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July 7, 2019  |  

Genomic and transcriptomic analyses reveal the characterization of a crude oil degrading bacterial strain: Pedobacter steynii DX4

Pedobacter steynii DX4, isolated from Qinghai-Tibet plateau, exhibited capability to effectively degrade crude oil at low temperature. In order to illustrate its biodegradation mechanism, whole genome and transcriptome sequencing were performed. It is the first genome of crude oil degrading strain in Pedobacter genus. The P. steynii DX4 genome consists of a single circular chromosome of 6,581,659 bp with an average G+C content of 41.31% and encodes 5464 genes in all. GIs were predicted and comparison analysis was performed between relative species. Genome annotation predicted several hydrocarbon oxygenases, chemotaxis proteins and biosurfactant synthetases. The transcriptional sequences profiled a lot of differently expressed genes when cells respectively grown on crude oil and pyruvate mediums. Crude oil significantly stimulated the expression of the genes related to the hydrocarbon oxidation and resparitory chain. Genomic and transcriptomic analysis of P. steynii DX4 have revealed the machenism of the crude oil degradation in Pedobacter steynii DX4 and provided us with valuable knowledge base to make effective strategy to mitigate the ecological damage caused by crude oil pollution.

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July 7, 2019  |  

Systems biology-guided biodesign of consolidated lignin conversion

Lignin is the second most abundant biopolymer on the earth, yet its utilization for fungible products is complicated by its recalcitrant nature and remains a major challenge for sustainable lignocellulosic biorefineries. In this study, we used a systems biology approach to reveal the carbon utilization pattern and lignin degradation mechanisms in a unique lignin-utilizing Pseudomonas putida strain (A514). The mechanistic study further guided the design of three functional modules to enable a consolidated lignin bioconversion route. First, P. putida A514 mobilized a dye peroxidase-based enzymatic system for lignin depolymerization. This system could be enhanced by overexpressing a secreted multifunctional dye peroxidase to promote a two-fold enhancement of cell growth on insoluble kraft lignin. Second, A514 employed a variety of peripheral and central catabolism pathways to metabolize aromatic compounds, which can be optimized by overexpressing key enzymes. Third, the ß-oxidation of fatty acid was up-regulated, whereas fatty acid synthesis was down-regulated when A514 was grown on lignin and vanillic acid. Therefore, the functional module for polyhydroxyalkanoate (PHA) production was designed to rechannel ß-oxidation products. As a result, PHA content reached 73% per cell dry weight (CDW). Further integrating the three functional modules enhanced the production of PHA from kraft lignin and biorefinery waste. Thus, this study elucidated lignin conversion mechanisms in bacteria with potential industrial implications and laid out the concept for engineering a consolidated lignin conversion route.

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July 7, 2019  |  

Complete genome sequence of a psychotrophic Pseudarthrobacter sulfonivorans strain Ar51 (CGMCC 4.7316), a novel crude oil and multi benzene compounds degradation strain.

Pseudarthrobacter sulfonivorans strain Ar51, a psychotrophic bacterium isolated from the Tibet permafrost of China, can degrade crude oil and multi benzene compounds efficiently in low temperature. Here we report the complete genome sequence of this bacterium. The complete genome sequence of Pseudarthrobacter sulfonivorans strain Ar51, consisting of a cycle chromosome with a size of 5.04Mbp and a cycle plasmid with a size of 12.39kbp. The availability of this genome sequence allows us to investigate the genetic basis of crude oil degradation and adaptation to growth in a nutrient-poor permafrost environment. Copyright © 2016 Elsevier B.V. All rights reserved.

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July 7, 2019  |  

Complete genome sequence of Marivivens sp. JLT3646, a potential aromatic compound degrader

Marivivens sp. JLT3646 (CGMCC 1.15778), belonging to the phylum Alphaproteobacteria, was isolated from seawater, Kueishan Islet, offshore northeast of Taiwan. Here, we present the complete genome sequence of Marivivens sp. JLT3646, which contains a circular 2,978,145 bp chromosome with 56.2% G + C content, and one circular plasmid which is 169,066 bp in length. The genome data suggested that Marivivens sp. JLT3646 has the potential to degrade aromatic monomers, which might provide insight into biotechnological applications and facilitate the investigation of environmental bioremediation.

