Publications by authors named "Vishakha Raina"

32 Publications

Genome-based identification and comparative analysis of enzymes for carotenoid biosynthesis in microalgae.

World J Microbiol Biotechnol 2021 Nov 27;38(1). Epub 2021 Nov 27.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024, India.

Microalgae are potential feedstocks for the commercial production of carotenoids, however, the metabolic pathways for carotenoid biosynthesis across algal lineage are largely unexplored. This work is the first to provide a comprehensive survey of genes and enzymes associated with the less studied methylerythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate pathway as well as the carotenoid biosynthetic pathway in microalgae through bioinformatics and comparative genomics approach. Candidate genes/enzymes were subsequently analyzed across 22 microalgae species of lineages Chlorophyta, Rhodophyta, Heterokonta, Haptophyta, Cryptophyta, and known Arabidopsis homologs in order to study the evolutional divergence in terms of sequence-structure properties. A total of 403 enzymes playing a vital role in carotene, lutein, zeaxanthin, violaxanthin, canthaxanthin, and astaxanthin were unraveled. Of these, 85 were hypothetical proteins whose biological roles are not yet experimentally characterized. Putative functions to these hypothetical proteins were successfully assigned through a comprehensive investigation of the protein family, motifs, intrinsic physicochemical features, subcellular localization, pathway analysis, etc. Furthermore, these enzymes were categorized into major classes as per the conserved domain and gene ontology. Functional signature sequences were also identified which were observed conserved across microalgal genomes. Additionally, the structural modeling and active site architecture of three vital enzymes, DXR, PSY, and ZDS catalyzing the vital rate-limiting steps in Dunaliella salina were achieved. The enzymes were confirmed to be stereochemically reliable and stable as revealed during molecular dynamics simulation of 100 ns. The detailed functional information about individual vital enzymes will certainly help to design genetically modified algal strains with enhanced carotenoid contents.
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http://dx.doi.org/10.1007/s11274-021-03188-yDOI Listing
November 2021

Combined biostimulation and bioaugmentation for chlorpyrifos degradation in laboratory microcosms.

3 Biotech 2021 Oct 18;11(10):439. Epub 2021 Sep 18.

Environmental Biotechnology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology-KIIT (Deemed to be University), Bhubaneswar, 751024 Odisha India.

Chlorpyrifos (CP) is a persistent organophosphorus pesticide (OP) used in soil ecosystem for insect control. Bioremediation process has been proven promising in degrading these toxic molecules and restoring the physio-chemical properties of soil. This work reports a laboratory microcosm study in both non-sterile & sterile conditions, conducted over a period of 56 days to examine the combined effect of additional supplements like biostimulants (BSs) such as N, P, and K in the presence of suitable carrier materials (compost, wheat straw, and corncob) along with bioaugmentation by a sp. CPD-03 on CP degradation from the contaminated soil. CP degradation was thoroughly monitored at an interval of 7 days over a period of 56 days. Results showed biostimulation and bioaugmentation along with compost as carrier material had shown higher CP degradation efficiency of 76 ± 2.8 and 74 ± 1.6% in non-sterile and sterile microcosms over a period of 56 days. Moreover, bacterial community profiling (16s rRNA and gene) demonstrated increased microbial counts, corroborating the efficiency of the bioremediation process. The survival of CPD-03 at the end of the assay validated its ability of colonizing modified soils. By this integrated method with compost as carrier material, bioremediation process could be enhanced for restoration CP-contaminated soils.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-021-02980-9.
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http://dx.doi.org/10.1007/s13205-021-02980-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8449756PMC
October 2021

Development of a Conserved Chimeric Vaccine for Induction of Strong Immune Response against Using Immunoinformatics Approaches.

Vaccines (Basel) 2021 Sep 18;9(9). Epub 2021 Sep 18.

Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 63243, Korea.

is one of the most notorious Gram-positive bacteria with a very high mortality rate. The WHO has listed as one of the ESKAPE pathogens requiring urgent research and development efforts to fight against it. Yet there is a major layback in the advancement of effective vaccines against this multidrug-resistant pathogen. SdrD and SdrE proteins are attractive immunogen candidates as they are conserved among all the strains and contribute specifically to bacterial adherence to the host cells. Furthermore, these proteins are predicted to be highly antigenic and essential for pathogen survival. Therefore, in this study, using the immunoinformatics approach, a novel vaccine candidate was constructed using highly immunogenic conserved T-cell and B-cell epitopes along with specific linkers, adjuvants, and consequently modeled for docking with human Toll-like receptor 2. Additionally, physicochemical properties, secondary structure, disulphide engineering, and population coverage analysis were also analyzed for the vaccine. The constructed vaccine showed good results of worldwide population coverage and a promising immune response. For evaluation of the stability of the vaccine-TLR-2 docked complex, a molecular dynamics simulation was performed. The constructed vaccine was subjected to in silico immune simulations by C-ImmSim and Immune simulation significantly provided high levels of immunoglobulins, T-helper cells, T-cytotoxic cells, and INF-γ. Lastly, upon cloning, the vaccine protein was reverse transcribed into a DNA sequence and cloned into a pET28a (+) vector to ensure translational potency and microbial expression. The overall results of the study showed that the designed novel chimeric vaccine can simultaneously elicit humoral and cell-mediated immune responses and is a reliable construct for subsequent in vivo and in vitro studies against the pathogen.
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http://dx.doi.org/10.3390/vaccines9091038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8470666PMC
September 2021

Comprehensive sequence and structure analysis of algal lipid catabolic enzyme Triacylglycerol lipase: an study to vitalize the development of optimum engineered strains with high lipid productivity.

J Biomol Struct Dyn 2021 Aug 20:1-19. Epub 2021 Aug 20.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India.

