Physiological alterations and heavy metal accumulation in the transplanted lichen Pyxine cocoes (Sw.) Nyl. in Lucknow city, Uttar Pradesh.

Air pollution has become a major concern due to its detrimental effects on living beings. The present study is aimed at assessing the current status of air pollution in Lucknow city using lichen transplantation technique and assesing its effect on physiology of Pyxine cocoes. The samples of P. cocoes were collected from relatively pollution-free area Malihabad and transplanted in 10 designated sites in five regions for 30 days. Various parameters such as heavy metals, chlorophyll pigments, carotenoid, chlorophyll degradation, and electrolyte conductivity were estimated in transplanted lichens. The study revealed that the concentration of all 10 heavy metals was higher in all transplanted samples than in the control sample, which was found in order of Al > Fe > Mn > Zn > Cu > Cr > Pb > Ni > Co > Cd. Among all 10 transplanted sites, the significantly increased accumulation of aluminum (5.11 to 5.47 µg L-1), iron (4.73 to 5.46 µg L-1), manganese (110.99 to 144.58 µg g-1), and zinc (87.96 to 97.40 µg g-1) was found in Charbagh, Qaisarbagh, and Alambagh sites. Further, in all samples, chlorophyll a (3.98 µg L-1), chlorophyll b (1.22 µg L-1), total chlorophyll (5.20 µg L-1), and chlorophyll degradation (0.55 µg g-1) were significantly decreased, whereas elevated levels of carotenoid (0.71 µg g-1), and electrolyte conductivity (64.99 µS cm-1), were observed. The scanning electron microscope (SEM) investigated the morphological changes in transplanted lichen samples, and significant damage to the anatomy of mycelium was found in most of the polluted site's samples, which correlated with the pollution levels. The present study clearly demonstrated that the transplanted lichen P. cocoes is an efficient bioaccumulator and bioindicator of air quality in urban environments.

Studies on the effect of ohmic heating on oil recovery and quality of sesame seeds.

This research describes a new technological process for sesame oil extraction. The process deals with the effect of ohmic heating on enhancement of oil recovery and quality of cleaned and graded sesame seed. The effect of ohmic heating parameters namely electric field strength (EFS), end point temperature (EPT) and holding time (HT) on oil extraction process were investigated. Three levels of electric field strength (600, 750 and 900 V/m), end point temperature (65, 75 and 85 °C) and holding time (5, 10 and 15 min.) were taken as independent variables using full factorial design. Percentage oil recovered from sesame seed through mechanical extracted oil by application of ohmic heating varies from 39.98 to 43.15 %. The maximum oil recovery 43.15 % was obtained when the sample was heated and maintained at 85 °C using EFS of 900 V/m for a holding time of 10 min as against 34.14 % in control sample. The free fatty acid (FFA) of the extracted oil was within the acceptable limit (1.52 to 2.26 % oleic acid) of 0.5 to 3 % as prescribed respectively by Prevention of Food Adulteration (PFA) and Bureau of Indian Standards (BIS). The peroxide value of extracted oil was also found within the acceptable limit (0.78 to 1.01 meq/kg). The optimum value for maximum oil recovery, minimum residual oil content, free fatty acid (FFA) and peroxide value were 41.24 %, 8.61 %, 1.74 % oleic acid and 0.86 meq/kg, respectively at 722.52 V/m EFS at EPT 65 °C for 5 min. holding time which was obtained by response surface methodology.

Bacterial diversity and real-time PCR based assessment of linA and linB gene distribution at hexachlorocyclohexane contaminated sites.