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July 7, 2019  |  

Draft genome sequence of Bacillus sp. strain UFRGS-B20, a hydrocarbon degrader.

Bacillus sp. strain UFRGS-B20 was isolated in 2012 from Brazilian land-farming soil contaminated with petrochemical oily sludge. This strain was subjected to hydrocarbon biodegradation tests, showing degradation rates of up to 60%. Here, we present the 6.82-Mb draft genome sequence of the strain, which contains 2,178 proteins with functional assignments.

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July 7, 2019  |  

Complete genome of Halomonas aestuarii Hb3, isolated from tidal flat

Halomonas aestuarii Hb3, a moderately halophilic bacterium belonging to the class Gammaproteobacteria, was isolated from a tidal flat. Herein, we report the complete genome sequence of its strain Hb3. Its size is estimated at 3.54Mbp with a mean G+C content of 67.9%. The genome includes 3238 open reading frames, 65 transfer RNAs, and four ribosomal RNA gene operons. Genes related to the degradation of monoaromatic compounds, detoxification of arsenic, and production of polymers were identified. These features indicate that this strain may be important for ecological and industrial application.

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July 7, 2019  |  

Complete genome sequence of Tsukamurella sp. MH1: A wide-chain length alkane-degrading actinomycete.

Tsukamurella sp. strain MH1, capable to use a wide range of n-alkanes as the only carbon source, was isolated from petroleum-contaminated soil (Pite?ti, Romania) and its complete genome was sequenced. The 4,922,396?bp genome contains only one circular chromosome with a G?+?C content of 71.12%, much higher than the type strains of this genus (68.4%). Based on the 16S rRNA genes sequence similarity, strain MH1 was taxonomically identified as Tsukamurella carboxydivorans. Genome analyses revealed that strain MH1 is harboring only one gene encoding for the alkB-like hydroxylase, arranged in a complete alkane monooxygenase operon. This is the first complete genome of the specie T. carboxydivorans, which will provide insights into the potential of Tsukamurella sp. MH1 and related strains for bioremediation of petroleum hydrocarbons-contaminated sites and into the environmental role of these bacteria. Copyright © 2017. Published by Elsevier B.V.

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July 7, 2019  |  

Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, Chile

Rhodococcus sp. H-CA8f was isolated from marine sediments obtained from the Comau fjord, located in Northern Chilean Patagonia. Whole-genome sequencing was achieved using PacBio RS II platform, comprising one closed, complete chromosome of 6,19?Mbp with a 62.45% G?+?C content. The chromosome harbours several metabolic pathways providing a wide catabolic potential, where the upper biphenyl route is described. Also, Rhodococcus sp. H-CA8f bears one linear mega-plasmid of 301?Kbp and 62.34% of G?+?C content, where genomic analyses demonstrated that it is constituted mostly by putative ORFs with unknown functions, representing a novel genetic feature. These genetic characteristics provide relevant insights regarding Chilean marine actinobacterial strains.

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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  |  

Finished genome sequence of a polyurethane-degrading Pseudomonas isolate.

Pseudomonas sp. strain WP001 is a laboratory isolate capable of polyurethane polymer degradation and harbors a predicted lipase precursor gene. The genome of strain WP001 is 6.15?Mb in size and is composed of seven scaffolds with a G+C content of 60.54%. Strain WP001 is closely related to Pseudomonas fluorescens based on ribosomal DNA comparisons. Copyright © 2018 Stamps 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  |  

Thauera sinica sp. nov., a phenol derivative-degrading bacterium isolated from activated sludge.