Microalgae as an alternative renewable resource for biofuel production have captured much significance. Nonetheless, its economic viability is a field of major concern for researchers. Unraveling the lipid catabolic pathway and gaining insights into the sequence-structural features of its primary functioning enzyme, Triacylglycerol lipase, will impart valuable information to target microalgae for augmented lipid content. In the present study, a genome-wide comparative study on putative Triacylglycerol lipase (TAGL) enzyme from algal species belonging to varied phylogenetic lineages was performed. The comprehensive sequence analysis revealed that TAGL comprises of three distinct conserved domains, such as, Patatin, Class III Lipase, and Abhydro_lipase, and also confirmed the ubiquitous presence of GXSXG motif in the sequences analyzed. In the absence of a crystal structure of algal TAGL till date, we developed the first 3D model of patatin domain of TAGL from an oleaginous microalga, , employing homology modeling, docking and molecular dynamic simulations methods. The domain-substrate complex having the low-ranking docking score revealed the binding of palmitic acid to the TAGL patatin domain surface with strong hydrogen bond interactions. The simulation results implied that the substrate-complexed patatin domain and the free enzyme adopted a more stable conformation after 40 ns. This is the first ever attempt to provide insights into the structural and dynamical insights on catalytic mechanism of the TAGL patatin domain. Subsequently, these findings aided our understanding on their structural stability, folding mechanism and protein-substrate interactions, which could be further utilized to design site-specific mutagenic experiments for engineering microalgal strains.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2021.1967194DOI Listing
August 2021

Draft genome sequence and potential identification of a biosurfactant from strain LS14 an isolate from fresh water Loktak Lake.

3 Biotech 2021 Jul 11;11(7):326. Epub 2021 Jun 11.

Environmental Biotechnology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology-KIIT (Deemed to be University), Bhubaneswar, Odisha 751024 India.

This study reports the whole-genome sequencing and sequence analysis of a bacterial isolate strain LS14, isolated from Loktak Lake, Imphal, India. The de novo assembled genome reported in this paper featured a size of 3,809,532 bp, has GC content of 68% and contains 3602 genomic features, including 3551 protein-coding genes, 46 tRNA and 5rRNA. A biosurfactant biosynthesis gene cluster in the genome of the isolated strain was identified using AntiSMASH online tool V3.0.5 and KAAS (KEGG Automatic Annotation Server). The presence of biosurfactant was demonstrated by drop collapse, oil displacement and emulsification index. Subsequent chemical characterization using FTIR and LC-MS analyses revealed surfactin and terpene containing biosurfactant moieties. Also, the presence of genes involved in terpenoid synthesis pathway in the genome sequence may account for biosurfactant terpenoid backbone, but genes for later-stage conversion of terpenoid to biosurfactant were not ascertained.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-021-02867-9.
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http://dx.doi.org/10.1007/s13205-021-02867-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196162PMC
July 2021

DBCOVP: A database of coronavirus virulent glycoproteins.

Comput Biol Med 2021 02 21;129:104131. Epub 2020 Nov 21.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, India; KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, India. Electronic address:

Since the emergence of SARS-CoV-1 (2002), novel coronaviruses have emerged periodically like the MERS- CoV (2012) and now, the SARS-CoV-2 outbreak which has posed a global threat to public health. Although, this is the third zoonotic coronavirus breakout within the last two decades, there are only a few platforms that provide information about coronavirus genomes. None of them is specific for the virulence glycoproteins and complete sequence-structural features of these virulence factors across the betacoronavirus family including SARS-CoV-2 strains are lacking. Against this backdrop, we present DBCOVP (http://covp.immt.res.in/), the first manually-curated, web-based resource to provide extensive information on the complete repertoire of structural virulent glycoproteins from coronavirus genomes belonging to betacoronavirus genera. The database provides various sequence-structural properties in which users can browse and analyze information in different ways. Furthermore, many conserved T-cell and B-cell epitopes predicted for each protein are present that may perform a significant role in eliciting the humoral and cellular immune response. The tertiary structure of the epitopes together with the docked epitope-HLA binding-complex is made available to facilitate further analysis. DBCOVP presents an easy-to-use interface with in-built tools for similarity search, cross-genome comparison, phylogenetic, and multiple sequence alignment. DBCOVP will certainly be an important resource for experimental biologists engaged in coronavirus research studies and will aid in vaccine development.
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http://dx.doi.org/10.1016/j.compbiomed.2020.104131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7679231PMC
February 2021

Designing an efficient multi-epitope vaccine displaying interactions with diverse HLA molecules for an efficient humoral and cellular immune response to prevent COVID-19 infection.

Expert Rev Vaccines 2020 09 24;19(9):871-885. Epub 2020 Sep 24.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU) , Bhubaneswar 751024, India.

Background: The novel SARS-CoV-2 coronavirus, the causative agent of the ongoing pandemic COVID-19 disease continues to infect people globally and has infected millions of humans worldwide. However, no effective vaccine against this virus exists.

Method: Using Immunoinformatics, epitopic sequences from multiple glycoproteins that play crucial role in pathogenesis were identified. Particularly, epitopes were mapped from conserved receptor-binding domain of spike protein which have been experimentally validated in SARS-CoV-1 as a promising target for vaccine development.

Results: A multi-epitopic vaccine construct comprising of B-cell, CTL, HTL epitopes was developed along with fusion of adjuvant and linkers. The epitopes identified herein are reported for the first time and were predicted to be highly antigenic, stable, nonallergen, nontoxic and displayed conservation across several SARS-CoV-2 isolates from different countries. Additionally, the epitopes associated with maximum HLA alleles and population coverage analysis shows the proposed epitopes would be a relevant representative of large proportion of the world population. A reliable three-dimensional structure of the vaccine construct was developed. Consequently, docking and molecular-dynamics simulation ensured the stable interaction between vaccine and innate-immune receptor.
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http://dx.doi.org/10.1080/14760584.2020.1811091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7544970PMC
September 2020

Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study.

J Biomol Struct Dyn 2021 11 7;39(18):7231-7245. Epub 2020 Aug 7.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.

