Dataset Information

Genome of Pseudomonas nitroreducens DF05 from dioxin contaminated sediment downstream of the San Jacinto River waste pits reveals a broad array of aromatic degradation gene determinants.

ABSTRACT: P. nitroreducens DF05 is a Gram negative, motile, aerobic, rod-shaped and psychrotrophic bacterium that was isolated from contaminated San Jacinto River sediment near River Terrace Park in Channelview, Texas. The draft genome of strain DF05 consists of a total of 192 contigs assembled at the scaffold level totaling 6,487,527 bp and encoding for 5862 functional proteins, 1116 of which are annotated as hypothetical proteins. The bacterial chromosome has a GC content of 65.15% and contains 22 rRNA and 70 tRNA loci. In addition, approximately 142 proteins localized on the bacterial chromosome are associated with metabolism of aromatic compounds. A single plasmid approximately 95 kb in size was also detected carrying copies of RNA genes and multiple phage assembly proteins.

SUBMITTER: Iyer R

PROVIDER: S-EPMC5565767 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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Genome of Pseudomonas nitroreducens DF05 from dioxin contaminated sediment downstream of the San Jacinto River waste pits reveals a broad array of aromatic degradation gene determinants.

Iyer Rupa R Iken Brian B Damania Ashish A

Genomics data 20170817

P. nitroreducens DF05 is a Gram negative, motile, aerobic, rod-shaped and psychrotrophic bacterium that was isolated from contaminated San Jacinto River sediment near River Terrace Park in Channelview, Texas. The draft genome of strain DF05 consists of a total of 192 contigs assembled at the scaffold level totaling 6,487,527 bp and encoding for 5862 functional proteins, 1116 of which are annotated as hypothetical proteins. The bacterial chromosome has a GC content of 65.15% and con ...[more]

PMID: 28856100

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Project description:Polychlorinated dibenzo-p-dioxin and polychlorinated dibenzofuran (PCDD/F) are persistent, toxic, and bioaccumulative. Currently, PCDD/F monitoring programs primarily use fish and birds with potentially large home ranges to monitor temporal trends over broad spatial scales; sentinel organisms that provide targeted sediment contaminant information across small geographic areas have yet to be developed. Riparian orb-weaving spiders, which typically have small home ranges and consume primarily adult aquatic insects, are potential PCDD/F sentinels. Recent studies have demonstrated that spider tissue concentrations indicate the source and magnitude of dioxin-like chlorinated compounds in contaminated sediments, including polychlorinated biphenyls (PCBs). Our aim in the present study was to assess the utility of riparian spiders as sentinels for PCDD/F-contaminated sediments. We measured PCDD/F (total [Σ] and homologs) in surface sediments and spiders collected from three sites within the St. Louis River basin (Minnesota and Wisconsin, USA). We then compared (1) patterns in ΣPCDD/F concentrations between sediment and spiders, (2) the distribution of homologs within sediments and spiders when pooled across sites, and (3) the relationship between sediment and spider concentrations of PCDD/F homologs across 13 stations sampled across the three sites. The ΣPCDD/F concentrations in sediment (mean ± standard error 286 591 ± 97 614 pg/g) were significantly higher than those in riparian spiders (2463 ± 977 pg/g, p < 0.001), but the relative abundance of homologs in sediment and spiders were not significantly different. Spider homolog concentrations were significantly and positively correlated with sediment concentrations across a gradient of sediment PCDD/F contamination (R2 = 0.47, p < 0.001). Our results indicate that, as has been shown for other legacy organic chemicals like PCBs, riparian spiders are suitable sentinels of PCDD/F in contaminated sediment. Environ Toxicol Chem 2023;42:414-420. © 2022 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Dataset Information

Genome of Pseudomonas nitroreducens DF05 from dioxin contaminated sediment downstream of the San Jacinto River waste pits reveals a broad array of aromatic degradation gene determinants.

Publications

Genome of <i>Pseudomonas nitroreducens</i> DF05 from dioxin contaminated sediment downstream of the San Jacinto River waste pits reveals a broad array of aromatic degradation gene determinants.

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