Complete Genome Sequence of a Bacterium Representing a Deep Uncultivated Lineage within the
            <i>Gammaproteobacteria</i>
            Associated with the Degradation of Polycyclic Aromatic Hydrocarbons

Singleton, David R.; Dickey, Allison N.; Scholl, Elizabeth H.; Wright, Fred A.; Aitken, Michael D.

doi:10.1128/genomea.01086-16

Cited by 16 publications

(12 citation statements)

References 15 publications

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“…Root189, and Gammaproteobacteria bacterium TR3.2 which were isolated from gasoline-contaminated sediment, ammonium sulfate bioreactor, contaminated soil, thiocyanate bioreactor, and root of Arabidopsis thaliana , respectively (Choi et al 2013 ; Wattam et al 2017 ). Strain BD-a59 has the ability to degrade benzene, toluene, ethylbenzene, and o -, m -, and p -xylene, in turn Gammaproteobacteria bacterium TR3.2 has the potential in degradation of PAH similarly to the strain PY97M which exhibit ability to degrade pyrene and fluoranthene (Choi et al 2013 ; Cui et al 2013 ; Singleton et al 2016 ). The presence of ipfABDEF cluster in the genomes of these strains suggests their ability to degrade ibuprofen among other cyclic compounds.…”

Section: Monocyclic Nonsteroidal Anti-inflammatory Drugsmentioning

confidence: 99%

Organic micropollutants paracetamol and ibuprofen—toxicity, biodegradation, and genetic background of their utilization by bacteria

Żur

Piński

Marchlewicz

et al. 2018

Environ Sci Pollut Res

198

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Currently, analgesics and nonsteroidal anti-inflammatory drugs (NSAIDs) are classified as one of the most emerging group of xenobiotics and have been detected in various natural matrices. Among them, monocyclic paracetamol and ibuprofen, widely used to treat mild and moderate pain are the most popular. Since long-term adverse effects of these xenobiotics and their biological and pharmacokinetic activity especially at environmentally relevant concentrations are better understood, degradation of such contaminants has become a major concern. Moreover, to date, conventional wastewater treatment plants (WWTPs) are not fully adapted to remove that kind of micropollutants. Bioremediation processes, which utilize bacterial strains with increased degradation abilities, seem to be a promising alternative to the chemical methods used so far. Nevertheless, despite the wide prevalence of paracetamol and ibuprofen in the environment, toxicity and mechanism of their microbial degradation as well as genetic background of these processes remain not fully characterized. In this review, we described the current state of knowledge about toxicity and biodegradation mechanisms of paracetamol and ibuprofen and provided bioinformatics analysis concerning the genetic bases of these xenobiotics decomposition.

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Section: Monocyclic Nonsteroidal Anti-inflammatory Drugsmentioning

confidence: 99%

Organic micropollutants paracetamol and ibuprofen—toxicity, biodegradation, and genetic background of their utilization by bacteria

Żur

Piński

Marchlewicz

et al. 2018

Environ Sci Pollut Res

198

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“…Log-phase cells grown in sRB2 stained with the Remel Flagella Stain (Thermo Scientific) and examined under oil-immersion light microscopy did not appear to have flagella. However, analysis of the genome of strain TR3.2 T indicated a complete set of genes required for assembly of a flagellum [22]. Expression of flagella by strain TR3.2 T therefore may be possible under some conditions, but was not observed under those tested here.…”

mentioning

confidence: 69%

“…The genome of strain TR3.2 T was acquired and annotated as described previously [22]. The genome was a singular, circular chromosome of 3 243 537 bp with a G+C content of 67.79 mol%.…”

mentioning

confidence: 99%

“…No extrachromosomal elements were detected. Annotation predicted 3114 total genes with 3054 protein coding genes, a single rRNA gene operon and 45 tRNAencoding genes [22]. The complete 16S rRNA gene of strain TR3.2 T was compared to publicly available sequences using BLASTN of the non-redundant GenBank database in separate searches including and excluding environmental sequences.…”

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confidence: 99%

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Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbon-degrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov.

