Deepika Pal
Council of Scientific and Industrial Research
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Featured researches published by Deepika Pal.
Journal of Hazardous Materials | 2013
Fazlurrahman Khan; Janmejay Pandey; Surendra Vikram; Deepika Pal; Swaranjit Singh Cameotra
An aerobic strain, Rhodococcus sp. strain FK48, capable of growing on 4-nitroaniline (4-NA) as the sole source of carbon, nitrogen, and energy has been isolated from enrichment cultures originating from contaminated soil samples. During growth studies with non- induced cells of FK48 catalyzed sequential denitrification (release of NO₂ substituent) and deamination (release of NH₂ substituent) of 4-NA. However, none of the degradation intermediates could be identified with growth studies. During resting cell studies, 4-NA-induced cells of strain FK48 transformed 4-NA via a previously unknown pathway which involved oxidative hydroxylation leading to formation of 4-aminophenol (4-AP). Subsequent degradation involved oxidated deamination of 4-AP and formation of 1,2,4-benzenetriol (BT) as the major identified terminal aromatic intermediate. Identification of these intermediates was ascertained by HPLC, and GC-MS analyses of the culture supernatants. 4-NA-induced cells of strain FK48 showed positive activity for 1,2,4-benzenetriol dioxygenase in spectrophotometric assay. This is the first conclusive study on aerobic microbial degradation of 4-NA and elucidation of corresponding metabolic pathway.
PLOS ONE | 2013
Fazlurrahman Khan; Deepika Pal; Surendra Vikram; Swaranjit Singh Cameotra
2-chloro-4-nitroaniline (2-C-4-NA) is used as an intermediate in the manufacture of dyes, pharmaceuticals, corrosion inhibitor and also used in the synthesis of niclosamide, a molluscicide. It is marked as a black-listed substance due to its poor biodegradability. We report biodegradation of 2-C-4-NA and its pathway characterization by Rhodococcus sp. strain MB-P1 under aerobic conditions. The strain MB-P1 utilizes 2-C-4-NA as the sole carbon, nitrogen, and energy source. In the growth medium, the degradation of 2-C-4-NA occurs with the release of nitrite ions, chloride ions, and ammonia. During the resting cell studies, the 2-C-4-NA-induced cells of strain MB-P1 transformed 2-C-4-NA stoichiometrically to 4-amino-3-chlorophenol (4-A-3-CP), which subsequently gets transformed to 6-chlorohydroxyquinol (6-CHQ) metabolite. Enzyme assays by cell-free lysates prepared from 2-C-4-NA-induced MB-P1 cells, demonstrated that the first enzyme in the 2-C-4-NA degradation pathway is a flavin-dependent monooxygenase that catalyzes the stoichiometric removal of nitro group and production of 4-A-3-CP. Oxygen uptake studies on 4-A-3-CP and related anilines by 2-C-4-NA-induced MB-P1 cells demonstrated the involvement of aniline dioxygenase in the second step of 2-C-4-NA degradation. This is the first report showing 2-C-4-NA degradation and elucidation of corresponding metabolic pathway by an aerobic bacterium.
Chemosphere | 2013
Fazlurrahman Khan; Deepika Pal; Anuradha Ghosh; Swaranjit Singh Cameotra
2,4-Dinitroanisole (DNAN) is an insensitive explosive ingredient used by many defense agencies as a replacement for 2,4,6-trinitrotoluene. Although the biotransformation of DNAN under anaerobic condition has been reported, aerobic microbial degradation pathway has not been elucidated. An n-methyl-4-nitroaniline degrading bacterium Pseudomonas sp. strain FK357 transformed DNAN into 2,4-dinitrophenol (2,4-DNP) as an end product. Interestingly, when strain FK357 was co-cultured with a 2,4-DNP degrading Rhodococcus imtechensis strain RKJ300, complete and high rate of DNAN degradation was observed with no accumulation of intermediates. Enzyme assay using cell extracts of strain FK357 demonstrated that O-demethylation reaction is the first step of DNAN degradation with formation of 2,4-DNP and formaldehyde as intermediates. Subsequently, 2,4-DNP was degraded by strain RKJ300 via the formation of hydride-Meisenheimer complex. The present study clearly demonstrates that complete degradation of DNAN occurs as a result of the metabolic cooperative activity of two members within a bacterial consortium.