A bacterial strain, K11T, capable of degrading phenol derivatives was isolated from activated sludge of a sewage treatment plant in China. This strain, which can degrade more than ten phenol derivatives, was identified as a Gram-stain negative, rod-shaped, asporogenous, facultative anaerobic bacterium with a polar flagellum. The strain was found to grow in tryptic soy broth in the presence of 0-2.5% (w/v) NaCl (optimum 0-1%), at 4-43 °C (optimum 30-35 °C) and pH 4.5-10.5 (optimum 7.5-8). Comparative analysis of nearly full-length 16S rRNA gene sequences showed that this strain belongs to the genus Thauera. The 16S rRNA gene sequence was found to show high similarity (97.5%) to that of Thauera chlorobenzoica 3CB-1T, with lesser similarity to other recognised Thauera strains. The G+C content of the DNA of the strain was determined to be 67.8 mol%. The DNA-DNA hybridization value between K11T and Thauera aromatica DSM6984T was 10.4 ± 4.5%. The genomic OrthoANI values of K11T with the other nine type strains of genus Thauera were less than 81.1%. Chemotaxonomic analysis of strain K11T revealed that Q-8 is the predominant quinone; the polar lipids contain phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and five uncharacterised lipids; the major cellular fatty acid was identified as summed feature 3 (C16:1 ?7c and/or iso-C15:0 2-OH; 45.9%), followed by C16:0 (20.5%) and C18:1 ?7c (15.8%). Based on the phenotypic and phylogenetic evidence, DNA-DNA hybridisation, OrthoANI, chemotaxonomic analysis and results of the physiological and biochemical tests, a new species named Thauera sinica sp. nov. is proposed with strain K11T (= CGMCC 1.15731T = KACC 19216T) designated as the type strain.

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July 7, 2019  |  

Complete genome sequence of Bacillus licheniformis BL-010.

The biodegradation of Aflatoxin B1 (AFB1) is an industry of increasing importance. Bacillus licheniformis BL-010 was isolated from the aflatoxin contaminated corn feed storage, and was shown to degrade AFB1 efficiently. Here we present the complete genome sequence of BL-010, the genome comprises 4,287,714 bp in a circular chromosome with a GC content of 46.12% and contains genes encoding AFB1 degrading enzymes. The genome sequence displayed that this strain contains genes involved in production of laccase, aromatic ring-opening dioxygenase which could detoxify AFB1. Complete genome sequence of the strain BL-010 can further provide the genomic basis for the biotechnological application of strain BL-010 as an effective way to degrade AFB1. Copyright © 2018 Elsevier Ltd. All rights reserved.

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July 7, 2019  |  

Low-level antimicrobials in the medicinal leech select for resistant pathogens that spread to patients.

Fluoroquinolones (FQs) and ciprofloxacin (Cp) are important antimicrobials that pollute the environment in trace amounts. Although Cp has been recommended as prophylaxis for patients undergoing leech therapy to prevent infections by the leech gut symbiont Aeromonas, a puzzling rise in Cp-resistant (Cpr) Aeromonas infections has been reported. We report on the effects of subtherapeutic FQ concentrations on bacteria in an environmental reservoir, the medicinal leech, and describe the presence of multiple antibiotic resistance mutations and a gain-of-function resistance gene. We link the rise of CprAeromonas isolates to exposure of the leech microbiota to very low levels of Cp (0.01 to 0.04 µg/ml), <1/100 of the clinical resistance breakpoint for Aeromonas Using competition experiments and comparative genomics of 37 strains, we determined the mechanisms of resistance in clinical and leech-derived Aeromonas isolates, traced their origin, and determined that the presence of merely 0.01 µg/ml Cp provides a strong competitive advantage for Cpr strains. Deep-sequencing the Cpr-conferring region of gyrA enabled tracing of the mutation-harboring Aeromonas population in archived gut samples, and an increase in the frequency of the Cpr-conferring mutation in 2011 coincides with the initial reports of CprAeromonas infections in patients receiving leech therapy.IMPORTANCE The role of subtherapeutic antimicrobial contamination in selecting for resistant strains has received increasing attention and is an important clinical matter. This study describes the relationship of resistant bacteria from the medicinal leech, Hirudo verbana, with patient infections following leech therapy. While our results highlight the need for alternative antibiotic therapies, the rise of Cpr bacteria demonstrates the importance of restricting the exposure of animals to antibiotics approved for veterinary use. The shift to a more resistant community and the dispersion of Cpr-conferring mechanisms via mobile elements occurred in a natural setting due to the presence of very low levels of fluoroquinolones, revealing the challenges of controlling the spread of antibiotic-resistant bacteria and highlighting the importance of a holistic approach in the management of antibiotic use. Copyright © 2018 Beka et al.

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