bacterial cultures, however without inhibiting their growth. The biosurfactant was more active against growing bacteria rather than resting cells, thus showing high biofilm-preventing properties. Contact angle measurements revealed more hydrophilic surface of the biosurfactant-covered polystyrene compared to bare polystyrene, which allowed less adhesion of hydrophobic bacteria. Furthermore, surface free-energy calculations showed a decrease in the Wan der Waals (γ(LW)) component and an increase in the acid-based (γ(AB)) component caused by the biosurfactant coating of polysterene. However, our results suggested that the biosurfactant inhibited the adhesion of bacteria independently on their surface charges. AFM scanning revealed three-type biosurfactant structures (micelles, cord-like assemblies and large vesicles) formed on glass, depending on concentrations used, that could lead to diverse anti-adhesive effects against different bacterial species.

Effect of cadmium stress and inoculation with a heavy-metal-resistant bacterium on the growth and enzyme activity of Sorghum bicolor

In this study, the influence of the heavy-metal-resistant rhizobacterial inoculant Rhodococcus ruber N7 on the growth and enzyme activity of Sorghum bicolor (L.) Moench. under cadmium stress was investigated in quartz sand pot experiments. The effect of cadmium and bacterium on the plant biomass accumulation, photosynthetic pigments, protein content, and the activities of plant-tissue enzymes such as peroxidase, laccase, and tyrosinase were estimated. It was shown that the presence of cadmium in the sand influenced the roots to a greater extent than it influenced the aerial parts of sorghum. This is manifested as increased protein content, reduced activity of peroxidase, and increased activity of laccase. Compared with cadmium stress, inoculation of plants with rhizobacterium R. ruber N7 has a stronger (and often opposite) effect on the biochemical parameters of sorghum, including a decrease in the concentration of protein in the plant, but increased the activity of peroxidase, laccase, and tyrosinase. Under cadmium contamination of sand, R. ruber N7 successfully colonizes the roots of Sorghum bicolor, survives in its root zone, and contributes to the accumulation of the metal in the plant roots, thereby reducing the concentration of the pollutant in the environment.

Individual or synchronous biodegradation of di-n-butyl phthalate and phenol by Rhodococcus ruber strain DP-2

The bacterial strain DP-2, identified as Rhodococcus ruber, is able to effectively degrade di-n-butyl phthalate (DBP) and phenol. Degradation kinetics of DBP and phenol at different initial concentrations revealed DBP and phenol degradation to fit modified first-order models. The half-life of DBP degradation ranged from 15.81 to 27.75h and phenol degradation from 14.52 to 45.52h under the initial concentrations of 600-1200mg/L. When strain DP-2 was cultured with a mixture of DBP (800mg/L) and phenol (700mg/L), DBP degradation rate was found to be only slightly influenced; however, phthalic acid (PA) accumulated, and phenol degradation was clearly inhibited during synchronous degradation. Transcriptional levels of degradation genes, phenol hydroxylase (pheu) and phthalate 3,4-dioxygenase (pht), decreased significantly more during synchronous degradation than during individual degradation. Quantitative estimation of individual or synchronous degradation kinetics is essential to manage mixed hazardous compounds through biodegradation in industrial waste disposal.