International Journal of Systematic and Evolutionary Microbiology | 2017
Deepika Pal; R Kumar Mathan; Navjot Kaur; Narender Kumar; Gurwinder Kaur; Nitin Kumar Singh; Srinivasan Krishnamurthi; Shanmugam Mayilraj
The taxonomic position of a Gram-stain-positive, endospore-forming bacterium, strain KS16-9T, isolated from a marine sediment sample collected from Kovalam, Kanyakumari coastal region of the Indian Ocean, India, was analysed by a polyphasic approach. Strain KS16-9T had typical phenotypic characteristics and chemotaxonomic features (menaquinones, fatty acids and lipids) that were consistent with the genus Bacillus. omparative analysis of the 16S rRNA gene sequence of the strain with previously published Bacillus type strains confirmed that it belongs to the genus Bacillus and is moderately related to Bacillus persicus B48T (98.42 % similarity), followed by Bacillus foraminis CV53T (97.67 %) and Bacillus rigiliprofundi (97.61 %). Other species in the genus Bacillusshared <97.6 % 16S rRNA gene sequence similarity. Strain KS16-9T contained MK-7 as the predominant menaquinone, meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, iso-C15 : 0 and anteiso-C15 : 0 as major fatty acids, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major phospholipids. The DNA G+C content of strain KS16-9T was 45.4 mol%. Based on data from this polyphasic taxonomic study, strain KS16-9T represents a novel species of the genus Bacillus, for which the name Bacillus maritimus sp. nov. is proposed. The type strain is KS16-9T (=MTCC 12305T=DSM 100413T=KCTC 33834T).
International Journal of Systematic and Evolutionary Microbiology | 2017
Aleksandra Checinska Sielaff; Rajendran Mathan Kumar; Deepika Pal; Shanmugam Mayilraj; Kasthuri Venkateswaran
A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterial strain, designated ISSFR-015T, was isolated from a high-efficiency particulate arrestance filter in the International Space Station and was characterized by polyphasic taxonomy. A comparative analysis of the 16S rRNA gene sequence (1494 bp) of strain ISSFR-015T showed highest similarity to Solibacillus isronensis B3W22T (98.9 %), followed by Solibacillus silvestris HR3-23T (98.6 %) and Bacillus cecembensis PN5T (96.7 %). DNA-DNA hybridization analysis revealed that the DNA relatedness values of strain ISSFR-015T with other closely related species were in the range of 41-47 % [S. silvestrisMTCC 10789T (47 %), S. isronensis MTCC 7902T (41 %) and B. cecembensis MTCC 9127T (43 %)]. The DNA G+C content of strain ISSFR-015T was 45.4 mol%. The major fatty acids were iso-C15 : 0 (45.2 %) and C17 : 1ω10c (12.1 %). The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and one unknown phospholipid. The isoprenoid quinones present in strain ISSFR-015T were MK-7 (86.8 %), MK-6 (11.6 %) and MK-8 (1.0 %). The peptidoglycan type of the cell wall was A4α l-Lys-d-Glu. Based on the phylogenetic analysis, strain ISSFR-015T belongs to the genus Solibacillus. The polyphasic taxonomic data, including low DNA-DNA hybridization values, and the chemotaxonomic analysis confirmed that strain ISSFR-015T represents a novel species, for which the name Solibacillus kalamii sp. nov. is proposed. The type strain for this proposed species is ISSFR-015T (=NRRL B-65388T=DSM 101595T).