Recent studies have pointed the role of angiotensin-converting enzyme-II (ACE2) in mediating the entry of SARS-CoV-2 to the host cell by binding to the receptor-binding domain (RBD) of viral spike protein, and successive priming by cellular proteases initiates the infection. SARS-CoV replication rate and disease severity is controlled by the binding affinity of RBD with ACE2. To understand, how mutations in the conserved residues of RBD affect the molecular interaction with ACE2, we generated five alanine mutants i.e. Y449A, N487A, Y489A, N501A and Y505A in the receptor binding motif (RBM) of the ACE2-RBD SARS-CoV-2 complex (PDB: 6M0J). Computational site directed mutagenesis induced dynamics in wild-type and mutant complexes were extensively studied through all-atoms molecular dynamics (MD) simulations of 150 ns. In silico mutational analysis revealed loss of important intermolecular hydrogen bonds and other non-bonded contacts, critical for molecular recognition of SARS-CoV-2 RBD to ACE2, which is well supported by saturation mutagenesis study of binding interface residues. MD simulations results showed that RBM motif is flexible, where mutant residues are relatively more mobile than corresponding wild-type residues. Global motion analysis through principal component studies revealed that RBD exhibits protuberant in-ward motion towards the human ACE2 binding interface which may be crucial for molecular interaction. Conclusively, the present finding are in congruence with previous experimental reports and provides detailed information on the structural basis of receptor binding by human SARS-CoV-2, which will crucial for the development of novel inhibitors or drugs to combat against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2020.1802348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7484587PMC
November 2021

Comparative Genomics of a Paddy Field Bacterial Isolate sp. CPD-03: Analysis of Chlorpyrifos Degradation Potential.

Indian J Microbiol 2020 Sep 2;60(3):325-333. Epub 2020 Apr 2.

Environmental Biotechnology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology-KIIT (Deemed to be University), Bhubaneswar, Odisha 751024 India.

genus is known to catabolize aromatic compounds. This study reports a complete genome sequence of sp. CPD-03 (~ 4.6 Mb of chromosomal features) responsible for chlorpyrifos (CP) isolated form a paddy field (20.3588° N, 85.8333° E) in Bhubaneswar, India. A comparative genomics approach was performed between CPD-03 and eight closely related genomes of other strains in order to deepen our knowledge, to establish its phylogenetic and functional relationships. The involvement of CP degrading genes indicated a versatile role of CPD-03 in additional field trails. This research would provide the genetic information for its use in natural environment for the depletion of organophosphorus (OP) compounds.
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http://dx.doi.org/10.1007/s12088-020-00864-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329950PMC
September 2020

Rheinheimera pleomorphica sp. nov., a Novel Alkali-Tolerant Bacteria Isolated from Chilika Lake, India.

Curr Microbiol 2020 Jan 8;77(1):158-165. Epub 2019 Nov 8.

School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India.

A novel Gram-negative gamma-proteobacterium, non-sporulating motile, rod or coccus-shaped bacterium designated as strain PKS7 was isolated from a sediment sample collected from Chilika Lake, Odisha, India and characterized taxonomically using a polyphasic approach. The major quinone was Q8 and major cellular fatty acids were C, C, Cw8c Cw8c, C3-OH. The chemotaxonomic features confirmed the isolate to be a member of genus Rheinheimera. 16SrRNA gene sequence of strain PKS7 was closest in similarity to R. aquimaris SW-353 (99.36% identity), R. muenzenbergensis E49 (98.63%), R. nanhaiensis E407-8 (98.35%), R. japonica KMM 9513 (98.35%) and R. baltica DSM-14885 (98.08%). The 16S rRNA gene sequence-based phylogenetic analysis and sequence similarity between the isolated strain and type strains also revealed its affiliation to genus Rheinheimera. DNA-DNA relatedness with closest type strain R. aquimaris SW-353 was 25.0% (±3.40) and in silico DDH showed values in the range of 17.7-37.1% with the type strains of the genus Rheinheimera for which whole genome sequence are available. Strain PKS7 was also distinguished by a multi-locus sequence analysis (MLST) by alingning gyrB gene sequences of the closest type strains of Rheinheimera. The draft genome of strain PKS7 contained 32 contigs of total size 3,963,569 bp comprising of 3763 predicted coding sequences with a G + C content of 50.7 mol%. Comparision of phenotypic and genotypic data with its closest neighbours and closely related species confirm the strain PKS7 to be recognised as a novel species within the genus Rheinheimera, for which the name Rheinheimera pleomorphica sp. nov. is proposed. The type strain is PKS7 (= KCTC 42365 = JCM 30460).
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http://dx.doi.org/10.1007/s00284-019-01802-9DOI Listing
January 2020

Optimization of media components for the production of N-acetylchitooligosaccharide from chitin by Streptomyces chilikensis through Taguchi experimental design.

J Microbiol Methods 2019 04 16;159:194-199. Epub 2019 Mar 16.

School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India; School of Law, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India. Electronic address:

Optimization of media composition for microbial growth is crucial particularly in industrial processes to obtain the desired end product. The waste from sea food industries includes the non-edible parts of shrimp, crabs and prawns which are rich in chitin as the major cause of pollution in coastal areas. Chitin degradation is carried out chemically. It can be degraded biologically also, particularly using microorganisms resulting in chitooligosaccahrides and the monomer N-acetylglucosamine. N-acetyl glucosamine and related chitooligosaccahrides have various applications such as treatment of cancer and metastasis, treatment of autoimmune reactions, as food supplements and increased plant stress tolerance against salinity and heavy metals. Thus, chitin waste can be efficiently degraded biologically using microorganisms to produce such useful products. Conventional methods such as One factor at a time (OFAT) are more time consuming and costly to address the problem. The current work focuses on the development of an experimental design to ascertain parameters optimized for chitin degradation by a Streptomyces chilikensis to produce various chitooligosaccharides. More than one factor was taken at a time to carry out the experiments and the data were fit into Taguchi Design to determine the contribution of the most important factors responsible for the production of the desired end product that is NAG and other chitooligosaccaharides. Highest NAG production (3741 μM/reaction) was observed in a media that contains 0.5% Raffinose (w/v), 0.5% peptone (w/v), 2.5% NaCl at pH 11.
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http://dx.doi.org/10.1016/j.mimet.2019.03.014DOI Listing
April 2019

Purification and characterization of an extracellular thermo-alkali stable, metal tolerant chitinase from RC1830 isolated from a brackish water lake sediment.

Biotechnol Rep (Amst) 2019 Mar 29;21:e00311. Epub 2019 Jan 29.

School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India.

