Rhodococcus Qingshengii Research Articles

Draft Genome Sequence of Rhodococcus qingshengii Strain PN_19, Isolated from a Moribund Individual of Pinna nobilis in Sardinia, Italy.

ABSTRACTDuring an epidemiological survey that aimed to discover the causes for the mass mortality of Pinna nobilis, a strain of Rhodococcus was found in a moribund individual. Here, we report its 7,037,134-bp draft genome sequence, which, after the annotation and genome survey, was identified as belonging to Rhodococcus qingshengii PN_19.

Complete Genome Sequence of Rhodococcus qingshengii Strain CL-05, Isolated from Concrete.

Here, we report the complete genome sequence of Rhodococcus qingshengii strain CL-05, which was isolated from pavement concrete in Newark, Delaware. The genome consists of a 6.29-Mbp chromosome and one plasmid (123,183 bp), encodes a total of 5,859 predicted proteins, and has a GC content of 62.5%.

Exploitation of extracellular organic matter from Micrococcus luteus to enhance ex situ bioremediation of soils polluted with used lubricants

Chronic pollution by used lubricant oils (ULOs) poses a serious challenge to the environment. Under stress conditions, microorganisms, including potential degraders, can enter a viable but non-culturable (VBNC) state, complicating the bioremediation of ULO-polluted areas. Resuscitation-promoting factors (Rpfs) can reverse this transition and/or enhance the biodegradation performance of both native and augmented strains. Here, Rpf-containing extracellular organic matter (EOM) from Micrococcus luteus was used to enhance the ex situ ULO removal in biostimulated and bioaugmented (with Rhodococcus qingshengii KAG C, R. erythropolis PR4) soils. ULO bioconversion, microbial activity, and CFUs were significantly higher in EOM-treated soils compared to corresponding control soils. After 60 days, the initial ULO concentration (52,500 mg kg−1) was reduced by 37% and 45% with EOM-supplemented biostimulation and bioaugmentation, respectively. Based on high-throughput 16S rRNA analysis, the enhancement was attributable both to the reactivation of EOM-responsive hydrocarbonoclastic bacterial genera (e.g., Pseudomonas, Comamonas, Stenotrophomonas, Gordonia) and to the long-term positive effect of EOM on the degradative efficacy of the introduced rhodococci. Ecotoxicological responses revealed that reduced ULO concentration did not correlate with decreased soil toxicity. Our findings provide an insight into the applicability of EOM in bioremediation and its effects on the soil microbial activity and community composition.

Toxicity evaluation of the metabolites derived from the degradation of phenanthrene by one of a soil ubiquitous PAHs-degrading strain Rhodococcus qingshengii FF

Rhodococcus qingshengii strain FF is a soil ubiquitous strain that has a high polycyclic aromatic hydrocarbons (PAHs) biodegradation capability. In this work, phenanthrene was used as a PAH model compound. The accumulated pattern of the metabolites of phenanthrene by strain FF was investigated, and their toxicity to Vibrio fischeri, effect on microbiota diversity of farmland soil and influence on seed of wheat were evaluated. Total of 29 main intermediates were observed for the phenanthrene degradation process. Pyrogallol was the predominant accumulated metabolite, and 59% of the accumulated metabolites were oxygen-containing PAHs that have only one benzene ring. The acute toxicity assessment showed the accumulated metabolites in later phase were more toxic to Vibrio fischeri. Microbe and wheat seed response to the different stages of phenanthrene metabolites indicated pollution significantly decreased microbial richness and evenness of farmland soil and lower germinal length, root length or root number of wheat seed. These results indicated that not only the elimination of PAHs, but also the easily accumulated metabolites produced during the PAHs degradation process should be paid enough attention. The comprehensive evaluation of toxicity during the degradation process would provide useful information for the use of microbe-orientated strategies in PAHs bioremediation.

