Whole genome sequence analysis of an Alachlor and Endosulfan degrading Pseudomonas strain W15Feb9B isolated from Ochlockonee River, Florida

Chauhan, Ashvini; Pathak, Ashish; Ewida, Ayman Y. I.; Griffiths, Zabrenna; Stothard, Paul

doi:10.1016/j.gdata.2016.05.008

Cited by 19 publications

(7 citation statements)

References 8 publications

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“…Briefly, genomic DNA from the strain was extracted and prepared for sequencing on an Illumina HiSeq2000 instrument as described previously [5], [6]. De novo assembly of the raw reads was performed with the SPAdes assembler [7] using default settings.…”

Section: Textmentioning

confidence: 99%

Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA

et al. 2017

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Savannah River Site (SRS), an approximately 800-km2 former nuclear weapons production facility located near Aiken, SC remains co-contaminated by heavy metals and radionuclides. To gain a better understanding on microbially-mediated bioremediation mechanisms, several bacterial strains resistant to high concentrations of Uranium (U) and Nickel (Ni) were isolated from the Steeds Pond soils located within the SRS site. One of the isolated strains, designated as strain SRS-W-2-2016, grew robustly on both U and Ni. To fully understand the arsenal of metabolic functions possessed by this strain, a draft whole genome sequence (WGS) was obtained, assembled, annotated and analyzed. Genome-centric evaluation revealed the isolate to belong to the Burkholderia genus with close affiliation to B. xenovorans LB400, an aggressive polychlorinated biphenyl-degrader. At a coverage of 90 ×, the genome of strain SRS-W-2-2016 consisted of 8,035,584 bases with a total number of 7071 putative genes assembling into 191 contigs with an N50 contig length of 134,675 bases. Several gene homologues coding for resistance to heavy metals/radionuclides were identified in strain SRS-W-2-2016, such as a suite of outer membrane efflux pump proteins similar to nickel/cobalt transporter regulators, peptide/nickel transport substrate and ATP-binding proteins, permease proteins, and a high-affinity nickel-transport protein. Also noteworthy were two separate gene fragments in strain SRS-W-2-2016 homologous to the spoT gene; recently correlated with bacterial tolerance to U. Additionally, a plethora of oxygenase genes were also identified in the isolate, potentially involved in the breakdown of organic compounds facilitating the strain's successful colonization and survival in the SRS co-contaminated soils. The WGS project of Burkholderia sp. strain SRS-W-2-2016 is available at DDBJ/ENA/GenBank under the accession #MSDV00000000.

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Section: Textmentioning

confidence: 99%

Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA

et al. 2017

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“…For example, in P. aeruginosa strains F9676 and DN1, P. alcaliphila strain JAB1, and Pseudomonas sp. strain W15Feb9B, the definite functional categories containing the largest number of genes are amino acid transport and metabolism, signal transduction mechanisms, transcription (Shi et al, 2015; Chauhan et al, 2016; Dong et al, 2017; Ridl et al, 2018), which are also top enriched categories in our tested strains. Thus, the genomic features responsible for AFB1 degradation should not be inherent elements of the genomes of genus Pseudomonas .…”

Section: Discussionmentioning

confidence: 77%

The genomic context for aflatoxin B1-degrading Pseudomonas strains

Tang

Deng²,

Song

et al. 2021

Preprint

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The whole genomes of three strains were sequenced and annotated. COG (Clusters of Orthologous Groups) and GO (Gene Ontology) annotations of the protein-coding genes from three strains show a conservation of genome-wide protein functions in genus Pseudomonas. However, the AFB1-degrading strains HAI2 and HT3 harbor much more genes belonged to the pathway of xenobiotics biodegradation and metabolism than non-degrading strain 48. Besides, the enzyme families potentially involved in the AFB1 degradation of bacteria are more abundant in the two AFB1-degrading strains. A pan-genome profile was then formed by comparing the genomes against other reference genomes of the corresponding Pseudomonas species. Accordingly, a total of 1,528 genes were found to be specific in AFB1-degrading strains, and 65 genes of them are related to oxidoreductase activity.

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“…Strains from Pseudomonas , Achromobacter or Stenotrophomonas genera which proliferated in presence of dimethachlor were previously reported to be able to degrade various acetanilide herbicides like alachlor 43 , acetochlor 44 , butolachlor 45 . Microorganisms capable of degrading herbicide are commonly also hyper-tolerant to this herbicide 46 which suggest finding dimethachlor degraders among groups which proliferated.…”

Section: Discussionmentioning

confidence: 99%

Changes in soil microbial community and activity caused by application of dimethachlor and linuron

Medo

Maková

Medová

et al. 2021

Sci Rep

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Soil microorganisms and their activities are essential for maintaining soil health and fertility. Microorganisms can be negatively affected by application of herbicides. Although effects of herbicides on microorganisms are widely studied, there is a lack of information for chloroacetamide herbicide dimethachlor. Thus, dimethachlor and well known linuron were applied to silty-loam luvisol and their effects on microorganisms were evaluated during112 days long laboratory assay. Dimethachlor and linuron were applied in doses 1.0 kg ha−1 and 0.8 kg ha−1 corresponding to 3.33 mg kg−1 and 2.66 mg kg−1 respectively. Also 100-fold doses were used for magnification of impacts. Linuron in 100-fold dose caused minor increase of respiration, temporal increase of soil microbial biomass, decrease of soil dehydrogenase activity, and altered microbial community. Dimethachlor in 100-fold dose significantly increased respiration; microbial biomass and decreased soil enzymatic activities. Microbial composition changed significantly, Proteobacteria abundance, particularly Pseudomonas and Achromobacter genera increased from 7 to 28th day. In-silico prediction of microbial gene expression by PICRUSt2 software revealed increased expression of genes related to xenobiotic degradation pathways. Evaluated characteristics of microbial community and activity were not affected by herbicides in recommended doses and the responsible use of both herbicides will not harm soil microbial community.

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Whole genome sequence analysis of an Alachlor and Endosulfan degrading Pseudomonas strain W15Feb9B isolated from Ochlockonee River, Florida

Cited by 19 publications

References 8 publications

Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA

Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA

The genomic context for aflatoxin B1-degrading Pseudomonas strains

Changes in soil microbial community and activity caused by application of dimethachlor and linuron

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