An extracellular thermo-alkali stable chitinase was obtained from RC1830, a novel actinobacterial strain isolated from the sediments of Chilika lake, India. Purification of the enzyme was carried out by concentrating the enzyme with centrifugal device followed by chromatographic separation by DEAE Sepharose ion exchange resin.The molecular weight of the enzyme was 10.5 kDa as determined by SDS-PAGE. The optimum pH and temperature for the partially purified chitinase was pH 7 and 60 °C. The chitinase showed 40% activity at pH 11 after 24 h exposure at room temperature. The chitinase exhibited Km and Vmax values are 0.02 mM and 3.184 mol/min/mg of enzyme respectively. The 6 residue N-terminal sequence of the enzyme was not found similar to any of the reported chitinase enzyme. Based on the SDS PAGE, zymogram analysis, activity assays and other characteristics, it is proposed that the purified enzyme from RC1830 is a chitinase.
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http://dx.doi.org/10.1016/j.btre.2019.e00311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6365541PMC
March 2019

A simple and rapid colorimetric method for the estimation of chitosan produced by microbial degradation of chitin waste.

J Microbiol Methods 2019 03 3;158:66-70. Epub 2019 Feb 3.

School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India; School of Law, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India. Electronic address:

Chitin is one of the most abundant biopolymers present in the environment. Chitosan being its major derivative can be obtained by hydrolysis of chitin, especially by microbial degradation. Estimation of resulting chitosan produced by chitin degradation is crucial to the process. Usefulness of the method of Badawy (Badawy, 2012) for estimation of chitosan is limited by interference resulting from susceptibility to variation in the pH of the sample and thiobarbituric acid. This work presents an improvement of the method proposed by Badawy for colorimetric determination of chitosan by using 3, 5-Dinitrosalicylic acid (DNSA) reagent instead of thiobarbituric acid, after one step depolymerization and deamination of chitosan with sodium nitrite (NaNO). Eventually colorimetric estimation was carried out at 540 nm. With the use of DNSA reagent, the limitation of thiobarbituric acid are overcome. This method is easy, cost effective, and sensitive for quantitative determination of chitosan. This new improved method was applied for evaluation and quantification of chitosan produced by microbial degradation of chitin waste by different novel Streptomyces strains.
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http://dx.doi.org/10.1016/j.mimet.2019.02.001DOI Listing
March 2019

Taxonomic description and genome sequence of Halobacillus marinus sp. nov., a novel strain isolated from Chilika Lake, India.

J Microbiol 2018 Apr 2;56(4):223-230. Epub 2018 Apr 2.

School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India.

moderately halophilic spore forming, motile, Gram-positive, rod-shaped bacterial strain designated as KGW1 was isolated from water sample of Chilika Lake and characterized taxonomically using polyphasic approach. The strain grew in the presence of 0-25% (w/v) NaCl in marine salt agar media, hydrolyzes casein, and gelatin and shows presence of alkaline proteases. The major cell wall menaquinone was MK7 and major cellular fatty acids were anteiso-C (44.89%), anteiso-C (6.18%), isoC (19.38%), and iso-C (7.39%). Several chemotaxonomic features conform the isolate be a member of genus Halobacillus. The isolate KGW1 contained A1γ meso-Dpm-direct type of peptidoglycan which is different from its phylogenetically closest neighbours. The 16S rRNA gene sequence based phylogenetic analysis also revealed the strain KGW1 was affiliated to the genus Halobacillus and sequence similarity between the isolated strain and the type strains of Halobacillus species were found closest to, H. dabanensis D-8 DSM 18199 (99.08%) and H. faecis IGA7-4 DSM 21559 (99.01%), H. trueperi SL-5 DSM 10404 (98.94%). The in silico DDH showed that the values in a range of 14.2-17.5% with the most closest strain H. dabanensis D-8 DSM 18199 and other type strains of the genus Halobacillus for which whole genome sequence is reported. DNA-DNA relatedness between strain KGW1 and the closest type strain Halobacillus trueperi DSM 10404 was 11.75% (± 1.15). The draft genome sequence includes 3,683,819 bases and comprises of 3898 predicted coding sequences with a G + C content of 46.98%. Thus, the significant distinctiveness supported by phenotypic and genotypic data with its closest neighbors and other closely related species confirm the strain KGW1 to be classified as a novel species within the genus Halobacillus, for which the name Halobacillus marinus sp. nov. is proposed. The type strain is KGW1 (= DSM 29522 = JCM 30443).
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http://dx.doi.org/10.1007/s12275-018-7387-xDOI Listing
April 2018

Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon.

Sci Total Environ 2017 Oct;595:472-485

Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India. Electronic address:

Brackish water coastal lagoons are least understood with respect to the seasonal and temporal variability in their sedimentary bacterial communities. These coastal lagoons are characterized by the steep environmental gradient and provide an excellent model system to decipher the biotic and abiotic factors that determine the bacterial community structure over time and space. Using Illumina sequencing of the 16S rRNA genes from a total of 100 bulk surface sediments, we investigated the sedimentary bacterial communities, their spatiotemporal distribution, and compared them with the rhizosphere sediment communities of a common reed; Phragmites karka and a native seagrass species; Halodule uninervis in Chilika Lagoon. Spatiotemporal patterns in bacterial communities were linked to specific biotic factors (e.g., presence and type of macrophyte) and abiotic factors (e.g., salinity) that drove the community composition. Comparative assessment of communities highlighted bacterial lineages that were responsible for segregating the sediment communities over distinct salinity regimes, seasons, locations, and presence and type of macrophytes. Several bacterial taxa were specific to one of these ecological factors suggesting that species-sorting processes drive specific biogeographical patterns in the bacterial populations. Modeling of proteobacterial lineages against salinity gradient revealed that α- and γ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed the opposite trend. The wide variety of biogeochemical functions performed by the rhizosphere microbiota of P. karka must be taken into consideration while formulating the management and conservation plan for this reed. Overall, this study provides a comprehensive understanding of the spatiotemporal dynamics and functionality of sedimentary bacterial communities and highlighted the role of biotic and abiotic factors in generating the biogeographical patterns in the bacterial communities of a tropical brackish water coastal lagoon.
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http://dx.doi.org/10.1016/j.scitotenv.2017.03.271DOI Listing
October 2017

Mangrovibacter phragmitis sp. nov., an endophyte isolated from the roots of Phragmites karka.

Int J Syst Evol Microbiol 2017 May 30;67(5):1228-1234. Epub 2017 May 30.

Wetland Research and Training Centre, Chilika Development Authority Odisha, Barkul, Balugaon 752030, India.

