Draft Genome Sequence of Klebsiella pneumoniae AWD5

Rajkumari, Jina; Singha, L. Paikhomba; Pandey, Piyush

doi:10.1128/genomea.01531-16

Cited by 8 publications

(4 citation statements)

References 3 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Luria Bertani (LB), and nutrient medium (NM) and constituents of growth media were purchased from HI Media. E. coli ATCC 25922 and S. aureus ATCC 25923 are type strains, which were taken from culture collection of department of Microbiology, while B. subtilis AST5-2, P. aeruginosa AL2-14B 32 and K. pneumoniae AWD5 33 , were isolated in an unrelated work, and identified by 16S rDNA sequence analysis. P. aeruginosa AL2-14b was plant endophyte while B. subtilis AST5-2 and K. pneumoniae AWD5 were isolated from soil.…”

Section: Methodsmentioning

confidence: 99%

Shape dependent physical mutilation and lethal effects of silver nanoparticles on bacteria

Acharya

Singha

Pandey

et al. 2018

Sci Rep

Self Cite

133

View full text Add to dashboard Cite

In this report, spherical silver nanoparticle (AgNP-sp) and rod-shaped silver nanoparticle (AgNR) were prepared by chemical reduction method and their antibacterial activity against various Gram-positive and Gram-negative bacteria had been evaluated for their efficiency. Minimal inhibitory concentration (MIC) tests were conducted to study the antibacterial properties, and substantiated with killing kinetics of silver nanoparticles (AgNPs). The study revealed that both AgNP-sp and AgNRs are good antibacterial candidates. Bacterial sensitivity to nanoparticles (NPs) was found to vary depending on microbial species. Disc diffusion studies revealed the greater effectiveness of AgNP-sp and AgNR against Klebsiella pneumoniae AWD5 at the doses of 249 and 392 µg. The dose dependent activities of prepared NPs were also observed on the batch studies of disc diffusion and MIC with various strains. The optical and morphological structures of NPs were analyzed by UV-visible, XRD, FE-SEM and TEM. Further, FESEM of bacterial culture treated with AgNPs confirmed antibacterial activity of NPs by showing rupture of bacterial cell wall. Also, the genome of test organism was found to have CusCFBA and CusRS operons. The killing kinetics confirmed that the death rate of K. pneumoniae was higher against AgNP-sp as compared to AgNR.

show abstract

Section: Methodsmentioning

confidence: 99%

Shape dependent physical mutilation and lethal effects of silver nanoparticles on bacteria

Acharya

Singha

Pandey

et al. 2018

Sci Rep

Self Cite

133

View full text Add to dashboard Cite

show abstract

“…The complete genomic DNA was sequenced using Next-Generation Sequencing System using Illumina HiSeq sequencing technology and assembled using CLC Genomics workbench v9.0. (Rajkumari et al 2017 ). The annotation of protein-coding genes was provided by NCBI Prokaryotic Genome Annotation pipeline version 3.3 on NCBI website; further gene prediction and functional annotation were performed by Bacterial annotation system server 3 (BASys) and Integrated Microbial Genome-expert Review (IMG) pipeline.…”

Section: Methodsmentioning

confidence: 99%

“…Irrespective to the available information on K. pneumoniae as an agent for biodegradation of hydrocarbons, only a few genomes have been reported with industrial or environmental applications and the genomes of different Klebsiella strains have been studied and described with perspective of virulence. Here, the genomic features of K. pneumoniae AWD5 are described which was isolated from rhizospheric soil of a contaminated site from Assam, India (Rajkumari et al 2017 ). K. pneumoniae AWD5 has excellent ability to degrade higher molecular weight (HMW) PAH; in addition, it also has plant growth promoting attributes like production of indole acetic acid (IAA), siderophore, and phosphate solubilization.…”

Section: Introductionmentioning

confidence: 99%

Genomic insights of aromatic hydrocarbon degrading Klebsiella pneumoniae AWD5 with plant growth promoting attributes: a paradigm of soil isolate with elements of biodegradation