The disposal of hexachlorocyclohexane (HCH) muck has created large number of HCH dumpsites all over the world from where the harmful HCH isomers are leaking into the environment. Bacteria have evolved at such contaminated sites that have the ability to degrade HCH. Degradation of various HCH isomers in bacterial strains is mediated primarily by two genes: linA and linB which encode dehydrochlorinase and haloalkane dehalogenase respectively. In this study we explored one such highly contaminated HCH dumpsite located in Lucknow, Uttar Pradesh, India. To assess the biostimulation potential of the contaminated site, microbial diversity study and real-time PCR based quantification of lin genes was carried out. The soil samples from dumpsite and surrounding areas were found to be highly contaminated with HCH residue levels as high as 1.8 × 10(5) mg kg(-1). The residues were detected in areas upto 13 km from the dumpsite. Sphingomonads, Chromohalobacter, and Marinobacter were the dominant genera present at the dump-site. Role of Sphingomonads in HCH degradation has been well documented. The highest copy numbers of linA and linB genes as determined using real-time PCR were 6.2 × 10(4) and 5.3 × 10(5), respectively, were found in sample from the dump site. The presence of Sphingomonads, linA, and linB genes from HCH contaminated soil indicates the presence of indigenous bacterial communities capable of HCH degradation.

Thermus parvatiensis RL(T) sp. nov., Isolated from a Hot Water Spring, Located Atop the Himalayan Ranges at Manikaran, India.

A Gram negative, yellow pigmented, rod shaped bacterium designated as RL(T) was isolated from a hot water spring (90-98 °C) located at Manikaran in Northern India. The isolate grows at 60-80 °C (optimum, 70 °C) and at pH 7.0-9.0 (optimum pH 7.2). Phylogenetic analysis of 16S rRNA gene sequences and levels of DNA-DNA relatedness together indicate that the new isolate represents a novel species of the genus Thermus with closest affinity to Thermus thermophilus HB8(T) (99.5 %) followed by Thermus arciformis (96.4 %). A comparative analysis of partial sequences of housekeeping genes (HKG) further revealed that strain RL(T) is a novel species belonging to the genus Thermus. The melting G+C content of strain RL(T) was calculated as 68.7 mol%. The DNA-DNA relatedness value of strain RL(T) with its nearest neighbours (>97 %) was found to be less than 70 % indicating that strain RL(T) represents a novel species of the genus Thermus. MK-8 was the predominant respiratory quinone. The presence of characteristic phospholipid and glycolipid further confirmed that strain RL(T) belongs to the genus Thermus. The predominant fatty acids of strain RL(T) were iso-C17:0 (23.67 %) and iso-C15:0 (24.50 %). The results obtained after DNA-DNA hybridization, biochemical and physiological tests clearly distinguished strain RL(T) from its closely related species. Thus, strain RL(T) represents a novel species of the genus Thermus for which the name Thermus parvatiensis is proposed (=DSM 21745(T)= MTCC 8932(T)).

Functional screening of enzymes and bacteria for the dechlorination of hexachlorocyclohexane by a high-throughput colorimetric assay.

Two distinct microbial dehalogenases are involved in the first steps of degradation of hexachlorocyclohexane (HCH) isomers. The enzymes, LinA and LinB, catalyze dehydrochlorination and dechlorination reactions of HCH respectively, each with distinct isomer specificities. The two enzymes hold great promise for use in the bioremediation of HCH residues in contaminated soils, although their kinetics and isomer specificities are currently limiting. Here we report the functional screening of a library of 700 LinA and LinB clones generated from soil DNA for improved dechlorination activity by means of a high throughput colorimetric assay. The assay relies upon visual colour change of phenol red in an aqueous medium, due to the pH drop associated with the dechlorination reactions. The assay is performed in a microplate format using intact cells, making it quick and simple to perform and it has high sensitivity, dynamic range and reproducibility. The method has been validated with quantitative gas chromatographic analysis of promising clones, revealing some novel variants of both enzymes with superior HCH degrading activities. Some sphingomonad isolates with potentially superior activities were also identified.

Germination and probiotic fermentation: a way to enhance nutritional and biochemical properties of cereals and millets.

