Draft Genome Sequence of Thiobacimonas sp. Strain D13, a Phthalate Ester-Degrading Bacterium Isolated from Deep-Sea Sediments.
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PROVIDER: S-EPMC6588033 | BioStudies |
REPOSITORIES: biostudies
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Project description:Datasets presented here were employed in the main work "Characterization of phthalate-degrading-bacteria from Asian carp microbiomes and riverine sediments" (Kolb et al., 2019a). The carcinogenic compounds dimethyl phthalate (DMP), diethyl phthalate (DEP), and dibutyl phthalate (DBP) are ubiquitous in the environment due to widespread production and distribution which can be taken up by aquatic organisms. Asian carp species silver (<i>Hypophthalmichthys molitrix</i>) and bighead (<i>Hypophthalmichthys nobilis</i>) are exposed to phthalates by ingestion and absorption. This article presents data on the characterization of phthalate-degrading bacteria isolated from Asian carp microbiomes and riverine sediments by means of sample collection, enrichment, and isolation. Graphical data presents substrate utilization profiles of consortium SK-1 and <i>Rhodococcus ruber</i> derived from the gut microbiome of <i>H. molitrix</i>. Additionally, phthalate-degrading microbes were isolated from the gut and scale microbiomes of Asian carp where scanning electron microscopy images show the morphology from samples of final enrichment cultures and isolates. Consortium SK-1 was subjected to amplicon sequencing where community data shows the distribution of taxa while enriched with 500 mg L<sup>-1</sup> DMP, DEP, and DBP combined. The data presented can provide insights to future research since other phthalate-degrading isolates and consortia can potentially be isolated from the microbiomes of aquatic organisms.
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Project description:Recent investigations have demonstrated that bacteria employ the volatile compounds they produce during interactions with other organisms, such as plants, fungi, nematodes and bacteria. However, studies focused on the antibacterial activity of plant growth-promoting rhizobacteria (PGPR) volatiles against bacterial phytopathogens are still rare. In this study, Bacillus strain D13, which is antagonistic to Xanthomonas oryzae pv. oryzae (Xoo), was isolated and screened. Volatile compounds emitted from strain D13 reduced the colony diameter and cell motility of Xoo cultured in divided Petri plates. Transmission electron micrograph analysis showed concentration in cytoplasm and altered surface morphology in the majority of Xanthomonas cells after co-cultivation with strain D13. Transcriptional expression of virulence-associated genes in Xoo was repressed. Based on gas chromatography/mass spectrometry (GC/MS) analysis, 12 volatile compounds specifically produced by strain D13 were identified. Among them, decyl alcohol and 3,5,5-trimethylhexanol inhibited the growth of Xoo at minimum inhibitory amounts of 0.48 and 2.4 mg, respectively. Furthermore, transcriptional expression of virulence-associated genes was also repressed by decyl alcohol and 3,5,5-trimethylhexanol. These results are useful for a better understanding of the biocontrol mechanisms of Bacillus.
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Project description:A newly isolated bacterial strain SHJ was found to be capable of degrading diethyl phthalate (DEP) very efficiently. Its growth characteristics and 16S rDNA gene sequence were analyzed. Its whole genome was also sequenced. Strain SHJ was identified as Sphingobium yanoikuyae SHJ.
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Project description:A bacterium capable of utilizing dimethyl phthalate (DMP), diethyl phthalate (DEP), di-<i>n</i>-butyl phthalate (DBP), and diisobuthyl phthalate (DIBP) as the sole carbon and energy source was isolated from shallow aquifer sediments. The strain was identified as <i>Sphingobium yanoikuyae</i> SHJ based on morphological characteristics, 16S rDNA gene phylogeny, and whole genome average nucleotide identity (ANI). The degradation half-life of DBP with substrate concentration of 8.5 and 50.0 mg/L by strain SHJ was 99.7 and 101.4 hours, respectively. The optimum degradation rate of DBP by SHJ was observed at 30°C and weak alkaline (pH 7.5). Genome sequence of the strain SHJ showed a circular chromosome and additional two circular plasmids with whole genome size of 5,669,383 bp and GC content of 64.23%. Functional annotation of SHJ revealed a total of 5,402 genes, with 5,183 protein-encoding genes, 143 pseudogenes, and 76 noncoding RNA genes. Based on genome annotation, 44 genes were identified to be involved in PAEs hydrolysis potentially. Besides, a region with size of about 6.9 kb comprised of seven ORFs, which is located on the smaller plasmid pSES189, was presumed to be responsible for the biodegradation of phthalate. These results provide insights into the genetic basis of DBP biodegradation in this strain.
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Project description:Phthalate esters (PEs) are important environmental pollutants. While the biodegradation of the parent compound, phthalate (PTH), is well characterized, the biodegradation of PEs is not well understood. In particular, prior to this study, genes involved in the uptake and hydrolysis of these compounds were not conclusively identified. We found that Rhodococcus jostii RHA1 could grow on a variety of monoalkyl PEs, including methyl, butyl, hexyl, and 2-ethylhexyl PTHs. Strain RHA1 could not grow on most dialkyl PEs, but suspensions of cells grown on PTH transformed dimethyl, diethyl, dipropyl, dibutyl, dihexyl and di-(2-ethylhexyl) PTHs. The major products of these dialkyl PEs were PTH and the corresponding monoalkyl PEs, and minor products resulted from the shortening of the alkyl side chains. RHA1 exhibited an inducible, ATP-dependent uptake system for PTH with a K(m) of 22 microM. The deletion and complementation of the patB gene demonstrated that the ATP-binding cassette (ABC) transporter encoded by patDABC is required for the uptake of PTH and monoalkyl PEs by RHA1. The hydrolase encoded by patE of RHA1 was expressed in Escherichia coli. PatE specifically hydrolyzed monoalkyl PEs to PTH but did not transform dialkyl PEs or other aromatic esters. This investigation of RHA1 elucidates key processes that are consistent with the environmental fate of PEs.