A facultatively anaerobic, Gram-stain-negative, rod-shaped, nitrogen-fixing, endophytic bacterial strain designated MP23T was isolated from the roots of Phragmites karka growing in Chilika Lagoon, Odisha, India. Strain MP23T was slightly halophilic, and the optimal NaCl concentration and temperature for growth were 1 % and 30 °C, respectively. On the basis of 16S rRNA gene sequence similarities, strain MP23T was affiliated to the family Enterobacteriaceae and most closely related to Mangrovibacter yixingensis KCTC 42181T and Mangrovibacter plantisponsor DSM 19579T with 99.71 % similarity, followed by Salmonella enterica subsp. salamae DSM 9220T (97.22 %), Cronobacter condimenti LMG 26250T (97.14 %) and Salmonella enterica subsp. diarizonae DSM 14847T (97 %). Sequence analysis of 16S rRNA, hsp60, gyrB and rpoB genes showed that strain MP23T formed a phylogenetic cluster with M. yixingensis KCTC 42181T and M. plantisponsor DSM 19579T indicating that it belongs to the genus Mangrovibacter. The major cellular fatty acids were C16 : 0, C18 : 1ω6c and/or C18 : 1ω7c, C16 : 1ω6c and/or C16 : 1ω7c, C14 : 0, C14 : 0 3-OH and/or iso-C16 : 1 I and C17 : 0 cyclo. Polar lipids of strain MP23T consisted of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 50.3 mol%. Based on experimental DNA-DNA hybridization values and average nucleotide identity derived from in silico comparison of whole-genome sequences, strain MP23T could be distinguished from its closest neighbours. We therefore conclude that strain MP23T represents a novel species of the genus Mangrovibacter for which the name Mangrovibacter phragmitis sp. nov. is proposed. The type strain is MP23T (=DSM 100250T=KCTC 42580T).
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http://dx.doi.org/10.1099/ijsem.0.001789DOI Listing
May 2017

The draft genome sequence of Mangrovibacter sp. strain MP23, an endophyte isolated from the roots of Phragmites karka.

Genom Data 2016 Sep 19;9:128-9. Epub 2016 Jul 19.

Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India.

Till date, only one draft genome has been reported within the genus Mangrovibacter. Here, we report the second draft genome shotgun sequence of a Mangrovibacter sp. strain MP23 that was isolated from the roots of Phargmites karka (P. karka), an invasive weed growing in the Chilika Lagoon, Odisha, India. Strain MP23 is a facultative anaerobic, nitrogen-fixing endophytic bacteria that grows optimally at 37 °C, 7.0 pH, and 1% NaCl concentration. The draft genome sequence of strain MP23 contains 4,947,475 bp with an estimated G + C content of 49.9% and total 4392 protein coding genes. The genome sequence has provided information on putative genes that code for proteins involved in oxidative stress, uptake of nutrients, and nitrogen fixation that might offer niche specific ecological fitness and explain the invasive success of P. karka in Chilika Lagoon. The draft genome sequence and annotation have been deposited at DDBJ/EMBL/GenBank under the accession number LYRP00000000.
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http://dx.doi.org/10.1016/j.gdata.2016.07.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971156PMC
September 2016

Draft Genome Sequence of Acinetobacter sp. Strain BMW17, a Cellulolytic and Plant Growth-Promoting Bacterium Isolated from the Rhizospheric Region of Phragmites karka of Chilika Lake, India.

Genome Announc 2016 Jun 30;4(3). Epub 2016 Jun 30.

School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India

We report the 3.16 Mb draft genome of Acinetobacter sp. strain BMW17, a Gram-negative bacterium in the class of Gammaproteobacteria, isolated from the rhizospheric region of Phragmites karka, an invasive weed in Chilika Lake, Odisha, India. The strain BMW17(T) is capable of degrading cellulose and is also an efficient plant growth promoter that can be useful for various phytoremedial and commercial applications.
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http://dx.doi.org/10.1128/genomeA.00395-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4929506PMC
June 2016

Draft Genome Sequence of Halobacillus sp. Strain KGW1, a Moderately Halophilic and Alkaline Protease-Producing Bacterium Isolated from the Rhizospheric Region of Phragmites karka from Chilika Lake, Odisha, India.

Genome Announc 2016 Jun 30;4(3). Epub 2016 Jun 30.

School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India

Halobacillus sp. strain KGW1 is a moderately halophilic, rod shaped, Gram-positive, yellow pigmented, alkaline protease-producing bacterium isolated from a water sample from Chilika Lake, Odisha, India. Sequencing of bacterial DNA assembled a 3.68-Mb draft genome. The genome annotation analysis showed various gene clusters for tolerance to stress, such as elevated pH, salt concentration, and toxic metals.
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http://dx.doi.org/10.1128/genomeA.00361-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4929504PMC
June 2016

Draft Genome Sequence of Pseudomonas sp. Strain BMS12, a Plant Growth-Promoting and Protease-Producing Bacterium, Isolated from the Rhizosphere Sediment of Phragmites karka of Chilika Lake, India.

Genome Announc 2016 Jun 30;4(3). Epub 2016 Jun 30.

School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India

We report the 4.51 Mb draft genome of Pseudomonas sp. strain BMS12, a Gram-negative bacterium in the class of Gammaproteobacteria, isolated from the rhizospheric sediment of Phragmites karka, an invasive weed in Chilika Lake, Odisha, India. The Pseudomonas sp. strain BMS12 is capable of producing proteases and is also an efficient plant growth promoter that can be useful for various phytoremedial and industrial applications.
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http://dx.doi.org/10.1128/genomeA.00342-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4929503PMC
June 2016

Streptomyces chitinivorans sp. nov., a chitinolytic strain isolated from estuarine lake sediment.

Int J Syst Evol Microbiol 2016 Sep 24;66(8):3241-3248. Epub 2016 May 24.

School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India.

