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July 7, 2019  |  

Use of WGS data for investigation of a long-term NDM-1-producing Citrobacter freundii outbreak and secondary in vivo spread of blaNDM-1 to Escherichia coli, Klebsiella pneumoniae and Klebsiella oxytoca.

An outbreak of NDM-1-producing Citrobacter freundii and possible secondary in vivo spread of blaNDM-1 to other Enterobacteriaceae were investigated.From October 2012 to March 2015, meropenem-resistant Enterobacteriaceae were detected in 45 samples from seven patients at Aalborg University Hospital, Aalborg, Denmark. In silico resistance genes, Inc plasmid types and STs (MLST) were obtained from WGS data from 24 meropenem-resistant isolates (13 C. freundii, 6 Klebsiella pneumoniae, 4 Escherichia coli and 1 Klebsiella oxytoca) and 1 meropenem-susceptible K. oxytoca. The sequences of the meropenem-resistant C. freundii isolates were compared by phylogenetic analyses. In vitro susceptibility to 21 antimicrobial agents was tested. Furthermore, in vitro conjugation and plasmid characterization was performed.From the seven patients, 13 highly clonal ST18 NDM-1-producing C. freundii were isolated. The ST18 NDM-1-producing C. freundii isolates were only susceptible to tetracycline, tigecycline, colistin and fosfomycin (except for the C. freundii isolates from Patient 2 and Patient 7, which were additionally resistant to tetracycline). The E. coli and K. pneumoniae from different patients belonged to different STs, indicating in vivo transfer of blaNDM-1 in the individual patients. This was further supported by in vitro conjugation and detection of a 154 kb IncA/C2 plasmid with blaNDM-1. Patient screenings failed to reveal any additional cases. None of the patients had a history of recent travel abroad and the source of the blaNDM-1 plasmid was unknown.To our knowledge, this is the first report of an NDM-1-producing C. freundii outbreak and secondary in vivo spread of an IncA/C2 plasmid with blaNDM-1 to other Enterobacteriaceae.© The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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July 7, 2019  |  

Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation.

A novel marine strain representing efficient degradation ability toward brown algae was isolated, identified, and assigned to Bacillus weihaiensis Alg07. The alga-associated marine bacteria promote the nutrient cycle and perform important functions in the marine ecosystem. The de novo sequencing of the B. weihaiensis Alg07 genome was carried out. Results of gene annotation and carbohydrate-active enzyme analysis showed that the strain harbored enzymes that can completely degrade alginate and laminarin, which are the specific polysaccharides of brown algae. We also found genes for the utilization of mannitol, the major storage monosaccharide in the cell of brown algae. To understand the process of brown algae decomposition by B. weihaiensis Alg07, RNA-seq transcriptome analysis and qRT-PCR were performed. The genes involved in alginate metabolism were all up-regulated in the initial stage of kelp degradation, suggesting that the strain Alg07 first degrades alginate to destruct the cell wall so that the laminarin and mannitol are released and subsequently decomposed. The key genes involved in alginate and laminarin degradation were expressed in Escherichia coli and characterized. Overall, the model of brown algae degradation by the marine strain Alg07 was established, and novel alginate lyases and laminarinase were discovered.

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July 7, 2019  |  

The genome of the toluene-degrading Pseudomonas veronii strain 1YdBTEX2 and its differential gene expression in contaminated sand.

The natural restoration of soils polluted by aromatic hydrocarbons such as benzene, toluene, ethylbenzene and m- and p-xylene (BTEX) may be accelerated by inoculation of specific biodegraders (bioaugmentation). Bioaugmentation mainly involves introducing bacteria that deploy their metabolic properties and adaptation potential to survive and propagate in the contaminated environment by degrading the pollutant. In order to better understand the adaptive response of cells during a transition to contaminated material, we analyzed here the genome and short-term (1 h) changes in genome-wide gene expression of the BTEX-degrading bacterium Pseudomonas veronii 1YdBTEX2 in non-sterile soil and liquid medium, both in presence or absence of toluene. We obtained a gapless genome sequence of P. veronii 1YdBTEX2 covering three individual replicons with a total size of 8 Mb, two of which are largely unrelated to current known bacterial replicons. One-hour exposure to toluene, both in soil and liquid, triggered massive transcription (up to 208-fold induction) of multiple gene clusters, such as toluene degradation pathway(s), chemotaxis and toluene efflux pumps. This clearly underlines their key role in the adaptive response to toluene. In comparison to liquid medium, cells in soil drastically changed expression of genes involved in membrane functioning (e.g., lipid composition, lipid metabolism, cell fatty acid synthesis), osmotic stress response (e.g., polyamine or trehalose synthesis, uptake of potassium) and putrescine metabolism, highlighting the immediate response mechanisms of P. veronii 1YdBTEX2 for successful establishment in polluted soil.