Corteselli

Aitken

Singleton

2017

International Journal of Systematic and Evolutionary Microbiology

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Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbondegrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov.Elizabeth M. Corteselli, Michael D. Aitken and David R. Singleton* AbstractThe bacterial strain TR3.2 T was isolated from aerobic bioreactor-treated soil from a polycyclic aromatic hydrocarbon (PAH)-contaminated site in Salisbury, NC, USA. Strain TR3.2 T was identified as a member of 'Pyrene Group 2' or 'PG2', a previously uncultivated cluster of organisms associated with the degradation of high-molecular-weight PAHs by stable-isotope probing. Based on its 16S rRNA gene sequence, the strain was classified as a member of the class Gammaproteobacteria but possessed only 90.5 % gene identity to its closest described relative, Methylococcus capsulatus strain Bath. Strain TR3.2 T grew on the PAHs pyrene, phenanthrene, anthracene, benz[a]anthracene and fluorene, as well as the azaarene carbazole, and could additionally metabolize a limited number of organic acids. Optimal growth occurred aerobically under mesophilic temperature, neutral pH and low salinity conditions. Strain TR3.2 T was catalase and oxidase positive. Predominant fatty acids were C 17 : 0 cyclo and C 16 : 0 . Genomic G+C content of the single chromosome was 67.79 mol% as determined by complete genome sequencing. Due to the high sequence divergence from any cultivated species and its unique physiological properties compared to its closest relatives, strain TR3.2 T is proposed as a representative of a novel order, family, genus and species within the class Gammaproteobacteria, for which the name Immundisolibacter cernigliae gen. nov., sp. nov. is proposed. The associated order and family are therefore proposed as Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov. The type strain of the species is

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“…Sequences were most similar to Immundisolibacter cernigliae strain TR3.2 (NR_156 801), a polycyclic aromatic hydrocarbon degrading bacterium (Singleton et al . 2016 ; Corteselli, Aitken and Singleton 2017b ). This group of bacteria was also present in the FW MM T (3.6% of the 16S rRNA gene reads) but virtually absent in the FW YBS T (0.1%).…”

Section: Resultsmentioning

confidence: 99%

Microbiomes in a manganese oxide producing ecosystem in the Ytterby mine, Sweden: impact on metal mobility

Sjöberg

Stairs

Allard

et al. 2020

FEMS Microbiology Ecology

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Microbe-mediated precipitation of Mn-oxides enriched in rare earth elements (REE) and other trace elements was discovered in tunnels leading to the main shaft of the Ytterby mine, Sweden. Defining the spatial distribution of microorganisms and elements in this ecosystem provide a better understanding of specific niches and parameters driving the emergence of these communities and associated mineral precipitates. Along with elemental analyses, high-throughput sequencing of the following four subsystems were conducted: (1) water seeping from a rock fracture into the tunnel, (2) Mn-oxides and associated biofilm; referred to as the Ytterby Black Substance (YBS) biofilm (3) biofilm forming bubbles on the Mn-oxides; referred to as the bubble biofilm, and (4) fracture water that has passed through the biofilms. Each subsystem hosts a specific collection of microorganisms. Differentially abundant bacteria in the YBS biofilm were identified within the Rhizobiales (e.g. Pedomicrobium), PLTA13 Gammaproteobacteria, Pirellulaceae, Hyphomonadaceae, Blastocatellia and Nitrospira. These taxa, likely driving the Mn-oxide production, were not detected in the fracture water. This biofilm binds Mn, REE and other trace elements in an efficient, dynamic process, as indicated by substantial depletion of these metals from the fracture water as it passes through the Mn deposit zone. Microbe-mediated oxidation of Mn(II) and formation of Mn(III/IV)-oxides can thus have considerable local environmental impact by removing metals from aquatic environments.

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Complete Genome Sequence of a Bacterium Representing a Deep Uncultivated Lineage within the Gammaproteobacteria Associated with the Degradation of Polycyclic Aromatic Hydrocarbons

Cited by 16 publications

References 15 publications

Organic micropollutants paracetamol and ibuprofen—toxicity, biodegradation, and genetic background of their utilization by bacteria

Organic micropollutants paracetamol and ibuprofen—toxicity, biodegradation, and genetic background of their utilization by bacteria

Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbon-degrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov.

Microbiomes in a manganese oxide producing ecosystem in the Ytterby mine, Sweden: impact on metal mobility

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