A novel actinobacterial strain RC1832T was isolated from the sediment of a fish dumping yard at Balugaon near Chilika Lake. The strain is halotolerant (15 % NaCl, w/v), alkali-tolerant (pH 7-10) and hydrolyzes chitin, starch, gelatin, cellulose, carboxymethyl cellulose, Tween 80, tributyrin, lecithin and casein. Apart from showing typical genus-specific morphological and chemotaxonomic features, the comparision and analysis of the near complete 16S rRNA gene sequence clearly revealed that the strain RC1832T represented a member of the genus Streptomyces. It exhibited the highest sequence similarities with the strains Streptomyces fenghuangensis GIMN4.003T (99.78 %), Streptomyces nanhaiensis DSM 41926T (99.07 %), Streptomyces radiopugnans R97T(98.71 %), Streptomyces atacamensis DSM 42065T (98.65 %) and Streptomyces barkulensis DSM 42082T (98.25 %). The DNA-DNA relatedness of strain RC 1832T with the closest phylogenetic neighbours S. fenghuangensis GIMN4.003T and S. nanhaiensis DSM 41926T were 20±2 % and 21±2 %, respectively. Thus, based on a range of phenotypic and genotypic properties, strain RC1832T was suggested to represent a novel species of the genus Streptomyces for which the name Streptomyces chitinivorans sp. nov. is proposed. The type strain is RC1832T (=JCM 30611=KCTC 29696).
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http://dx.doi.org/10.1099/ijsem.0.001176DOI Listing
September 2016

Streptomyces barkulensis sp. nov., isolated from an estuarine lake.

Int J Syst Evol Microbiol 2014 Apr 16;64(Pt 4):1365-1372. Epub 2014 Jan 16.

School of Biotechnology, KIIT University, Bhubaneswar - 751024, Odisha, India.

The taxonomic position of a novel actinomycete, strain RC 1831(T), isolated from the sediment of a fish dumping yard at Barkul village near Chilika Lake, Odisha, India, was determined by a polyphasic approach. Based on morphological and chemotaxonomic characteristics the isolate was determined to belong to the genus Streptomyces. The phylogenetic tree based on its nearly complete 16S rRNA gene sequence (1428 nt) with representative strains showed that the strain consistently falls into a distinct phyletic line together with Streptomyces glaucosporus DSM 41689(T) (98.22% similarity) and a subclade consisting of Streptomyces atacamensis DSM 42065(T) (98.40%), Streptomyces radiopugnans R97 DSM 41901(T) (98.27%), Streptomyces fenghuangensis GIMN4.003(T) (98.33 %), Streptomyces nanhaiensis DSM 41926(T) (98.13%), Streptomyces megasporus NBRC 14749(T) (97.37%) and Streptomyces macrosporus NBRC 14748(T) (98.22%). However, the levels of DNA-DNA relatedness between strain RC 1831(T) and phylogenetically related strains Streptomyces atacamensis DSM 42065(T) (28.75 ± 3.25%) and Streptomyces glaucosporus DSM 41689(T) (15 ± 2.40%) were significantly lower than the 70% threshold value for delineation of genomic species. Furthermore, the isolate could be distinguished phenotypically on the basis of physiological, morphological and biochemical differences from its closest phylogenetic neighbours and other related reference strains. Strain RC 1831(T) is therefore considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces barkulensis sp. nov. is proposed. The type strain is RC 1831(T) ( = JCM 18754(T) = DSM 42082(T)).
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http://dx.doi.org/10.1099/ijs.0.056614-0DOI Listing
April 2014

Streptomyces chilikensis sp. nov., a halophilic streptomycete isolated from brackish water sediment.

Int J Syst Evol Microbiol 2013 Aug 4;63(Pt 8):2757-2764. Epub 2013 Jan 4.

School of Biotechnology, Campus 11, KIIT University, Patia, Bhubaneswar-751024, Odisha, India.

A novel actinobacterial strain, designated RC 1830(T), was isolated from the sediment of estuarine coastal brackish water lagoon of Chilika Lake, in Khurdha district of Odisha, India, and characterized using a polyphasic approach. Strain RC 1830(T) was halophilic and alkali-tolerant and found to hydrolyse chitin, starch, tributyrin, lecithin, Tween 80, cellulose, gelatin and casein. The diagnostic presence of ll-diaminopimelic acid, iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, C16 : 0, iso-C17 : 0, anteiso-C17 : 0 as major cellular fatty acids and MK-9(H4 and H6) as major menaquinones noticeably associated the strain to the genus Streptomyces. After comparison and analysis of the near complete 16S rRNA gene sequence with representative strains of other streptomycetes, it was evident that strain RC 1830(T) belonged to the genus Streptomyces, and exhibited the highest sequence similarities of 99.53 %, 99.25 %, 99.11 %, 99.10 % and 99. 06 % to Streptomyces fragilis DSM 40044(T), Streptomyces coelicoflavus NBRC 15399(T), Streptomyces flaveolus NBRC 3715(T), Streptomyces lavenduligrisesus NBRC 13405(T) and Streptomyces eurythermus ATCC 14975(T), respectively. Reconstruction of a phylogenetic tree for the genus Streptomyces revealed that strain RC 1830(T) formed a distinct phyletic line and clustered with its most closely related neighbour S. fragilis DSM 40044(T). The DNA-DNA relatedness values between strain RC 1830(T) and the most closely related type strain S. fragilis DSM 40044(T) were determined to be 17.7 ± 4.55 %. Additionally, morphological, biochemical and physiological tests were able to distinguish the strain from the most closely related type strain S. fragilis DSM 40044(T) and other closely related neighbours, S. coelicoflavus DSM 41471(T) and Streptomyces flaveolus DSM 40061(T). Based on a range of phenotypic and genotypic properties, strain RC 1830(T) is suggested to represent a novel species of the genus Streptomyces for which the name Streptomyces chilikensis sp. nov. is proposed. The type strain is RC 1830(T) ( = JCM 18411(T) = DSM 42072(T)).
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http://dx.doi.org/10.1099/ijs.0.046284-0DOI Listing
August 2013

High prevalence of bacterial spore-formers active against mosquito larvae in temporary monsoon flooded sites in Orissa, India.

J Am Mosq Control Assoc 2011 Jun;27(2):159-61

School of Biotechnology, KIIT University, Bhubaneswar, Orissa-751024, India.