Potential effects of Rhodococcus qingshengii strain djl-6 on the bioremediation of carbendazim-contaminated soil and the assembly of its microbiome

As a widely used fungicide, the environmental fate of carbendazim and its residues in agricultural products have caused great concern. However, its effects on soil microbial communities are largely unknown. Herein, we used high-throughput sequencing to reveal the effects of high and low dose of carbendazim and its degrading strain, Rhodococcus qingshengii strain djl-6, on the composition, diversity, and interrelationship of soil bacterial and fungal communities in short- and medium-term under laboratory conditions. The results showed that carbendazim exhibited an increased negative impact on bacterial communities and reduced the proportion of dominant fungal phylum Ascomycota during a 14-day incubation period. Only the impacts of low-dose carbendazim (2 mg·kg−1 dry soil) on fungal community were weakened. Network analysis showed that carbendazim increased the connectivity and modularity of microbial co-occurrence networks. Strain djl-6 exhibited good potential for bioremediation of carbendazim-contaminated soils. Moreover, it driven the assembly of potential carbendazim-degrading consortia from indigenous microbial communities; and members of the genera Arthrobacter, Bacillus, Brevundimonas, Lysinibacillus, Massilia, Mycobacterium, Paenibacillus, and Pseudarthrobacter might be participated in the degradation of carbendazim. Taken together, our study provides a relatively comprehensive understanding of the effects of carbendazim and its degrading strain djl-6 on soil microbial communities.

Complete Genome Sequence of the Cesium-Accumulating Bacterium Rhodococcus qingshengii CS98, Isolated from Soil in Japan.

Rhodococcus qingshengii CS98 is a bacterium isolated from soil in Japan that shows strong cesium-accumulating ability. Here, we report the complete genome sequence of R. qingshengii (6.7 Mb), which may provide useful genetic information supporting its bioremediation features.

Enhanced degradation and mineralization of phenol by combining two highly efficient strains with divergent ring-cleavage pathways

Pseudomonas stutzeri N2 and Rhodococcus qingshengii FF were combined to enhance phenol degradation, and the interaction mechanism of microorganisms was investigated. The cells in the culture of mixed strain degrading 1000 mg/L phenol exhibited a rapid growth and proliferation, and the maximum cell density of mixed strain was 34.6 ± 0.3% and 60.8 ± 0.2% higher than the single strain N2 and strain FF respectively. The degradation of phenol by mixed strain was completed within 24 h, and the phenol mineralization efficiency was up to 84.9 ± 0.4%. In addition, two ring-cleavage products of catechol accumulating from the culture of mixed strain were markedly reduced. Through the analysis of intermediates and functional groups, the enhanced phenol degradation by mixed strain was found to mainly depend on the synergistic effect of strain N2 served as an oxidant and strain FF acted as a reductant. Based on the synergic mechanism, the mixed strain might be used as a promising bacterial agent for removing phenolic compounds from the industrial wastewater.

Metagenomic Analysis Reveals Bacterial and Fungal Diversity and Their Bioremediation Potential From Sediments of River Ganga and Yamuna in India.

In this study, we report the presence of a microbial community of bioremediation potential in terms of relative abundance and taxonomic biodiversity in sediment samples of river Ganga and Yamuna, India at nine different sites. Metagenomic libraries were constructed using TruSeq Nano DNA Library Prep Kit and sequenced on NextSeq 500 by Illumina Next Generation Sequencing (NGS) technology. Bioremediation bacteria belong to 45 genera with 92 species and fungi belong to 13 genera with 24 species have been classified using Kaiju taxonomical classification. The study revealed that Proteobacteria was the most dominant bacterial flora, followed by Actinobacteria, Firmicutes, and Deinococcus–Thermus. PCA analysis revealed that bioremediation bacteria viz. Streptomyces bikiniensis, Rhodococcus qingshengii, Bacillus aerophilus, Pseudomonas veronii, etc., were more dominant in highly polluted river stretch as compared to less polluted river stretch. Similarly, the relative abundance of bioremediation fungi viz. Phanerochaete chrysosporium and Rhizopus oryzae, etc., were significantly correlated with the polluted Kanpur stretch of river Ganga. Several protein domains, which play a pivotal role in bioremediation in the polluted environments, including urea ABC transporter, UrtA, UrtD, UrtE, zinc/cadmium/mercury/lead-transporting ATPase, etc., were identified using protein domain analysis. The protein domains involved in pesticide biodegradation viz. P450, short-chain dehydrogenases/reductases (SDR), etc., were also discovered in river sediment metagenomics data. This is the first report on the richness of bioremediation microbial communities in the Ganga and Yamuna riverine ecosystems, highlighting their importance in aquatic pollution management.