Probiotics have become increasingly popular as consumers demand balanced nutrition and health benefits from their diet. However, lactose intolerance and allergies to milk proteins may make dairy-based probiotics unsuitable for some individuals. Thus, probiotics derived from cereals and millets have shown promise as an alternative to dairy probiotics. Soaking, germination, and fermentation can reduce the anti-nutritional factors present in cereal grains and improve nutrient quality and bioactive compounds. Biochemical properties of probiotics are positively influenced by fermentation and germination. Thus, the current review provides an overview of the effect of fermentation and germination on the biochemical properties of probiotics. Further, probiotics made from non-dairy sources may prevent intestinal infections, improve lactose metabolism, reduce cholesterol, enhance immunity, improve calcium absorption, protein digestion, and synthesize vitamins. Finally, health-conscious consumers seeking non-dairy probiotic options can now choose from a wider variety of low-cost, phytochemically rich probiotics derived from germinated and fermented cereal grains.

Whole genome sequence of the rifamycin B-producing strain Amycolatopsis mediterranei S699.

Amycolatopsis mediterranei S699 is an actinomycete that produces an important antibiotic, rifamycin B. Semisynthetic derivatives of rifamycin B are used for the treatment of tuberculosis, leprosy, and AIDS-related mycobacterial infections. Here, we report the complete genome sequence (10.2 Mb) of A. mediterranei S699, with 9,575 predicted coding sequences.

Pseudoxanthomonas indica sp. nov., isolated from a hexachlorocyclohexane dumpsite.

A bacterial strain, designated P15(T), was isolated from the soil of an open hexachlorocyclohexane dumpsite. Comparative sequence analysis showed that strain P15(T) displayed high 16S rRNA gene sequence similarities (94.4-97.2 %) with members of the genus Pseudoxanthomonas. The isolate was most closely related to Pseudoxanthomonas mexicana AMX 26B(T) (97.2 % 16S rRNA gene sequence similarity) and Pseudoxanthomonas japonensis 12-3(T) (97.2 %). DNA-DNA relatedness studies showed unambiguously that strain P15(T) represented a novel species that was separate from P. mexicana DSM 17121(T) (7.7 %) and P. japonensis DSM 17109(T) (9.4 %). The predominant cellular fatty acids of strain P15(T) were iso-C16:0 (21.4 %), iso-C15:0 (16.1 %), summed feature 9 (comprising iso-C17:1ω9c and/or 10-methyl C16:0; 14.9 %), iso-C11:0 3-OH (8.3 %) and iso-C14:0 (7.0 %). The polar lipid profile of strain P15(T) showed the presence of large amounts of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol in addition to unknown glycolipids, phospholipids and an amino-group-containing polar lipid. Ubiquinone 8 was found as the major quinone. The polyamine profile showed the presence of spermidine. The DNA G+C content was 62.9±2 mol%. Strain P15(T) is described as representing a new member of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas indica sp. nov. is proposed. The type strain is P15(T) ( = MTCC 8596(T) = CCM 7430(T)).

From bacterial genomics to metagenomics: concept, tools and recent advances.

In the last 20 years, the applications of genomics tools have completely transformed the field of microbial research. This has primarily happened due to revolution in sequencing technologies that have become available today. This review therefore, first describes the discoveries, upgradation and automation of sequencing techniques in a chronological order, followed by a brief discussion on microbial genomics. Some of the recently sequenced bacterial genomes are described to explain how complete genome data is now being used to derive interesting findings. Apart from the genomics of individual microbes, the study of unculturable microbiota from different environments is increasingly gaining importance. The second section is thus dedicated to the concept of metagenomics describing environmental DNA isolation, metagenomic library construction and screening methods to look for novel and potentially important genes, enzymes and biomolecules. It also deals with the pioneering studies in the area of metagenomics that are offering new insights into the previously unappreciated microbial world.

Pseudomonas sp. to Sphingobium indicum: a journey of microbial degradation and bioremediation of Hexachlorocyclohexane.

The unusual process of production of hexachlorocyclohexane (HCH) and extensive use of technical HCH and lindane has created a very serious problem of HCH contamination. While the use of technical HCH and lindane has been banned all over the world, India still continues producing lindane. Bacteria, especially Sphingomonads have been isolated that can degrade HCH isomers. Among all the bacterial strains isolated so far, Sphingobium indicum B90A that was isolated from HCH treated rhizosphere soil appears to have a better potential for HCH degradation. This conclusion is based on studies on the organization of lin genes and degradation ability of B90A. This strain perhaps can be used for HCH decontamination through bioaugmentation.