2018

Self Cite

View full text Add to dashboard Cite

This research employs draft genome sequence data of Klebsiella pneumoniae AWD5 to explore genes that contribute to the degradation of polyaromatic hydrocarbon (PAH) and stimulate plant growth, for rhizosphere-mediated bioremediation. Annotation analysis suggests that the strain AWD5 not only possess gene clusters for PAH utilization, but also for utilization of benzoate, fluorobenzoate, phenylacetate (paa), hydroxyphenylacetic acid (hpa), 3-hydroxyphenyl propionate (mhp). A comparative genome analysis revealed that the genome of AWD5 was highly similar with genomes of environmental as well as clinical K. pneumoniae isolates. The artemis output confirmed that there are 139 different genes present in AWD5 which were absent in genome of clinical strain K. pneumoniae ATCC BAA-2146, and 25 genes were identified to be present in AWD5 genome but absent in genome of environmental strain K. pneumoniae KP-1. Pathway analyzed using Kyoto Encyclopedia of Genes and Genomes enzyme database revealed the presence of gene clusters that code for enzymes to initiate the opening of aromatic rings. The polyaromatic hydrocarbon and benzoate degradation were found to be metabolized through ortho-cleavage pathway, mineralizing the compounds to TCA cycle intermediates. Genes for plant growth promoting attributes such as Indole acetic acid (IAA) synthesis, siderophore production, and phosphate solubilization were detected in the genome. These attributes were verified in vitro, including IAA (14.75 µg/ml), siderophore production (13.56%), phosphate solubilization (198.28 ng/ml), and ACC deaminase (0.118 mM α-ketobutyrate/mg) in the presence of pyrene, and also compared with results obtained in glucose amended medium. K. pneumoniae AWD5 enhanced the growth of Jatropha curcas in the presence of pyrene-contaminated soil. Moreover, AWD5 harbors heavy metal resistance genes indicating adaptation to contaminants. The study revealed the genomic attributes of K. pneumoniae AWD5 for its catabolic characteristics for different aromatic compounds, which makes it suitable for rhizoremediation of PAH-contaminated soil.Electronic supplementary materialThe online version of this article (10.1007/s13205-018-1134-1) contains supplementary material, which is available to authorized users.

show abstract

“…Pure culture of bacterial strain AWD5 used in this study was obtained from the Soil and Environmental Microbiology Laboratory (SEML), Department of Microbiology, Assam University, Silchar, India. The isolate AWD5 had already been identified ( Klebsiella pneumoniae ) and characterized at the genomic level ( Rajkumari et al, 2017 , 2018 ). The strain grows best at a pH range of 4–8 in a nutrient medium at 30°C ( Rajkumari et al, 2018 ).…”

Section: Methodsmentioning

confidence: 99%

Rhizodegradation of Pyrene by a Non-pathogenic Klebsiella pneumoniae Isolate Applied With Tagetes erecta L. and Changes in the Rhizobacterial Community

et al. 2021

Self Cite

View full text Add to dashboard Cite

The non-clinical Klebsiella pneumoniae variants, isolated from different environments, are now well acknowledged for their role in plant-growth promotion and biodegradation of pollutants. In the present study, a non-clinical environmental isolate K. pneumoniae AWD5 is being described for rhizoremediation of pyrene, applied through the rhizosphere of an ornamental plant, Tagetes erecta L (marigold). The non-pathogenic nature of AWD5 was established using an in vivo mouse model experiment, where AWD5 was unable to cause lung infection in tested mice. Degradation of pyrene, in the presence of succinate as co-substrate, was observed to be 87.5% by AWD5, after 21 days of incubation in minimal (Bushnell–Hass) medium in vitro conditions. Consequently, the bacterial inoculation through the rhizosphere of T. erecta L. plants resulted in 68.61% degradation of pyrene, which was significantly higher than control soil. Inoculation of AWD5 also improved plant growth and exhibited an increase in root length (14.64%), dry root weight (80.56%), shoot length (3.26%), and dry shoot weight (45.35%) after 60 days of incubation. T. erecta L., an ornamental plant, was also found to be suitable for bioremediation of pyrene. The effect of AWD5 application, and rhizoremediation process, on rhizosphere bacterial diversity and community structure has been studied using the metagenomic analysis of the 16S (V3–V4) region of rRNA. 37 bacterial phyla constituted the core microbiome, which was dominated by Proteobacteria followed by Actinobacteria, Actinobacteria, and Planctomycetes for all the treatments. AWD5 inoculation enhanced the relative abundance of Firmicutes and Acidobacteria as compared with other treatments. Genus Kaistobacter and Verrucomicrobia were found to be an abundant indigenous population in pyrene-spiked soils. Bacterial richness and diversity were analyzed using the Shannon–Wiener (H) index. A lower diversity index was observed in pyrene-spiked soils. Canonical correspondence analysis (CCA) showed a possible linkage with plant growth attributes and available nitrogen content that influences diversity and abundance of the bacterial community.

show abstract

Draft Genome Sequence of Klebsiella pneumoniae AWD5

Cited by 8 publications

References 3 publications

Shape dependent physical mutilation and lethal effects of silver nanoparticles on bacteria

Shape dependent physical mutilation and lethal effects of silver nanoparticles on bacteria

Genomic insights of aromatic hydrocarbon degrading Klebsiella pneumoniae AWD5 with plant growth promoting attributes: a paradigm of soil isolate with elements of biodegradation

Rhizodegradation of Pyrene by a Non-pathogenic Klebsiella pneumoniae Isolate Applied With Tagetes erecta L. and Changes in the Rhizobacterial Community

Contact Info

Product

Resources

About