Genomic and phenotypic analysis of siderophore-producing Rhodococcus qingshengii strain S10 isolated from an arid weathered serpentine rock environment

The success of members of the genus Rhodococcus in colonizing arid rocky environments is owed in part to desiccation tolerance and an ability to extract iron through the secretion and uptake of siderophores. Here, we report a comprehensive genomic and taxonomic analysis of Rhodococcus qingshengii strain S10 isolated from eathered serpentine rock at the arid Khalilovsky massif, Russia. Sequence comparisons of whole genomes and of selected marker genes clearly showed strain S10 to belong to the R. qingshengii species. Four prophage sequences within the R. qingshengii S10 genome were identified, one of which encodes for a putative siderophore-interacting protein. Among the ten non-ribosomal peptides synthase (NRPS) clusters identified in the strain S10 genome, two show high homology to those responsible for siderophore synthesis. Phenotypic analyses demonstrated that R. qingshengii S10 secretes siderophores and possesses adaptive features (tolerance ofup to 8% NaCland pH 9) that should enable survival in its native habitat within dry serpentine rock.

Immobilization of Rhodococcus qingshengii strain FF on the surface of polyethylene and its adsorption and biodegradation of mimic produced water

Low pH and high salinity characteristic of produced water (PW) posed a big challenge for the direct biological treatment. The immobilization of R. qingshengii strain FF, which degraded petroleum effectively under low pH, and application of immobilized R. qingshengii strain FF in treating mimic PW was studied in this work. The immobilization of R. qingshengii strain FF on the surface of polyethylene foam (PEF), one type of waste packaging materials, was optimized using the response surface methodology. Under optimum conditions, cell density of R. qingshengii strain FF immobilized on the surface of PEF reached 388 mg (cells)/g(PEF). In addition, a few factors, including hydraulic retention time (HRT), pH and salinity, were studied for treating mimic PW using immobilized R. qingshengii strain FF. The result of this study demonstrated that TPH degradation efficiency of PW by immobilized R. qingshengii strain FF reached above 90% when HRT was longer than 8 h. Weak acid and high salinity conditions only moderately decreased TPH. Asphalt, alkanes and aromatic hydrocarbon contained in petroleum can be degraded to some extent. These results indicated that immobilized R. qingshengii strain FF can be used as a highly efficient strain which could be used in biological treatment of real PW.

Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8.

Rhodococcus strain IGTS8 is the most extensively studied model bacterium for biodesulfurization of fossil fuels via the non–destructive sulfur–specific 4S pathway. This strain was initially assigned to Rhodococcus rhodochrous and later to Rhodococcus erythropolis thus making its taxonomic status debatable and reflecting the limited resolution of methods available at the time. In this study, phylogenomic analyses of the whole genome sequences of strain IGTS8 and closely related rhodococci showed that R. erythropolis and Rhodococcus qingshengii are very closely related species, that Rhodococcus strain IGTS8 is a R. qingshengii strain and that several strains identified as R. erythropolis should be re-classified as R. qingshengii. The genomes of strains assigned to these species contain potentially novel biosynthetic gene clusters showing that members of these taxa should be given greater importance in the search for new antimicrobials and other industrially important biomolecules. The plasmid-borne dsz operon encoding fossil fuel desulfurization enzymes was present in R. qingshengii IGTS8 and R. erythropolis XP suggesting that it might be transferable between members of these species.

Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency

Protein-based biomarkers can be a promising approach for identification and real-time monitoring of the bio-inoculants employed under sustainable agricultural plans. In this perspective, differential proteomics of psychrophilic diazotroph Rhodococcus qingshengii S10107 (JX173283) was performed to unravel its adaptive responses towards low-temperature nitrogen deficiency and identification of a biomarker for respective physiological conditions. LC-MS/MS-based proteome analysis mapped more than 4830 proteins including 77 up-regulated and 47 down-regulated proteins (p ≤ 0.05). Differential expression of the structural genes of nif regulon viz. nifH, nifD, and nifK along with their response regulators i.e. nifA, nifL, and nifB indicated that the nitrogenase complex was activated successfully. Besides up-regulating the biosynthesis of certain amino acids viz. Leucine, Lysine, and Alanine; the expression of the peptidoglycan synthesis proteins were also increased; while, the enzymes involved in Lipid biosynthesis were found to decrease. Furthermore, two important enzymes of the pentose phosphate pathway viz. Transketolase and Transaldolase along with Ribose import ATP-binding protein RbsA were also found to induce significantly under low temperature a nitrogen deficient condition, which suggests the cellular need for ample ribose sugar instantly. Additionally, comparative protein profiling of S10107 strain with our previous studies revealed that CowN protein was significantly up-regulated in all the cases under low-temperature nitrogen deficient conditions and therefore, can be developed as a biomarker. Conclusively, present study for the first time provides an in-depth proteome profiling of R. qingshengii S10107 and proclaims CowN as a potential protein biomarker for monitoring BNF under cold niches.

English

Two East Asian finless porpoises (Neophocaena asiaeorientalis sunameri) in Ningbo, East China Sea, China, were observed to be bacterially infected between the fat layer and muscle layer. The microbial communities in pus samples were identified by metagenome sequencing 16S in the PacBio platform and explored the relationship between emaciation and bacterial infection. The present paper was the first report on bacterial diversity in infected tissue pus of finless porpoise. In total, 101 bacterial species were identified, and the top nine species were Rhodococcus qingshengii (26.25%), Rhodococcus jialingiae (22.43%), Ralstonia pickettii (16.03%), Moraxella osloensis (9.97%), Psychrobacter cibarius (2.97%), Flavobacterium johnsoniae (2.11%), Flavobacterium chungbukense (1.80%), Stenotrophomonas maltophilia (1.73%) and Serratia marcescens (1.62%). These main bacteria could cause various diseases or metabolic disorder, such as endocarditis, meningitis, bacteraemia, septicaemia, and so on; they also involve microbiome metabolism of amino acids (12.47%), carbohydrates (11.58%), xenobiotic biodegradation (7.81%), lipids (6.01%) and energy (4.98%). Regardless of the type of disease metabolic disorder will firstly cause body weight loss. In conclusion, these bacteria could cause diseases or metabolic disorders, resulting in emaciation of East Asian finless porpoises. Admittedly, pathogenic assay is furthermore needed to determine the mechanisms regarding the pathological phenomena.   Key words: Bacterial diversity, East Asian finless porpoises, Metagenome sequencing 16S.

De Novo Genome Assembly of a Plant-Associated Rhodococcus qingshengii Strain (RL1) Isolated from Eruca sativa Mill. and Showing Plant Growth-Promoting Properties.

Rhodococcus qingshengii RL1 was isolated from surface-sterilized leaves of Eruca sativa Mill. and shows plant growth-promoting (PGP) properties. The de novo genome assembly consists of one chromosome with 6,253,838 bp and two plasmids with 144,038 bp and 448,745 bp. Many genes could be identified reflecting its PGP potential.