Different ecosystems were probed in the vicinity of the city of Bhubaneswar in the Indian state of Orissa for the presence of bacterial spore-formers with activity against mosquito larvae. The most productive sites were places that were flooded during the monsoon season, including roadside ditches and shorelines of ponds. Among 630 isolates screened, 44 (7%) showed larvicidal activity against larvae of Aedes aegypti. The specific activity of the bacterial spore-formers varied greatly. Isolates were found with specific activities superior to the Bacillus thuringiensis israelensis reference strain of the Pasteur Institute. All mosquitocidal strains produced crystal proteins, and based on the biochemical analyses could be classified into the species B. thuringiensis. Such strains possess the potential for the development of new microbial products for mosquito control in India.
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http://dx.doi.org/10.2987/10-6067.1DOI Listing
June 2011

Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation.

Microbiol Mol Biol Rev 2010 Mar;74(1):58-80

Department of Zoology, University of Delhi, Delhi 110007, India.

Lindane, the gamma-isomer of hexachlorocyclohexane (HCH), is a potent insecticide. Purified lindane or unpurified mixtures of this and alpha-, beta-, and delta-isomers of HCH were widely used as commercial insecticides in the last half of the 20th century. Large dumps of unused HCH isomers now constitute a major hazard because of their long residence times in soil and high nontarget toxicities. The major pathway for the aerobic degradation of HCH isomers in soil is the Lin pathway, and variants of this pathway will degrade all four of the HCH isomers although only slowly. Sequence differences in the primary LinA and LinB enzymes in the pathway play a key role in determining their ability to degrade the different isomers. LinA is a dehydrochlorinase, but little is known of its biochemistry. LinB is a hydrolytic dechlorinase that has been heterologously expressed and crystallized, and there is some understanding of the sequence-structure-function relationships underlying its substrate specificity and kinetics, although there are also some significant anomalies. The kinetics of some LinB variants are reported to be slow even for their preferred isomers. It is important to develop a better understanding of the biochemistries of the LinA and LinB variants and to use that knowledge to build better variants, because field trials of some bioremediation strategies based on the Lin pathway have yielded promising results but would not yet achieve economic levels of remediation.
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http://dx.doi.org/10.1128/MMBR.00029-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832351PMC
March 2010

New metabolites in the degradation of alpha- and gamma-hexachlorocyclohexane (HCH): pentachlorocyclohexenes are hydroxylated to cyclohexenols and cyclohexenediols by the haloalkane dehalogenase LinB from Sphingobium indicum B90A.

J Agric Food Chem 2008 Aug 4;56(15):6594-603. Epub 2008 Jul 4.

Swiss Federal Institute of Aquatic Science and Technology, Eawag, CH-8600 Dübendorf, Switzerland.

Technical hexachlorocyclohexane (HCH) and lindane are obsolete pesticides whose former production and use led to widespread contaminations posing serious and lasting health and environmental risks. Out of nine possible stereoisomers, alpha-, beta-, gamma-, and delta-HCH are usually present at contaminated sites, and research for a better understanding of their biodegradation has become essential for the development of appropriate remediation technologies. Because haloalkane dehalogenase LinB was recently found responsible for the hydroxylation of beta-HCH, delta-HCH, and delta-pentachlorocyclohexene (delta-PCCH), we decided to examine whether beta- and gamma-PCCH, which can be formed by LinA from alpha- and gamma-HCH, respectively, were also converted by LinB. Incubation of such substrates with Escherichia coli BL21 expressing functional LinB originating from Sphingobium indicum B90A showed that both beta-PCCH and gamma-PCCH were direct substrates of LinB. Furthermore, we identified the main metabolites as 3,4,5,6-tetrachloro-2-cyclohexene-1-ols and 2,5,6-trichloro-2-cyclohexene-1,4-diols by nuclear magnetic resonance spectroscopy and gas chromatography-mass spectrometry. In contrast to alpha-HCH, gamma-HCH was not a substrate for LinB. On the basis of our data, we propose a modified gamma-HCH degradation pathway in which gamma-PCCH is converted to 2,5-cyclohexadiene-1,4-diol via 3,4,5,6-tetrachloro-2-cyclohexene-1-ol and 2,5,6-trichloro-2-cyclohexene-1,4-diol.
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http://dx.doi.org/10.1021/jf800465qDOI Listing
August 2008

Hydroxylated metabolites of beta- and delta-hexachlorocyclohexane: bacterial formation, stereochemical configuration, and occurrence in groundwater at a former production site.

Environ Sci Technol 2007 Jun;41(12):4292-8

Environmental Microbiology, Swiss Federal Institute for Aquatic Science and Technology (Eawag), CH-8600 Dübendorf, Switzerland.

Although the use of hexachlorocyclohexane (HCH), one of the most popular insecticides after the Second World War, has been discontinued in many countries, problems remain from former production and waste sites. Despite the widespread occurrence of HCHs, the environmental fate of these compounds is not fully understood. In particular, environmental metabolites of the more persistent beta-HCH and delta-HCH have not been fully identified. Such knowledge, however, is important to follow degradation and environmental fate of the HCHs. In the present study, several hydroxy metabolites that formed during incubation of beta- and delta-HCH with the common soil microorganism Sphingobium indicum B90A were isolated, characterized, and stereochemically identified by gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance spectroscopy (NMR). The metabolites were identified as isomeric pentachlorocyclohexanols (B1, D1) and tetrachlorocyclohexane-1,4-diols (B2, D2); delta-HCH additionally formed a tetrachloro-2-cyclohexen-1-ol (D3) and a trichloro-2-cyclohexene-1,4-diol (D4), most likely by hydroxylation of delta-pentachlorocyclohexene (delta-PCCH), initially formed by dehydrochlorination. The dehydrochlorinase LinA was responsible for conversion of delta-HCH into delta-PCCH, and the haloalkane dehalogenase LinB was responsible for the transformation of beta-HCH and delta-HCH into B1 and D1, respectively, and subsequently into B2 and D2, respectively. LinB was also responsible for transforming delta-PCCH into D3 and subsequently into D4. These hydroxylations proceeded in accordance with SN2 type reactions with initial substitution of equatorial Cls and formation of axially hydroxylated stereoisomers. The apparently high reactivity of equatorial Cls in beta- and delta-HCH toward initial hydroxylation by LinB of Sphingobium indicum B90A is remarkable when considering the otherwise usually higher reactivity of axial Cls. Several of these metabolites were detected in groundwater from a former HCH production site in Switzerland. Their presence indicates that these reactions proceed under natural environmental conditions and that the metabolites are of environmental relevance.
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http://dx.doi.org/10.1021/es062908gDOI Listing
June 2007

Enhanced biodegradation of hexachlorocyclohexane (HCH) in contaminated soils via inoculation with Sphingobium indicum B90A.