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Project description:Sphingobium yanoikuyae TJ is a halotolerant di-n-butyl-phthalate-degrading bacterium, isolated from the Haihe estuary in Bohai Bay, Tianjin, China. Here, we report the 5.1-Mb draft genome sequence of this strain, which will provide insights into the diversity of Sphingobium spp. and the mechanism of phthalate ester degradation in the estuary.
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Project description:Despites lots of characterized microorganisms that are capable of degrading phthalic acid esters (PAEs), there are few isolated strains with high activity towards PAEs under a broad range of environmental conditions. In this study, Gordonia sp. YC-JH1 had advantages over its counterparts in terms of di(2-ethylhexyl) phthalate (DEHP) degradation performance. It possessed an excellent degradation ability in the range of 20?50 °C, pH 5.0?12.0, or 0?8% NaCl with the optimal degradation condition 40 °C and pH 10.0. Therefore, strain YC-JH1 appeared suitable for bioremediation application at various conditions. Metabolites analysis revealed that DEHP was sequentially hydrolyzed by strain YC-JH1 to mono(2-ethylhexyl) phthalate (MEHP) and phthalic acid (PA). The hydrolase MphG1 from strain YC-JH1 hydrolyzed monoethyl phthalate (MEP), mono-n-butyl phthalate (MBP), mono-n-hexyl phthalate (MHP), and MEHP to PA. According to molecular docking and molecular dynamics simulation between MphG1 and monoalkyl phthalates (MAPs), some key residues were detected, including the catalytic triad (S125-H291-D259) and the residues R126 and F54 potentially binding substrates. The mutation of these residues accounted for the reduced activity. Together, the mechanism of MphG1 catalyzing MAPs was elucidated, and would shed insights into catalytic mechanism of more hydrolases.
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Project description:A bacterial strain QH-12 isolated from activated sludge was identified as Gordonia sp. based on analysis of 16S rRNA gene sequence and was found to be capable of utilizing dibutyl phthalate (DBP) and other common phthalate esters (PAEs) as the sole carbon and energy source. The degradation kinetics of DBP under different concentrations by the strain QH-12 fit well with the modified Gompertz model (R² > 0.98). However, strain QH-12 could not utilize the major intermediate product phthalate (phthalic acid; PA) as the sole carbon and energy source, and only a little amount of PA was detected. The QH-12 genome analysis revealed the presence of putative hydrolase/esterase genes involved in PAEs-degradation but no phthalic acid catabolic gene cluster was found, suggesting that a novel degradation pathway of PAEs was present in Gordonia sp. QH-12. This information will be valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs-degrading Gordonia sp. strains.
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Project description:The microbial populations responsible for anaerobic degradation of phthalate isomers were investigated by enrichment and isolation of those microbes from anaerobic sludge treating wastewater from the manufacturing of terephthalic acid. Primary enrichments were made with each of three phthalate isomers (ortho-, iso-, and terephthalate) as the sole energy source at 37 degrees C with two sources of anaerobic sludge (both had been used to treat wastewater containing high concentrations of phthalate isomers) as the inoculum. Six methanogenic enrichment cultures were obtained which not only degraded the isomer used for the enrichment but also had the potential to degrade part of other phthalate isomers as well as benzoate with concomitant production of methane, presumably involving strictly syntrophic substrate degradation. Our 16S rRNA gene-cloning analysis combined with fluorescence in situ hybridization revealed that the predominant bacteria in the enrichment cultures were affiliated with a recently recognized non-sulfate-reducing subcluster (subcluster Ih) in the group 'Desulfotomaculum lineage I' or a clone cluster (group TA) in the class delta-PROTEOBACTERIA: Several attempts were made to isolate these microbes, resulting in the isolation of a terephthalate-degrading bacterium, designated strain JT, in pure culture. A coculture of the strain with the hydrogenotrophic methanogen Methanospirillum hungatei converted terephthalate to acetate and methane within 3 months of incubation, whereas strain JT could not degrade terephthalate in pure culture. During the degradation of terephthalate, a small amount of benzoate was transiently accumulated as an intermediate, indicative of decarboxylation of terephthalate to benzoate as the initial step of the degradation. 16S rRNA gene sequence analysis revealed that the strain was a member of subcluster Ih of the group 'Desulfotomaculum lineage I', but it was only distantly related to other known species.
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Project description:Azoarcus sp. strain PA01(T) belongs to the genus Azoarcus, of the family Rhodocyclaceae within the class Betaproteobacteria. It is a facultatively anaerobic, mesophilic, non-motile, Gram-stain negative, non-spore-forming, short rod-shaped bacterium that was isolated from a wastewater treatment plant in Constance, Germany. It is of interest because of its ability to degrade o-phthalate and a wide variety of aromatic compounds with nitrate as an electron acceptor. Elucidation of the o-phthalate degradation pathway may help to improve the treatment of phthalate-containing wastes in the future. Here, we describe the features of this organism, together with the draft genome sequence information and annotation. The draft genome consists of 4 contigs with 3,908,301 bp and an overall G?+?C content of 66.08 %. Out of 3,712 total genes predicted, 3,625 genes code for proteins and 87 genes for RNAs. The majority of the protein-encoding genes (83.51 %) were assigned a putative function while those remaining were annotated as hypothetical proteins.
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