Inoculation with abscisic acid (ABA)-catabolizing bacteria can improve phytoextraction of heavy metal in contaminated soil

Promotion of plant capacity for accumulation of heavy metals (HMs) is one of the key strategies in enhancing phytoremediation in contaminated soils. Here we report that, Rhodococcus qingshengii, an abscisic acid (ABA)-catabolizing bacteria, clearly boosts levels of Cd, Zn, and Ni in wild-type Arabidopsis by 47, 24, and 30%, respectively, but no increase in Cu was noted, when compared with non-inoculated Arabidopsis plants in contaminated growth substrate. Furthermore, when compared with wild-type plants, R.qingshengii-induced increases in Cd, Zn, and Ni concentrations were more pronounced in abi1/hab1/abi2 (ABA-sensitive mutant) strains of Arabidopsis, whereas little effect was observed in snrk2.2/2.3 (ABA insensitive mutant). This demonstrates that metabolizing ABA might be indispensable for R. qingshengii to improve metal accumulation in plants. Bacterial inoculation significantly elevated the expression of Cd, Zn, and Ni-related transporters; whereas the transcript levels of Cu transporters remained unchanged. This result may be a reasonable explanation for why the uptake of Cd, Zn, and Ni in plants was stimulated by bacterial inoculation, while no effect was observed on Cu levels. From our results, we clearly demonstrate that R. qingshengii can increase the accumulation of Cd, Zn, and Ni in plants via an ABA-mediated HM transporters-associated mechanism. Metabolizing ABA in the plants by ABA-catabolizing bacterial inoculation might be an alternative strategy to improve phytoremediation efficiency in HMs contaminated soil.

Characterization of trehalose lipids produced by a unique environmental isolate bacterium Rhodococcus qingshengii strain FF.

The aim of this study was to elucidate the chemical properties and applications of trehalose lipids produced by Rhodococcus qingshengii strain FF and optimize its production yield. Strain FF was identified as R. qingshengii. It was observed to produce biosurfactants in the presence of n-hexadecane. The biosurfactants were identified as the mixture of trehalose triesters and trehalose tetraesters, mainly consisting of TrehC12 C3 C6 C12 :10, TrehC11 C8 C6 :6, TrehC11 C6 C4 :5 and TrehC6 C4 C6 :5 based on the analysis of thin layer chromatography, Fourier transform infrared and flight tandem mass spectrometry. The best carbon source and nitrogen source for producing trehalose lipids was the mixture of n-hexadecane and oleic acid (m:m=1:1) and the organic nitrogen, urea. Under this condition, the production of trehalose lipids could reach 7·97gl-1 . The crude trehalose lipids showed extremely high surface-active properties and were proven to promote the degradation of naphthalene. The trehalose lipids produced by R. qingshengii strain FF exhibited high surfactant activity under various conditions and were proven to promote the degradation of naphthalene. Rhodococcus qingshengii strain FF is a potential candidate for bioremediation. The trehalose lipids might be used as unique biosurfactants in cosmetic industries, biological formulations and other applications.

Impacts of Bioinoculants Pseudomonas jesenii MP1 and Rhodococcus qingshengii S10107 on Chickpea (Cicer arietinum L.) Yield and Soil Nitrogen Status

Cold-adapted bioinoculants are considered as harbingers of sustainable hill agriculture. Therefore, two previously characterized psychrotolerant diazotrophs, Pseudomonas jesenii MP1 and Rhodococcus qingshengii S10107, were evaluated for their plant growth-promoting potential for chickpea (Cicer arietinum L.) grown under natural field conditions. Comparative analysis of agronomical and biochemical crop parameters revealed the irrelevance of chemical fertilizers for chickpea production; the diazotrophs alone were sufficient to fulfil the crop’s nutritional requirement. However, the integrated use of bacterial strains in combination with urea at 20 kg N ha–1 as urea was being recommended for higher crop yield and better soil nitrogen status. Quantitative polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE)-based soil bacterial dynamics unveiled the persistence of both diazotrophs until the end of the crop maturation period without affecting the native micro-flora. Therefore, these bioinoculants can be explored as natural nitrogen resource, and an additional incentive in their bio-formulation will be a step towards agricultural sustainability.

