The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity ... more The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity of Pseudomonas putida strain SF-1 at a genomic scale. Annotation analysis proposes that the strain SF1 not only possesses the gene cluster for PNP utilization but also for the utilization of benzoate, catechol, hydroxybenzoate, protocatechuate, and homogentisate. Further, the analysis was carried out to understand more details of PNP 4-monooxygenase and its regulator. A comparative analysis of PNP 4-monooxygenase from SF1 was carried out for prediction of its tertiary structure; and also its binding affinity with PNP, FAD, NADH and NADPH using FlexX docking. The tertiary structure of regulator was also predicted along with its conserved DNA binding residues. Regulator binding site (RBS) and promoter region were mapped for the PNP degradation gene cluster. Based on genome sequence analysis, the study unveiled the genomic attributes for a versatile catabolic potential of Pseudomonas putida...
Alcaligenes sp. HPC 1271 demonstrated antibacterial activity against multidrug resistant bacteria... more Alcaligenes sp. HPC 1271 demonstrated antibacterial activity against multidrug resistant bacteria, Enterobacter sp., resistant to sulfamethoxazole, ampicillin, azithromycin, and tetracycline, as well as against Serratia sp. GMX1, resistant to the same antibiotics with the addition of netilmicin. The cell-free culture supernatant was analyzed for possible antibacterials by HPLC, and the active fraction was further identified by LC-MS. Results suggest the production of tunicamycin, a nucleoside antibiotic. The draft genome of this bacterial isolate was analyzed, and the 4.2 Mb sequence data revealed six secondary metabolite-producing clusters, identified using antiSMASH platform as ectoine, butyrolactone, phosphonate, terpene, polyketides, and nonribosomal peptide synthase (NRPS). Additionally, the draft genome demonstrated homology to the tunicamycin-producing gene cluster and also defined 30 ORFs linked to protein secretion that could also play a role in the antibacterial activity o...
Alcaligenes sp. HPC 1271 demonstrated antibacterial activity against multidrug resistant bacteria... more Alcaligenes sp. HPC 1271 demonstrated antibacterial activity against multidrug resistant bacteria, Enterobacter sp., resistant to sulfamethoxazole, ampicillin, azithromycin, and tetracycline, as well as against Serratia sp. GMX1, resistant to the same antibiotics with the addition of netilmicin. The cell-free culture supernatant was analyzed for possible antibacterials by HPLC, and the active fraction was further identified by LC-MS. Results suggest the production of tunicamycin, a nucleoside antibiotic. The draft genome of this bacterial isolate was analyzed, and the 4.2 Mb sequence data revealed six secondary metabolite-producing clusters, identified using antiSMASH platform as ectoine, butyrolactone, phosphonate, terpene, polyketides, and nonribosomal peptide synthase (NRPS). Additionally, the draft genome demonstrated homology to the tunicamycin-producing gene cluster and also defined 30 ORFs linked to protein secretion that could also play a role in the antibacterial activity observed. Gene expression analysis demonstrated that both NRPS and dTDP-glucose 4,6-dehydratase gene clusters are functional and could be involved in antibacterial biosynthesis.
We report the draft genome sequences of two tropical bacterial isolates capable of degrading the ... more We report the draft genome sequences of two tropical bacterial isolates capable of degrading the herbicide atrazine. Alcaligenes sp. strain EGD-AK7 and Arthrobacter sp. strain AK-YN10 were isolated from Indian agricultural soil in which sugarcane is grown, with a reported history of atrazine use. EGD-AK7 has the atzABCDEF genes and AK-YN10 has the trzN and atzBC genes for atrazine degradation. A. 2014. Draft genome sequence of atrazine-utilizing bacteria isolated from Indian agricultural soil. Genome Announc. 2(1):e01149-13. doi:10.1128/genomeA.01149-13. A trazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-tri-azine) is a member of the s-triazine group of herbicides. Due to their excessive usage, high persistence, and mobility, atrazine and its metabolites are found in soil and water bodies. The accumulation of atrazine in the environment is of great concern, as several studies have shown that atrazine is a potent endocrine disruptor (1). This study reports the draft genomes of t...
We report whole-genome sequences of two clinical isolates of Mycobacterium tuberculosis isolated ... more We report whole-genome sequences of two clinical isolates of Mycobacterium tuberculosis isolated from patients in Odisha, India. The sequence analysis revealed that these isolates are of an ancestral type and might represent some of the "pristine" isolates in India that have not admixed with other lineages.