International Journal of Systematic and Evolutionary Microbiology | 2018
Deepika Pal; Ayanka Bhardwaj; Sarabjeet Kour Sudan; Navjot Kaur; Munesh Kumari; Bhawana Bisht; Bhawna Vyas; Srinivasan Krishnamurthi; Shanmugam Mayilraj
A Gram-stain-negative, non-endospore-producing, short-rod strain, KNDSS-Mac4T, was isolated from a downstream sediment sample of the river Ganges, Kanpur, India and studied by using the polyphasic taxonomic approach. 16S rRNA gene sequence analysis uncovered that the strain had similarity to species of the genus Thauera and formed a distinct phylogenetic cluster with Thauera humireducens KACC16524T. However, KNDSS-Mac4T showed closest phylogenetic affiliation to Thauera aminoaromatica DSM 14742T with 16S rRNA gene sequence similarity of 98.7 % followed by Thauera phenylacetica DSM 14743T (98.6 %), Thauera chlorobenzoica (98.2 %), T. humireducens KACC16524T (98.2 %), Thauera selenatis ATCC 55363T (98.2 %) and Thauera mechernichensis DSM 12266T (98.0 %). The digital DNA-DNA hybridization and average nucleotide identity values between strain KNDSS-Mac4T and the two most closely related taxa, T. aminoaromatica DSM 14742T and T. phenylacetica DSM 14743T, were 26.0, 26.7 and 84.0, 84.3 % respectively. Major lipids present were phosphatidylglycerol, three unknown aminophospholipids, phosphatidylmethylethanolamine, two unidentified lipids and Q-8 as the only ubiquonone. The major cellular fatty acids present were C16 : 1 ω6c/C16 : 1ω7c and C16 : 0. The DNA G+C content of strain KNDSS-Mac4T was 65.9 %. Based on data from phenotypic tests and the genotypic differences of strain KNDSS-Mac4T from its closest phylogenetic relatives, it is evident that this isolate should be regarded as a new species. It is proposed that strain KNDSS-Mac4T should be classified in the genus Thauera as a novel species, Thauerapropionica sp. nov. The type strain is KNDSS-Mac4T (=KCTC 52820T=VTCC-B-910017T).
International Journal of Systematic and Evolutionary Microbiology | 2018
Sarabjeet Kour Sudan; Deepika Pal; Bhawana Bisht; Narender Kumar; Vasvi Chaudhry; Prabhu B. Patil; Girish Sahni; Shanmugam Mayilraj; Srinivasan Krishnamurthi
A bacterial strain, designated ASS-1T, was isolated and identified from a sediment sample of the river Ganges, Allahabad, India. The strain was Gram-stain-negative, formed straw-yellow pigmented colonies, was strictly aerobic, motile with a single polar flagellum, and positive for oxidase and catalase. The major fatty acids were C16 : 1ω7c/ 16 : 1 C16 : 1ω6c, C18 : 1ω7c and C16 : 0. Sequence analysis based on the 16S rRNA gene revealed that strain ASS-1T showed high similarity to Pseudomonas guguanensis CC-G9AT (98.2 %), Pseudomonas alcaligenes ATCC 14909T (98.2 %), Pseudomonas oleovorans DSM 1045T (98.1 %), Pseudomonas indolxydans IPL-1T (98.1 %) and Pseudomonas toyotomiensis HT-3T (98.0 %). Analysis of its rpoB and rpoD housekeeping genes confirmed its phylogenetic affiliation and showed identities lower than 93 % with respect to the closest relatives. Phylogenetic analysis based on the 16S rRNA, rpoB, rpoD genes and the whole genome assigned it to the genus Pseudomonas. The results of digital DNA-DNA hybridization based on the genome-to-genome distance calculator and average nucleotide identity revealed low genome relatedness to its close phylogenetic neighbours (below the recommended thresholds of 70 and 95 %, respectively, for species delineation). Strain ASS-1T also differed from the related strains by some phenotypic characteristics, i.e. growth at pH 5.0 and 42 °C, starch and casein hydrolysis, and citrate utilization. Therefore, based on data obtained from phenotypic and genotypic analysis, it is evident that strain ASS-1T should be regarded as a novel species within the genus Pseudomonas, for which the name Pseudomonasfluvialis sp. nov. is proposed. The type strain is ASS-1T (=KCTC 52437T=CCM 8778T).