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July 7, 2019  |  

Genome sequence of Pseudomonas citronellolis SJTE-3, an estrogen- and polycyclic aromatic hydrocarbon-degrading bacterium.

Pseudomonas citronellolis SJTE-3, isolated from the active sludge of a wastewater treatment plant in China, can utilize a series of environmental estrogens and estrogen-like toxicants. Here, we report its whole-genome sequence, containing one circular chromosome and one circular plasmid. Genes involved in estrogen biodegradation in this bacterium were predicted. Copyright © 2016 Zheng et al.

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July 7, 2019  |  

Draft whole-genome sequence of the fluorene-degrading Sphingobium sp. strain LB126, isolated from polycyclic aromatic hydrocarbon-contaminated soil.

We report here the draft whole-genome sequence of a fluorene-degrading bacterium, Sphingobium sp. strain LB126. The genes involved in the upper biodegradation pathway of fluorene are located on a plasmid, and the lower pathway that generates tricarboxylic acid cycle intermediates is initiated by the meta-cleavage of protocatechuic acid that is chromosomally encoded. Copyright © 2018 Augelletti et al.

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July 7, 2019  |  

Complete genome sequence of Gordonia sp. YC-JH1, a bacterium efficiently degrading a wide range of phthalic acid esters.

Phthalic acid esters (PAEs) are a family of recalcitrant pollutants mainly used as plasticizer. The strain Gordonia sp.YC-JH1, isolated from petroleum-contaminated soil, is capable of efficiently degrading a wide range of PAEs. In order to pertinently investigate the genetic mechanism of PAEs catabolism by strain YC-JH1, its complete genome sequencing has been performed by SMRT sequencing technology. The genome comprises a circular chromosome and a plasmid with a size of 4,101,557 bp and 91,767 bp respectively. Based on the genome sequence, 3563 protein-coding genes are predicted, of which the genes responsible for PAEs degradation are identified, including the two genes of PAEs hydrolase and the gene clusters for phthalic acid and protocatechuic acid degradation. The genome information provides genomic basis of PAEs degradation to allow the complete metabolism of PAEs. The wide substrate spectrum and its genetic basis of this strain should expand its application potential for environments bioremediation, provide novel gene resources involved in PAEs degradation for biotechnology and gene engineering, and contribute to shed light on the mechanism of PAEs metabolism. Copyright © 2018. Published by Elsevier B.V.

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July 7, 2019  |  

Complete genome sequence of the dissimilatory azo reducing thermophilic bacterium Novibacillus thermophiles SG-1.

With the isolation and identification of efficient azo-dye degradation bacteria, bioaugmentation with specific microbial strains has now become an effective strategy to promote the bioremediation of azo dye. However, Azo dye wastewater discharged at high temperature restricted the extensive application of the known mesophilic azoreducing microorganisms. Here we present the complete genome sequence of a bacterium capable of reducing azo dye under thermophilic condition, Novibacillus thermophiles SG-1 (=KCTC 33118T =CGMCC 1.12363T). The complete genome of strain SG-1 contains a circular chromosome of 3,629,225 bp with a G?+?C content of 50.44%. Genome analysis revealed that strain SG-1 possessed genes encoding riboflavin biosynthesis protein that would secrete riboflavin, which could act as electron shuttles to transport the electrons to extracellular azo dye in decolorization process. HPLC analysis showed that the concentration of riboflavin increased from 0.01?µM to 0.255?µM with the growth of strain SG-1 under azo dye reduction. Quantitative real-time PCR analysis further demonstrated that the gene encoding riboflavin biosynthesis protein would be involved in the azo dye decolorization. The results from this study would be beneficial to research the mechanism of anaerobic reduction of azo dye under thermophilic conditions. Copyright © 2018 Elsevier B.V. All rights reserved.

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July 7, 2019  |  

Complete genome sequence of Bacillus sp. HBCD-sjtu, an efficient HBCD-degrading bacterium.

Environmental pollution caused by the release of industrial chemicals is currently one of the most important environmental harms. Manufacturing chemicals can be biodegraded, and valuable intermediates can be used as pharmacophores in drug targeting and have several other useful purposes. Hexabromocyclododecane (HBCD), a non-aromatic brominated flame retardant, is a toxic compound that consists of a cycloaliphatic ring of 12 carbon atoms to which six bromine atoms are attached. It is formed by bromination of cis-trans-trans-1,5,9-cyclododecatriene, but its use is now restricted in several countries, because it is an environmental pollutant. Little is known about whether bacteria can degrade HBCD. A bacterial strain that degrades HBCD was recently isolated using enrichment culture techniques. Based on morphological, biochemical and phylogenetic analysis this isolate was categorized as Bacillus cereus and named strain HBCD-sjtu. Maximum growth and HBCD-degrading activity were observed when this strain was grown at 30 °C, pH 7.0 and 200 RPM in mineral salt medium containing 0.5 mm HBCD. The genome of strain HBCD-sjtu, which consists of only one circular chromosome, was sequenced. This whole genome sequence will be crucial for illuminating the molecular mechanisms of HBCD degradation.