The whole genome of a pigment-producing isolate from a lake in northern India, Pseudogulbenkiania... more The whole genome of a pigment-producing isolate from a lake in northern India, Pseudogulbenkiania ferrooxidans strain EGD-HP2, has been sequenced to study the spectrum of biosynthesis of secondary metabolites. The genome annotation data revealed an operon for violacein, which showed homology with the reported operon of a Chromobacterium sp., and also a quinone cofactor.
We present a draft genome sequence of Lactobacillus plantarum strain EGD-AQ4, isolated from nonal... more We present a draft genome sequence of Lactobacillus plantarum strain EGD-AQ4, isolated from nonalcoholic fermented bamboo shoot products of Northeast India. The size of the draft genome sequence is the largest among all the reported genome sequences of Lactobacillus plantarum, thus enabling the exploration of new gene clusters involved in various functional and probiotic attributes.
We report the draft genome sequences of two tropical bacterial isolates capable of degrading the ... more We report the draft genome sequences of two tropical bacterial isolates capable of degrading the herbicide atrazine. Alcaligenes sp. strain EGD-AK7 and Arthrobacter sp. strain AK-YN10 were isolated from Indian agricultural soil in which sugarcane is grown, with a reported history of atrazine use. EGD-AK7 has the atzABCDEF genes and AK-YN10 has the trzN and atzBC genes for atrazine degradation.
A bacterial consortium has been isolated containing Pseudomonas spp. strains S1 and S2, which was... more A bacterial consortium has been isolated containing Pseudomonas spp. strains S1 and S2, which was able to degrade p-nitrophenol (PNP). The strains were isolated from agricultural soil contaminated with organophosphorus pesticides. Pseudomonas spp. strain S2 could convert p-nitrophenol to 4nitrocatechol (4NC) after pre-exposure to phenol, when PNP was used as the only carbon source in the medium. Pseudomonas spp. strain S2, when mixed with strain S1 in the ratio 1:5 respectively, decolorised PNP completely.
Arthrobacter sp. HPC1223 (Genebank Accession No. AY948280) isolated from activated biomass of eff... more Arthrobacter sp. HPC1223 (Genebank Accession No. AY948280) isolated from activated biomass of effluent treatment plant was capable of utilizing 2,4,6 trinitrophenol (TNP) under aerobic condition at 30°C and pH 7 as nitrogen source. It was observed that the isolated bacteria utilized TNP up to 70 % (1 mM) in R2A media with nitrite release. The culture growth media changed into orange-red color hydride-meisenheimer complex at 24 h as detected by HPLC. Oxygen uptake of Arthrobacter HPC1223 towards various nitro/amino substituted phenols such as dinitrophenol (1.2 nmol/min/mg cells), paranitrophenol (0.9 nmol/ min/mg cells), 2-aminophenol (0.75 nmol/min/mg cells), p-aminophenol (0.4 nmol/min/mg cells), phenol (0.56 nmol/min/mg cells) and TNP (2.42 nmol/min/mg cell) was analysed, which showed its additional characteristic of broad substrate catabolic capacity. The present study thus report a novel indigenous bacteria isolated from activated sludge utilized TNP and has broad catabolic potential towards substituted phenols.
A bacterial consortium has been isolated containing Pseudomonas spp. strains S1 and S2, which was... more A bacterial consortium has been isolated containing Pseudomonas spp. strains S1 and S2, which was able to degrade p-nitrophenol (PNP). The strains were isolated from agricultural soil contaminated with organophosphorus pesticides. Pseudomonas spp. strain S2 could convert p-nitrophenol to 4nitrocatechol (4NC) after pre-exposure to phenol, when PNP was used as the only carbon source in the medium. Pseudomonas spp. strain S2, when mixed with strain S1 in the ratio 1:5 respectively, decolorised PNP completely.
We report a draft genome sequence of Alcaligenes sp. strain HPC1271, which demonstrates antimicro... more We report a draft genome sequence of Alcaligenes sp. strain HPC1271, which demonstrates antimicrobial activity against multidrug-resistant bacteria. Antibiotic production by Alcaligenes has not been frequently reported, and hence, the availability of the genome sequence should enable us to explore new antibiotic-producing gene clusters.