Kinetic and sequence-structure-function analysis of LinB enzyme variants with ß- and δ-hexachlorocyclohexane.

Organochlorine insecticide hexachlorocyclohexane (HCH) has recently been classified as a 'Persistent Organic pollutant' by the Stockholm Convention. The LinB haloalkane dehalogenase is a key upstream enzyme in the recently evolved Lin pathway for the catabolism of HCH in bacteria. Here we report a sequence-structure-function analysis of ten naturally occurring and thirteen synthetic mutants of LinB. One of the synthetic mutants was found to have ∼80 fold more activity for ß- and δ-hexachlorocyclohexane. Based on detailed biophysical calculations, molecular dynamics and ensemble docking calculations, we propose that the latter variant is more active because of alterations to the shape of its active site and increased conformational plasticity.

Kinetic and sequence-structure-function analysis of known LinA variants with different hexachlorocyclohexane isomers.

BACKGROUND: Here we report specific activities of all seven naturally occurring LinA variants towards three different isomers, α, γ and δ, of a priority persistent pollutant, hexachlorocyclohexane (HCH). Sequence-structure-function differences contributing to the differences in their stereospecificity for α-, γ-, and δ-HCH and enantiospecificity for (+)- and (-)-α -HCH are also discussed. METHODOLOGY/PRINCIPAL FINDINGS: Enzyme kinetic studies were performed with purified LinA variants. Models of LinA2(B90A) A110T, A111C, A110T/A111C and LinA1(B90A) were constructed using the FoldX computer algorithm. Turnover rates (min(-1)) showed that the LinAs exhibited differential substrate affinity amongst the four HCH isomers tested. α-HCH was found to be the most preferred substrate by all LinA's, followed by the γ and then δ isomer. CONCLUSIONS/SIGNIFICANCE: The kinetic observations suggest that LinA-γ1-7 is the best variant for developing an enzyme-based bioremediation technology for HCH. The majority of the sequence variation in the various linA genes that have been isolated is not neutral, but alters the enantio- and stereoselectivity of the encoded proteins.

Competing S(N)2 and E2 reaction pathways for hexachlorocyclohexane degradation in the gas phase, solution and enzymes.

Quantum chemistry calculations have been used alongside experimental kinetic analysis to investigate the competition between S(N)2 and E2 mechanisms for the dechlorination of hexachlorocyclohexane isomers, revealing that enzyme specificity reflects the intrinsic reactivity of the various isomers.

Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation.

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.

Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant.

A phenanthrene- and citronellol-degrading bacterium, strain RLD-1(T), was isolated from the fly ash dumping site of a thermal power plant in Delhi, India. The 16S rRNA gene sequence indicated that this strain belongs to the genus Pseudomonas; high levels of sequence similarity were found with respect to Pseudomonas citronellolis DSM 50332(T) (98.9 %), Pseudomonas jinjuensis DSM 16612(T) (97.6 %) and Pseudomonas nitroreducens DSM 14399(T) (97.5 %). Phylogenetic analysis based on 16S rRNA gene sequences placed the strain within the clade represented by these three strains. Strain RLD-1(T) showed low levels of DNA-DNA hybridization with respect to P. citronellolis DSM 50332(T) (36 %), P. jinjuensis DSM 16612(T) (4 %) and P. nitroreducens (13.7 %). Strain RLD-1(T) can also be distinguished from these three strains on the basis of several biochemical and physiological attributes. The novel strain contained high levels of cellular fatty acids 18 : 1omega7c, 16 : 0 and 16 : 1omega7c, along with 10 : 0 3-OH and 12 : 0 3-OH. Thus, strain RLD-1(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas delhiensis sp. nov. is proposed. The type strain is RLD-1(T) (=MTCC 7601(T)=CCM 7361(T)).