Biodegradation 2008 Feb 27;19(1):27-40. Epub 2007 Mar 27.

Department of Zoology, University of Delhi, Delhi 110007, India.

Soil pollution with hexachlorocyclohexane (HCH) has caused serious environmental problems. Here we describe the targeted degradation of all HCH isomers by applying the aerobic bacterium Sphingobium indicum B90A. In particular, we examined possibilities for large-scale cultivation of strain B90A, tested immobilization, storage and inoculation procedures, and determined the survival and HCH-degradation activity of inoculated cells in soil. Optimal growth of strain B90A was achieved in glucose-containing mineral medium and up to 65% culturability could be maintained after 60 days storage at 30 degrees C by mixing cells with sterile dry corncob powder. B90A biomass produced in water supplemented with sugarcane molasses and immobilized on corncob powder retained 15-20% culturability after 30 days storage at 30 degrees C, whereas full culturability was maintained when cells were stored frozen at -20 degrees C. On the contrary, cells stored on corncob degraded gamma-HCH faster than those that had been stored frozen, with between 15 and 85% of gamma-HCH disappearance in microcosms within 20 h at 30 degrees C. Soil microcosm tests at 25 degrees C confirmed complete mineralization of [(14)C]-gamma-HCH by corncob-immobilized strain B90A. Experiments conducted in small pits and at an HCH-contaminated agricultural site resulted in between 85 and 95% HCH degradation by strain B90A applied via corncob, depending on the type of HCH isomer and even at residual HCH concentrations. Up to 20% of the inoculated B90A cells survived under field conditions after 8 days and could be traced among other soil microorganisms by a combination of natural antibiotic resistance properties, unique pigmentation and PCR amplification of the linA genes. Neither the addition of corncob nor of corncob immobilized B90A did measurably change the microbial community structure as determined by T-RFLP analysis. Overall, these results indicate that on-site aerobic bioremediation of HCH exploiting the biodegradation activity of S. indicum B90A cells stored on corncob powder is a promising technology.
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http://dx.doi.org/10.1007/s10532-007-9112-zDOI Listing
February 2008

Haloalkane dehalogenase LinB is responsible for beta- and delta-hexachlorocyclohexane transformation in Sphingobium indicum B90A.

Appl Environ Microbiol 2006 Sep;72(9):5720-7

Department of Zoology, University of Delhi, Delhi 110007, India.

Incubation of resting cells of Sphingobium indicum B90A, Sphingobium japonicum UT26, and Sphingobium francense Sp+ showed that they were able to transform beta- and delta-hexachlorocyclohexane (beta- and delta-HCH, respectively), the most recalcitrant hexachlorocyclohexane isomers, to pentachlorocyclohexanols, but only resting cells of strain B90A could further transform the pentachlorocyclohexanol intermediates to the corresponding tetrachlorocyclohexanediols. Moreover, experiments with resting cells of Escherichia coli expressing the LinB proteins of strains B90A, UT26, and Sp+ indicated that LinB was responsible for these transformations. Purified LinB proteins from all three strains also effected the formation of the respective pentachlorocyclohexanols. Although the three LinB enzymes differ only marginally with respect to amino acid sequence, they showed interesting differences with respect to substrate specificity. When LinB from strain B90A was incubated with beta- and delta-HCH, the pentachlorocyclohexanol products were further transformed and eventually disappeared from the incubation mixtures. In contrast, the LinB proteins from strains UT26 and Sp+ could not catalyze transformation of the pentachlorocyclohexanols, and these products accumulated in the incubation mixture. A mutant of strain Sp+ lacking linA and linB did not degrade any of the HCH isomers, including beta-HCH, and complementation of this mutant by linB from strain B90A restored the ability to degrade beta- and delta-HCH.
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http://dx.doi.org/10.1128/AEM.00192-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1563659PMC
September 2006

Enantioselective transformation of alpha-hexachlorocyclohexane by the dehydrochlorinases LinA1 and LinA2 from the soil bacterium Sphingomonas paucimobilis B90A.

Appl Environ Microbiol 2005 Dec;71(12):8514-8

Department of Zoology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Ueberlandstrasse 133, P.O. Box 611, CH-8600 Dübendorf, Switzerland.

Sphingomonas paucimobilis B90A contains two variants, LinA1 and LinA2, of a dehydrochlorinase that catalyzes the first and second steps in the metabolism of hexachlorocyclohexanes (R. Kumari, S. Subudhi, M. Suar, G. Dhingra, V. Raina, C. Dogra, S. Lal, J. R. van der Meer, C. Holliger, and R. Lal, Appl. Environ. Microbiol. 68:6021-6028, 2002). On the amino acid level, LinA1 and LinA2 were 88% identical to each other, and LinA2 was 100% identical to LinA of S. paucimobilis UT26. Incubation of chiral alpha-hexachlorocyclohexane (alpha-HCH) with Escherichia coli BL21 expressing functional LinA1 and LinA2 S-glutathione transferase fusion proteins showed that LinA1 preferentially converted the (+) enantiomer, whereas LinA2 preferred the (-) enantiomer. Concurrent formation and subsequent dissipation of beta-pentachlorocyclohexene enantiomers was also observed in these experiments, indicating that there was enantioselective formation and/or dissipation of these enantiomers. LinA1 preferentially formed (3S,4S,5R,6R)-1,3,4,5,6-pentachlorocyclohexene, and LinA2 preferentially formed (3R,4R,5S,6S)-1,3,4,5,6-pentachlorocyclohexene. Because enantioselectivity was not observed in incubations with whole cells of S. paucimobilis B90A, we concluded that LinA1 and LinA2 are equally active in this organism. The enantioselective transformation of chiral alpha-HCH by LinA1 and LinA2 provides the first evidence of the molecular basis for the changed enantiomer composition of alpha-HCH in many natural environments. Enantioselective degradation may be one of the key processes determining enantiomer composition, especially when strains that contain only one of the linA genes, such as S. paucimobilis UT26, prevail.
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http://dx.doi.org/10.1128/AEM.71.12.8514-8518.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317435PMC
December 2005
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