BACKGROUND: Pesticide-formulating industries are contaminating the environment through various ac... more BACKGROUND: Pesticide-formulating industries are contaminating the environment through various activities. Bioremediation is the best method for decontamination, as chemical and physical methods are not only costly but also not very effective in open field systems. In the present study, in situ bioremediation of organochlorine-contaminated soil was demonstrated by combined biostimulation and bioaugmentation strategies, followed by evaluation using a molecular method.
A bacterial strain HPC 135 capable of growing on 4-nitroaniline (NA) as a source of carbon and en... more A bacterial strain HPC 135 capable of growing on 4-nitroaniline (NA) as a source of carbon and energy was isolated from contaminated site after enrichment. Experiments revealed that the strain HPC 135 utilized 4NA as analyzed by high-performance liquid chromatography (HPLC). The presence of acetate as co-substrate did not affect the utilization of 4-nitroaniline by the isolate but cell growth was increased. Oxygen consumption studies demonstrated that strain HPC 135 could utilize various substrates such as 4-chloro-2-nitrophenol, 4-chlorobenzonitrile, 4-nitrophenol as well as 4NA. On partial 16S rDNA sequence analysis, strain HPC 135 showed highest homology with Stenotrophomonas strain based on FASTA program. r
Resorcinol was utilized as the sole carbon and energy source by Enterobacter cloacae (identificat... more Resorcinol was utilized as the sole carbon and energy source by Enterobacter cloacae (identification by 16S rDNA nucleotide sequencing Genbank Accession Number JN093148). The different concentration of resorcinol utilized by the bacterial isolate ranged between 55 and 220 mg l -1 at 30°C and pH of 7.0. It was observed that the batch experimental results were best fitted for Michaelis-Menten and Monod models (for 220 mg l -1 resorcinol) with time under defined conditions. The kinetics constants for the Michaelis-Menten equation (enzyme kinetics) were K m = 11.00 mM and V max = 0.03 mM min -1 and for the Monod equation (growth kinetics) was μ max = 0.0371 h -1 in the inhibitory region and K S = 22.09 mg l -1 . It was assumed that enzyme reactions limit biomass production (Monod kinetics) during resorcinol degradation by E. cloacae. The enzyme kinetic model (Michaelis-Menten) used was fit to the resorcinol degradation profiles with a set of model parameters such as using pre-induced E. cloacae cells on 220 mg l -1 resorcinol.
The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity ... more The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity of Pseudomonas putida strain SF-1 at a genomic scale. Annotation analysis proposes that the strain SF1 not only possesses the gene cluster for PNP utilization but also for the utilization of benzoate, catechol, hydroxybenzoate, protocatechuate, and homogentisate. Further, the analysis was carried out to understand more details of PNP 4-monooxygenase and its regulator. A comparative analysis of PNP 4-monooxygenase from SF1 was carried out for prediction of its tertiary structure; and also its binding affinity with PNP, FAD, NADH and NADPH using FlexX docking. The tertiary structure of regulator was also predicted along with its conserved DNA binding residues. Regulator binding site (RBS) and promoter region were mapped for the PNP degradation gene cluster. Based on genome sequence analysis, the study unveiled the genomic attributes for a versatile catabolic potential of Pseudomonas putida...
Alcaligenes sp. HPC 1271 demonstrated antibacterial activity against multidrug resistant bacteria... more Alcaligenes sp. HPC 1271 demonstrated antibacterial activity against multidrug resistant bacteria, Enterobacter sp., resistant to sulfamethoxazole, ampicillin, azithromycin, and tetracycline, as well as against Serratia sp. GMX1, resistant to the same antibiotics with the addition of netilmicin. The cell-free culture supernatant was analyzed for possible antibacterials by HPLC, and the active fraction was further identified by LC-MS. Results suggest the production of tunicamycin, a nucleoside antibiotic. The draft genome of this bacterial isolate was analyzed, and the 4.2 Mb sequence data revealed six secondary metabolite-producing clusters, identified using antiSMASH platform as ectoine, butyrolactone, phosphonate, terpene, polyketides, and nonribosomal peptide synthase (NRPS). Additionally, the draft genome demonstrated homology to the tunicamycin-producing gene cluster and also defined 30 ORFs linked to protein secretion that could also play a role in the antibacterial activity o...