Isolation, characterization and effect of plant-growth-promoting rhizobacteria on pine seedlings (Pinus pseudostrobus Lindl.)

In this study, 10 bacterial strains were isolated from the rhizosphere of coniferous trees on Mount Tlaloc in Mexico. The strains were characterized by their capacity to produce auxins, solubilize phosphates and stimulate mycelial growth of the ectomycorrhizal fungus Suillus sp. All isolates were identified at the molecular level. Moreover, an experiment was established to evaluate the response of Pinus pseudostrobus seedlings to inoculation with the rhizobacteria strains. The isolated strains belonged to the species Cupriavidus basilensis, Rhodococcus qingshengii, R. erythropolis, Pseudomonas spp., P. gessardii, Stenotrophomonas rhizophila and Cohnella sp. All of the strains produced auxins; the best producer was R. erythropolis CPT9 (76.4 µg mL−1). P. gessardii CPT6 solubilized phosphate at a significant level (443 µg mL−1). The strain S. rhizophila CPT8 significantly increased the radial growth of the ectomycorrhizal fungus Suillus sp. by 18.8%. Five strains increased the dry mass of the shoots; R. qingshengii CPT4 and R. erythropolis CPT9 increased growth the most, by more than 20%. Inoculation with plant-growth-promoting rhizobacteria can be a very useful practice in a forest nursery to produce healthy, vigorous plants.

Oil biodegradation: Interactions of artificial marine snow, clay particles, oil and Corexit

During the Deepwater Horizon (DwH) oil spill, interactions between oil, clay particles and marine snow lead to the formation of aggregates. Interactions between these components play an important, but yet not well understood, role in biodegradation of oil in the ocean water. The aim of this study is to explore the effect of these interactions on biodegradation of oil in the water. Laboratory experiments were performed, analyzing respiration and n-alkane and BTEX biodegradation in multiple conditions containing Corexit, alginate particles as marine snow, and kaolin clay. Two oil degrading bacterial pure cultures were added, Pseudomonas putida F1 and Rhodococcus qingshengii TUHH-12. Results show that the presence of alginate particles enhances oil biodegradation. The presence of Corexit alone or in combination with alginate particles and/or kaolin clay, hampers oil biodegradation. Kaolin clay and Corexit have a synergistic effect in increasing BTEX concentrations in the water and cause delay in oil biodegradation.

BIOACTIVITIES OF THE ETHYL ACETATE EXTRACT OF RHODOCOCCUS QINGSHENGII STRAIN BJC15-A38 AN ENDOPHYTE OF AZADIRACHTA INDICA A. JUSS

Objective: This study evaluated the antidiabetic activities of the ethyl acetate-methanol (4:1) extract (EA) of Rhodococcus qingshengii strain BJC15-A38 supernatant.Methods: In vitro alpha-amylase and alpha-glucosidase inhibitory assays, were used to determine the antidiabetic activity of EA (100, 250, 500, 750 and 1000 μg/ml). Also, the total phenol content of the extract was determined, followed by understanding the mode of α-amylase inhibition.Results: The crude extract from Azadirachta indica A. Juss. endophytic actinomycete Rhodococcus qingshengii strain BJC15-A38 was found to have significant inhibition against α-amylase (IC50 = 65.93 µg/ml) and α-glucosidase (IC50 = 929.56 µg/ml). The total phenol content of the crude was found to be 97.25±6.47 and 15.40±0.43 mg/g of the extract in terms of catechol and gallic acid equivalents respectively. Purification of the extract was carried out using silica gel column chromatography. Kinetic analysis revealed the mixed competitive with mixed competitive of inhibition towards α-amylase.Conclusion: The findings suggest that the extract of Rhodococcus qingshengii strain BJC15-A38 possesses antidiabetic effects.