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July 7, 2019  |  

Bioaugmentated activated sludge degradation of progesterone: Kinetics and mechanism

Progesterone (PGT) is not completely removed in conventional treatment plants, and the processing results may have adverse effects on aquatic organisms. In this study, an effective PGT-degradation bacterium, Rhodococcus sp. HYW, was newly isolated from the pharmaceutical plant and was used to augment degradation of PGT. When grown in a mineral medium (MM) containing a trace amount of PGT (500?µg/L) as the sole carbon and energy source, the results show that 99% of PGT was degraded within 1?h and followed the first-order reaction kinetics. Bioaugmentation of PGT-contaminated activated sludge greatly enhanced the PGT degradation rate (~91%) and its derivatives degradation rate were also greatly improved (>83%). The process of PGT degradation in non-bioaugmented PGT-contaminated activated sludge (NBS) and bioaugmentation activated sludge with the bacterial consortium(BS) also conforms to the first-order kinetic model. Furthermore, 12 and 11 biodegradation products for PGT in the NBS and BS were identified using HPLC-LTQ-Orbitrap XL™, respectively. Based on these biodegradation products, two degradation pathways for PGT in NBS and BS were proposed, respectively. Comparing the degradation kinetics and metabolites, it was found that BS degrades PGT more rapidly and can further convert PGT to a small molecular acid. Finally, to reveal the probable cause for the differences in the PGT degradation efficiency and products in the NBS and BS.

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July 7, 2019  |  

Identification and genome analysis of Deinococcus actinosclerus SJTR1, a novel 17ß-estradiol degradation bacterium.

Biodegradation with microorganisms is considered as an efficient strategy to remove the environmental pollutants. In this work, Deinococcus actinosclerus SJTR1 isolated from the wastewater was confirmed with great degradation capability to 17ß-estradiol, one typical estrogen chemical. It could degrade nearly 90% of 17ß-estradiol (10 mg/L) in 5 days and transform it into estrone; its degradation kinetics fitted for the first-order kinetic equation. The whole genome sequence of D. actinosclerus SJTR1 was obtained and annotated, containing one chromosome (3,315,586 bp) and four plasmids (ranging from 17,267 bp to 460,244 bp). A total of 3913 CDSs and 73 RNA genes (including 12 rRNA genes, 50 tRNA genes, and 11 ncRNA genes) were identified in its whole genome sequence. On this basis, a series of potential genes involved in steroid metabolism and stress responses of D. actinosclerus SJTR1 were predicted. It is the first report of Deinococcus strain with the degradation capability to estrogens. This work could enrich the genome sources of the estrogen-degrading strains and promote the degradation mechanism study of 17ß-estradiol in bacteria.

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July 7, 2019  |  

Genome analysis of Rhodococcus Sp. DSSKP-R-001: A highly effective ß-estradiol-degrading bacterium.

We screened bacteria that use E2 as its sole source of carbon and energy for growth and identified them as Rhodococcus, and we named them DSSKP-R-001. For a better understanding of the metabolic potential of the strain, whole genome sequencing of Rhodococcus DSSKP-R-001 and annotation of the functional genes were performed. The genomic sketches included a predicted protein-coding gene of approximately 5.4?Mbp with G?+?C content of 68.72% and 5180. The genome of Rhodococcus strain DSSKP-R-001 consists of three replicons: one chromosome and two plasmids of 5.2, 0.09, and 0.09, respectively. The results showed that there were ten steroid-degrading enzymes distributed in the whole genome of the strain. The existence and expression of estradiol-degrading enzymes were verified by PCR and RTPCR. Finally, comparative genomics was used to compare multiple strains of Rhodococcus. It was found that Rhodococcus DSSKP-R-001 had the highest similarity to Rhodococcus sp. P14 and there were 2070 core genes shared with Rhodococcus sp. P14, Rhodococcus jostii RHA1, Rhodococcus opacus B4, and Rhodococcus equi 103S, showing evolutionary homology. In summary, this study provides a comprehensive understanding of the role of Rhodococcus DSSKP-R-001 in estradiol-efficient degradation of these assays for Rhodococcus. DSSKP-R-001 in bioremediation and evolution within Rhodococcus has important meaning.

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