Alcaligenes sp. HPC 1271 demonstrated antibacterial activity against multidrug resistant bacteria... more Alcaligenes sp. HPC 1271 demonstrated antibacterial activity against multidrug resistant bacteria, Enterobacter sp., resistant to sulfamethoxazole, ampicillin, azithromycin, and tetracycline, as well as against Serratia sp. GMX1, resistant to the same antibiotics with the addition of netilmicin. The cell-free culture supernatant was analyzed for possible antibacterials by HPLC, and the active fraction was further identified by LC-MS. Results suggest the production of tunicamycin, a nucleoside antibiotic. The draft genome of this bacterial isolate was analyzed, and the 4.2 Mb sequence data revealed six secondary metabolite-producing clusters, identified using antiSMASH platform as ectoine, butyrolactone, phosphonate, terpene, polyketides, and nonribosomal peptide synthase (NRPS). Additionally, the draft genome demonstrated homology to the tunicamycin-producing gene cluster and also defined 30 ORFs linked to protein secretion that could also play a role in the antibacterial activity observed. Gene expression analysis demonstrated that both NRPS and dTDP-glucose 4,6-dehydratase gene clusters are functional and could be involved in antibacterial biosynthesis.
We report the draft genome sequences of two tropical bacterial isolates capable of degrading the ... more We report the draft genome sequences of two tropical bacterial isolates capable of degrading the herbicide atrazine. Alcaligenes sp. strain EGD-AK7 and Arthrobacter sp. strain AK-YN10 were isolated from Indian agricultural soil in which sugarcane is grown, with a reported history of atrazine use. EGD-AK7 has the atzABCDEF genes and AK-YN10 has the trzN and atzBC genes for atrazine degradation. A. 2014. Draft genome sequence of atrazine-utilizing bacteria isolated from Indian agricultural soil. Genome Announc. 2(1):e01149-13. doi:10.1128/genomeA.01149-13. A trazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-tri-azine) is a member of the s-triazine group of herbicides. Due to their excessive usage, high persistence, and mobility, atrazine and its metabolites are found in soil and water bodies. The accumulation of atrazine in the environment is of great concern, as several studies have shown that atrazine is a potent endocrine disruptor (1). This study reports the draft genomes of t...
We report whole-genome sequences of two clinical isolates of Mycobacterium tuberculosis isolated ... more We report whole-genome sequences of two clinical isolates of Mycobacterium tuberculosis isolated from patients in Odisha, India. The sequence analysis revealed that these isolates are of an ancestral type and might represent some of the "pristine" isolates in India that have not admixed with other lineages.
The whole genome of a pigment-producing isolate from a lake in northern India, Pseudogulbenkiania... more The whole genome of a pigment-producing isolate from a lake in northern India, Pseudogulbenkiania ferrooxidans strain EGD-HP2, has been sequenced to study the spectrum of biosynthesis of secondary metabolites. The genome annotation data revealed an operon for violacein, which showed homology with the reported operon of a Chromobacterium sp., and also a quinone cofactor.
We present a draft genome sequence of Lactobacillus plantarum strain EGD-AQ4, isolated from nonal... more We present a draft genome sequence of Lactobacillus plantarum strain EGD-AQ4, isolated from nonalcoholic fermented bamboo shoot products of Northeast India. The size of the draft genome sequence is the largest among all the reported genome sequences of Lactobacillus plantarum, thus enabling the exploration of new gene clusters involved in various functional and probiotic attributes.
We report the draft genome sequences of two tropical bacterial isolates capable of degrading the ... more We report the draft genome sequences of two tropical bacterial isolates capable of degrading the herbicide atrazine. Alcaligenes sp. strain EGD-AK7 and Arthrobacter sp. strain AK-YN10 were isolated from Indian agricultural soil in which sugarcane is grown, with a reported history of atrazine use. EGD-AK7 has the atzABCDEF genes and AK-YN10 has the trzN and atzBC genes for atrazine degradation.
A bacterial consortium has been isolated containing Pseudomonas spp. strains S1 and S2, which was... more A bacterial consortium has been isolated containing Pseudomonas spp. strains S1 and S2, which was able to degrade p-nitrophenol (PNP). The strains were isolated from agricultural soil contaminated with organophosphorus pesticides. Pseudomonas spp. strain S2 could convert p-nitrophenol to 4nitrocatechol (4NC) after pre-exposure to phenol, when PNP was used as the only carbon source in the medium. Pseudomonas spp. strain S2, when mixed with strain S1 in the ratio 1:5 respectively, decolorised PNP completely.