International Journal of Systematic and Evolutionary Microbiology | 2018
Deepika Pal; Ayanka Bhardwaj; Navjot Kaur; Sarabjeet Kour Sudan; Bhawana Bisht; Munesh Kumari; Bhawna Vyas; Srinivasan Krishnamurthi; Shanmugam Mayilraj
A Gram-stain-positive, facultatively anaerobic bacterial strain, GDSW-R2A3T, was isolated from a downstream water sample collected from the river Ganges, India. Analysis of the 16S rRNA gene sequence of strain GDSW-R2A3T revealed its affiliation to the family Bacillaceae. Further analysis using a polyphasic approach revealed that strain GDSW-R2A3T was most closely related to the genus Fictibacillus. Analysis of the almost-complete (1488 bp) 16S rRNA gene sequence of strain GDSW-R2A3T revealed the highest level of sequence similarity with Fictibacillus phosphorivorans CCM 8426T (98.3 %) and Fictibacillus nanhaiensis KCTC 13712T (98.3 %) followed by Fictibacillus barbaricus DSM 14730T (98.0 %). The digital DNA-DNA hybridization and average nucleotide identity (ANI) values between strain GDSW-R2A3T and the most closely related taxon, F. phosphorivorans CCM 8426T, were 20.3 and 78.2 %, respectively. The DNA G+C content of the strain was 44.2 mol%. The cell-wall amino acid was meso-diaminopimelic acid. Polar lipids present were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three aminophospholipids, two phospholipids and one unidentified lipid; the major menaquinone was MK-7; iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0 were the major fatty acids. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it can be concluded that strain GDSW-R2A3T represents a novel species of the genus Fictibacillus, for which the name Fictibacillus aquaticus sp. nov. is proposed. The type strain is GDSW-R2A3T (=VTCC-B-910015T=CCM 8782T).
International Journal of Systematic and Evolutionary Microbiology | 2018
Deepika Pal; Navjot Kaur; Sarabjeet Kour Sudan; Bhawana Bisht; Srinivasan Krishnamurthi; Shanmugam Mayilraj
A Gram-stain-negative, rod-shaped, aerobic, straw yellow, motile strain, designated KNDSW-TSA6T, belonging to the genus Acidovorax, was isolated from a water sample of the river Ganges, downstream of the city of Kanpur, Uttar Pradesh, India. Cells were aerobic, non-endospore-forming and motile with single polar flagella. It differed from its phylogenetically related strains by phenotypic characteristics such as hydrolysis of urea, gelatin, casein and DNA, and the catalase reaction. The major fatty acids were C16 : 1ω7c/C16 : 1ω6c, C16 : 0 and C18 : 1ω7c/C18 : 1ω6c. Phylogenetic analysis based on 16S rRNA and housekeeping genes (gyrb, recA and rpoB gene sequences), confirmed its placement within the genus Acidovorax as a novel species. Strain KNDSW-TSA6T showed highest 16S rRNA sequence similarity to Acidovorax soli BL21T (98.9 %), Acidovorax delafieldii ATCC 17505T (98.8 %), Acidovorax temperans CCUG 11779T (98.2 %), Acidovorax caeni R-24608T (97.9 %) and Acidovorax radicis N35T (97.6 %). The digital DNA-DNA hybridization and average nucleotide identity values calculated from whole genome sequences between strain KNDSW-TSA6T and the two most closely related strains A. soli BL21T and A. delafieldii ATCC 17505T were below the threshold values of 70 and 95 % respectively. Thus, the data from the polyphasic taxonomic analysis clearly indicates that strain KNDSW-TSA6T represents a novel species, for which the name Acidovorax kalamii sp. nov. is proposed. The type strain is Acidovorax kalamii (=MTCC 12652T=KCTC 52819T=VTCC-B-910010T).
Journal of Hazardous Materials | 2017
Fazlurrahman Khan; Janmejay Pandey; Surendra Vikram; Deepika Pal; Swaranjit Singh Cameotra
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editors because of concerns about the validity of the results reported in this publication. Arising from a complaint by a third party questioning the veracity of the data in this paper an Official Committee of the Institute of Microbial Technology (CSIR), Chandigarh, India was formed to examine the circumstances of this publication. During the course of its investigation the Committee determined that a number of experiments had not actually been conducted to generate the associated data. This represents an abuse of the scientific publishing system and a clear violation of publishing ethics. All of the authors of the paper have asked that the paper be retracted. Publication of an article in a peer-reviewed journal is an important building-block in the development of science. Elsevier has defined policies and ethical guidelines that have to be obeyed by authors and editors, and Elsevier takes its duties of guardianship over the scholarly record extremely seriously. Upon investigation, the Editors of the Journal of Hazardous Materials found the above concerns to be sufficiently compelling that they have decided that this paper should be retracted.