Arthrobacter sp. HPC1223 (Genebank Accession No. AY948280) isolated from activated biomass of eff... more Arthrobacter sp. HPC1223 (Genebank Accession No. AY948280) isolated from activated biomass of effluent treatment plant was capable of utilizing 2,4,6 trinitrophenol (TNP) under aerobic condition at 30°C and pH 7 as nitrogen source. It was observed that the isolated bacteria utilized TNP up to 70 % (1 mM) in R2A media with nitrite release. The culture growth media changed into orange-red color hydride-meisenheimer complex at 24 h as detected by HPLC. Oxygen uptake of Arthrobacter HPC1223 towards various nitro/amino substituted phenols such as dinitrophenol (1.2 nmol/min/mg cells), paranitrophenol (0.9 nmol/ min/mg cells), 2-aminophenol (0.75 nmol/min/mg cells), p-aminophenol (0.4 nmol/min/mg cells), phenol (0.56 nmol/min/mg cells) and TNP (2.42 nmol/min/mg cell) was analysed, which showed its additional characteristic of broad substrate catabolic capacity. The present study thus report a novel indigenous bacteria isolated from activated sludge utilized TNP and has broad catabolic potential towards substituted phenols.
A bacterial consortium has been isolated containing Pseudomonas spp. strains S1 and S2, which was... more A bacterial consortium has been isolated containing Pseudomonas spp. strains S1 and S2, which was able to degrade p-nitrophenol (PNP). The strains were isolated from agricultural soil contaminated with organophosphorus pesticides. Pseudomonas spp. strain S2 could convert p-nitrophenol to 4nitrocatechol (4NC) after pre-exposure to phenol, when PNP was used as the only carbon source in the medium. Pseudomonas spp. strain S2, when mixed with strain S1 in the ratio 1:5 respectively, decolorised PNP completely.
We report a draft genome sequence of Alcaligenes sp. strain HPC1271, which demonstrates antimicro... more We report a draft genome sequence of Alcaligenes sp. strain HPC1271, which demonstrates antimicrobial activity against multidrug-resistant bacteria. Antibiotic production by Alcaligenes has not been frequently reported, and hence, the availability of the genome sequence should enable us to explore new antibiotic-producing gene clusters.
BACKGROUND: Pesticide-formulating industries are contaminating the environment through various ac... more BACKGROUND: Pesticide-formulating industries are contaminating the environment through various activities. Bioremediation is the best method for decontamination, as chemical and physical methods are not only costly but also not very effective in open field systems. In the present study, in situ bioremediation of organochlorine-contaminated soil was demonstrated by combined biostimulation and bioaugmentation strategies, followed by evaluation using a molecular method.
A bacterial strain HPC 135 capable of growing on 4-nitroaniline (NA) as a source of carbon and en... more A bacterial strain HPC 135 capable of growing on 4-nitroaniline (NA) as a source of carbon and energy was isolated from contaminated site after enrichment. Experiments revealed that the strain HPC 135 utilized 4NA as analyzed by high-performance liquid chromatography (HPLC). The presence of acetate as co-substrate did not affect the utilization of 4-nitroaniline by the isolate but cell growth was increased. Oxygen consumption studies demonstrated that strain HPC 135 could utilize various substrates such as 4-chloro-2-nitrophenol, 4-chlorobenzonitrile, 4-nitrophenol as well as 4NA. On partial 16S rDNA sequence analysis, strain HPC 135 showed highest homology with Stenotrophomonas strain based on FASTA program. r
Resorcinol was utilized as the sole carbon and energy source by Enterobacter cloacae (identificat... more Resorcinol was utilized as the sole carbon and energy source by Enterobacter cloacae (identification by 16S rDNA nucleotide sequencing Genbank Accession Number JN093148). The different concentration of resorcinol utilized by the bacterial isolate ranged between 55 and 220 mg l -1 at 30°C and pH of 7.0. It was observed that the batch experimental results were best fitted for Michaelis-Menten and Monod models (for 220 mg l -1 resorcinol) with time under defined conditions. The kinetics constants for the Michaelis-Menten equation (enzyme kinetics) were K m = 11.00 mM and V max = 0.03 mM min -1 and for the Monod equation (growth kinetics) was μ max = 0.0371 h -1 in the inhibitory region and K S = 22.09 mg l -1 . It was assumed that enzyme reactions limit biomass production (Monod kinetics) during resorcinol degradation by E. cloacae. The enzyme kinetic model (Michaelis-Menten) used was fit to the resorcinol degradation profiles with a set of model parameters such as using pre-induced E. cloacae cells on 220 mg l -1 resorcinol.
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